From Simon.Sham at USU.Edu Wed Jun 1 07:08:15 2011 From: Simon.Sham at USU.Edu (Simon Sham) Date: Wed, 1 Jun 2011 14:08:15 +0000 Subject: [Chimera-users] Secondary Structures in MD data Message-ID: <7EDE6B59B687D44FB317A960F906CD16302304AF@mb01.aggies.usu.edu> Hi, I am interested in analysizing the secondary structures from a period of MD trajectories. Is it possible to do that in Chimera? Thanks for your insight. Best, Simon -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Wed Jun 1 09:34:41 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 1 Jun 2011 09:34:41 -0700 Subject: [Chimera-users] Secondary Structures in MD data In-Reply-To: <7EDE6B59B687D44FB317A960F906CD16302304AF@mb01.aggies.usu.edu> References: <7EDE6B59B687D44FB317A960F906CD16302304AF@mb01.aggies.usu.edu> Message-ID: <2B22A4A7-C0BD-4255-983E-6426A84003D4@cgl.ucsf.edu> Hi Simon, I don't know what exactly you mean by "analyze," but there is a command "ksdssp" for assigning secondary structure. You could run that command on each frame of your trajectory. Chimera has a tool for trajectory viewing and analysis, MD Movie. You would first need to have or generate one of the formats that it knows, see "Startup and Input" in the man page: MD Movie is in the menu under Tools... MD/Ensemble Analysis. Choose input format and then browse to your files. With MD Movie you can "play" the trajectory frame by frame or continuously, record as a movie, etc. You can define a Chimera script to be run at each frame (see "Per-Frame Scripts" in the man page, link above). The script could be as simple as just the command "ksdssp," or it could do lots of other stuff too. Alternatively, if your trajectory is really large, many frames with many atoms, and it takes too much memory to put the whole thing in MD Movie, you could instead use a python script to loop through your structures, where each one is a separate PDB file, as discussed in this recent post. You would have to generate these PDB files first. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jun 1, 2011, at 7:08 AM, Simon Sham wrote: > Hi, > I am interested in analysizing the secondary structures from a period of MD trajectories. Is it possible to do that in Chimera? > Thanks for your insight. > Best, > Simon > From Simon.Sham at USU.Edu Wed Jun 1 10:02:23 2011 From: Simon.Sham at USU.Edu (Simon Sham) Date: Wed, 1 Jun 2011 17:02:23 +0000 Subject: [Chimera-users] Secondary Structures in MD data In-Reply-To: <2B22A4A7-C0BD-4255-983E-6426A84003D4@cgl.ucsf.edu> References: <7EDE6B59B687D44FB317A960F906CD16302304AF@mb01.aggies.usu.edu>, <2B22A4A7-C0BD-4255-983E-6426A84003D4@cgl.ucsf.edu> Message-ID: <7EDE6B59B687D44FB317A960F906CD1630230504@mb01.aggies.usu.edu> Hi Elaine, Thank for the info. I will try what you suggested. Best, Simon ________________________________________ From: Elaine Meng [meng at cgl.ucsf.edu] Sent: Wednesday, June 01, 2011 10:34 AM To: Simon Sham Cc: chimera-users at cgl.ucsf.edu Subject: Re: [Chimera-users] Secondary Structures in MD data Hi Simon, I don't know what exactly you mean by "analyze," but there is a command "ksdssp" for assigning secondary structure. You could run that command on each frame of your trajectory. Chimera has a tool for trajectory viewing and analysis, MD Movie. You would first need to have or generate one of the formats that it knows, see "Startup and Input" in the man page: MD Movie is in the menu under Tools... MD/Ensemble Analysis. Choose input format and then browse to your files. With MD Movie you can "play" the trajectory frame by frame or continuously, record as a movie, etc. You can define a Chimera script to be run at each frame (see "Per-Frame Scripts" in the man page, link above). The script could be as simple as just the command "ksdssp," or it could do lots of other stuff too. Alternatively, if your trajectory is really large, many frames with many atoms, and it takes too much memory to put the whole thing in MD Movie, you could instead use a python script to loop through your structures, where each one is a separate PDB file, as discussed in this recent post. You would have to generate these PDB files first. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jun 1, 2011, at 7:08 AM, Simon Sham wrote: > Hi, > I am interested in analysizing the secondary structures from a period of MD trajectories. Is it possible to do that in Chimera? > Thanks for your insight. > Best, > Simon > From goddard at sonic.net Fri Jun 3 15:16:27 2011 From: goddard at sonic.net (Tom Goddard) Date: Fri, 03 Jun 2011 15:16:27 -0700 Subject: [Chimera-users] Smooth edge when masking volume data In-Reply-To: References: <4DD172D5.9050505@virginia.edu> <4DD17869.4080201@sonic.net> Message-ID: <4DE95D3B.8060803@sonic.net> > Thanks, Tom. That helped a lot. However, is there anyway to smooth out the masked edge? I end up with chopped voxels (looks like stair-steps), rather than getting an interpolated smooth surface at the edge. This is true whether I am masking directly, or the inverted view. > > Kelly Hi Kelly, When you mask volume data in Chimera using Volume Eraser or the mask command it sets the density values to zero outside the surface. In places where high density crosses the surface the masked result looks horrible -- volume contour surface is jagged with stair-steps following the pattern of the volume grid. I don't have any trick to make that surface look smooth. I have two ideas about how to approach the problem. One is to not have the density fall to zero immediately outside the surface. If it rolled off gradually the contour surface of the masked data would look better. I'm not optimistic that that will produce a good result. The second approach is to do something different from masking. Instead clip the volume surface with the sphere surface and cover the resulting holes with patches of the actual smooth sphere surface. I think this would look very nice and the patches of sphere could be a different coloring which would give a nice visual indication that you have cut through high density. I have not implemented either of these two ideas. Just last week I had a lengthy discussion on this problem with Greg Pintilie and Ernesto Arias. Greg said he might try the gradual fall-off technique. I include that email discussion below. Tom -------- Original Message -------- From: Greg Pintilie To: Tom Goddard Date: 5/24/11 6:10 PM > Right - it's numpy to the rescue; I'll give it a shot... I think if we > use a smoothing filter with relatively high width the staircase effect > may not be as bad as you think... though then the boundaries may > become exceedingly smooth; so it will be a fine balance. Will let you > know how it goes! > > Greg > > > > On Tue, May 24, 2011 at 7:42 PM, Tom Goddard wrote: >> Hi Greg, >> >> It's an interesting idea. But it seems to me there will still be a >> discontinuity in map values. For example imagine you have a box shaped >> region with density values 1 inside and 0 outside. The Gaussian filter of >> that will give values approximately equal to 0.5 at the surface (if the >> Gaussian is half in the 1 region and half in the 0 region). So I think the >> drop from 1 to 0.5 on the surface is likely to give the same ugly artifacts. >> That said, implementation would be trivial. Just compute the Gaussian >> smoothing and copy it only where the original map has zeros (can be done >> with a line or two of tricky numpy Python code). >> >> You know Gaussian smoothing is what the heat equation produces. If you >> modify your idea so the non-zero density points are fixed temperature >> sources, and the heat flows to the zero grid points (by averaging neighbor >> temperatures) then you would get a continuous fall-off. Again it is a >> pretty easy calculation in Python/numpy. But I'm not optimistic about the >> results. The trouble is we've created this horrible stair step surface and >> it will take pretty long range smoothing to get rid of the stair steps. I >> think a good smooth cut is going to require stepping back and not producing >> the stair steps in the first place -- you need a boundary definition that is >> smooth instead of discretized. For instance when we make a contour surface >> we trilinear interpolate the 8 nearest grid points and the surface comes out >> smooth. Not quite sure how to do the equivalent for watershed regions. >> >> Tom >> >>> Sounds good - thanks for all those insights, Tom. I agree that >>> solution is not ideal, but I'm glad it helps at least a bit. I just >>> got an idea that might be interesting to try - I mentioned that you >>> can Gaussian-filter the masked map, which would lessen that huge drop >>> in density values at the boundary, but this removes good detail from >>> the actual map as well. What I'm thinking to try is to do the filter, >>> but only apply it to voxels with 0 density values (the masked >>> portion); that way the original density map gets left alone, and the >>> boundary no longer has a drop from some density value to 0... what do >>> you think Tom, could there be an easy way to implement this using >>> current functions? Done voxel by voxel in python would probably be >>> exceedingly slow... >>> >>> Greg >>> >>> >>> >>> On Tue, May 24, 2011 at 7:04 PM, Ernesto Arias >>> wrote: >>>> Hi, >>>> >>>> I tried and is working. The problem is that I'm visualizing the volume >>>> close >>>> to the noise level, so the segmentation at lower thresholds could be >>>> trickier, but I think I'll can deal with it. >>>> >>>> I really appreciate your help. >>>> Ernesto. >>>> >>>> >>>> >>>> >>>> On Tue, May 24, 2011 at 4:20 PM, Tom Goddard wrote: >>>>> Hi Ernesto, >>>>> >>>>> Yes, now I understand. The Segger regions only include grid points >>>>> above the contour level that was displayed when you made the >>>>> segmentation. >>>>> So when you mask to one of those regions, then use a contour level that >>>>> is >>>>> the same or lower (or even a little higher) than the Segger contour >>>>> level >>>>> you get a horrible surface because the density has been set to zero >>>>> everywhere below the segmentation contour level. The solution is to use >>>>> a >>>>> low contour level when you do the segmentation -- a contour level >>>>> substantially lower than what you plan to use to actually view the >>>>> masked >>>>> regions, so that the zero density values are not near the eventual >>>>> contour >>>>> surface you will be displaying. The Color Zone approach is effectively >>>>> doing this, since it includes all the density out to a specified >>>>> distance. >>>>> >>>>> Tom >>>>> >>>>> Hi, >>>>> >>>>> I see what you mean, but I'm not sure why I get different results. Maybe >>>>> I'm not explaining well what I'm doing There are attached some images >>>>> and >>>>> volumes to illustrate it better. >>>>> >>>>> When I segment the map using segger, mask the original map using the >>>>> segger "Regions->mask map with selected" I get the segger.mrc map or the >>>>> segger_masked_region.png that I'm attaching. >>>>> However, when I place some markers around the same region of the >>>>> original >>>>> map, color the map using Color Zone, and do the Split map option I get >>>>> much >>>>> better results (color_zone.mrc and color_zone_masked_region.png). >>>>> >>>>> One thing I noticed is that the histograms of segger.mrc and >>>>> color_zone.mrc are completely different. The segger.mrc volume has a >>>>> sharp >>>>> cutoff at low threshold values whereas color_zone.mrc has a more >>>>> continuous >>>>> histogram. Could it be the problem? >>>>> >>>>> Thanks so much for your help. >>>>> Ernesto. >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> On Tue, May 24, 2011 at 10:10 AM, Tom Goddard wrote: >>>>>> Hi Ernesto, Greg, >>>>>> >>>>>> The Color Zone splitting tool uses the same method of setting density >>>>>> values to zero outside the region. So the jagged surface appearance >>>>>> should >>>>>> be every bit as bad looking as the Segger ones. If color zone really >>>>>> does >>>>>> look better you'd have to show me an example. It shouldn't look any >>>>>> better. >>>>>> >>>>>> The problem is fundamentally that Segger defined the boundary between >>>>>> regions by saying which grid point are in the region and which are >>>>>> outside >>>>>> the region. So the surface has stair steps matching the volume grid >>>>>> points. >>>>>> I don't have a good idea of how to smooth this jagged surface out. >>>>>> Ideally >>>>>> I'd want to see the jagged surface as smooth, but colored differently >>>>>> from >>>>>> the other parts of the surface. I'd like the different coloring >>>>>> because at >>>>>> this surface patch you have cut through high density -- it is an >>>>>> artificial >>>>>> boundary. When you hide that by masking it makes misleading images. I >>>>>> have >>>>>> an idea about how to achieve both these goals but it is not implemented >>>>>> yet. >>>>>> Basically I don't mask the volume. Instead I intersect the volume >>>>>> surface >>>>>> with the masking surface. By "intersect" I mean I show the mask >>>>>> surface >>>>>> wherever it lies inside the volume surface, and the volume surface >>>>>> wherever >>>>>> it lies inside the mask, and hide everything else. The mask surface >>>>>> and >>>>>> volume surface can have two different colors. Another way to think of >>>>>> this >>>>>> idea is that I clip the volume surface using the mask surface. We >>>>>> already >>>>>> allow you to clip a surface with a plane in Chimera. This is just a >>>>>> generalization where you can clip a surface with some arbitrary other >>>>>> surface. This isn't too hard to implement, but I want the boundary >>>>>> where >>>>>> the volume surface and the mask surface meet to be a smooth curve. >>>>>> That >>>>>> requires cutting up the the triangles of the original surfaces. I've >>>>>> been >>>>>> meaning to try this for years now. I think it would look great. >>>>>> >>>>>> One further comment. Segger makes its region surfaces using the list >>>>>> grid points in the regions, so how does it make the surface look >>>>>> smooth? >>>>>> The main trick it uses is "surface smoothing", 5 iterations with >>>>>> smoothing >>>>>> factor 0.25. You can enable this for the volume surfaces using the >>>>>> Surface >>>>>> and Mesh Options panel and see if it helps. Segger also rebins the >>>>>> grid >>>>>> points which may help the appearance and that is possible but not so >>>>>> easy to >>>>>> duplicate with a volume surface using standard Chimera features. >>>>>> >>>>>> Tom >>>>>> >>>>>>> Hi Ernesto, >>>>>>> >>>>>>> That is a good point, I'm not completely familiar with how the color >>>>>>> zone tool splits out a subsection of the map, so I am cc-ing Tom >>>>>>> Goddard, who I think wrote that tool, and is a developer of Chimera >>>>>>> and co-developer of Segger. Tom, could you look at the message Ernesto >>>>>>> sent and my reply, both below? Let us know if you have any further >>>>>>> insights into how we can make segmented-region-masked maps have nicer >>>>>>> boundaries... >>>>>>> >>>>>>> Greg >>>>>>> >>>>>>> >>>>>>> >>>>>>> On Sun, May 22, 2011 at 8:26 PM, Ernesto >>>>>>> Arias >>>>>>> wrote: >>>>>>>> Hi Greg, >>>>>>>> >>>>>>>> Thanks so much for answering my question. Everything is crystal >>>>>>>> clear. >>>>>>>> For illustrating the segmentation results I can use the segmented >>>>>>>> regions, >>>>>>>> but I wanted to make a morphing and some movies using the segmented >>>>>>>> regions >>>>>>>> and I would be easier if I could save the maps without loosing >>>>>>>> details. >>>>>>>> I >>>>>>>> tried to use a lower threshold and also to filter the volume before >>>>>>>> segmenting it, but the results are not much better. >>>>>>>> >>>>>>>> I'm not a programmer so I'm sorry if I say nonsenses. Using Chimera >>>>>>>> "Color >>>>>>>> zone" tool you can color different regions in the volume using >>>>>>>> markers >>>>>>>> or >>>>>>>> atoms, and it has the option of splitting the colored regions into >>>>>>>> different >>>>>>>> maps and save them. In that case I don't notice a a coarser surface >>>>>>>> in >>>>>>>> the >>>>>>>> manually segmented maps. Could I use the segger information to color >>>>>>>> the >>>>>>>> volume with Color zone, and use the split map option to segment the >>>>>>>> map? >>>>>>>> >>>>>>>> Thanks again for your help, >>>>>>>> Ernesto. >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On Fri, May 20, 2011 at 7:50 AM, Greg Pintilie >>>>>>>> wrote: >>>>>>>>> Hi Ernesto, >>>>>>>>> >>>>>>>>> Sorry for the slow response - but thanks for the message and the >>>>>>>>> question. I believe the artefact you are noticing is that when you >>>>>>>>> mask the map with the segmented region, the map densities are set to >>>>>>>>> 0 >>>>>>>>> everywhere except inside the region. Hence instad of a gradual >>>>>>>>> decrease in density at the boundary, making the surface smooth, as >>>>>>>>> you >>>>>>>>> can see in your original map, now there is a sudden drop from some >>>>>>>>> density value to 0 in the segment-masked map. This manifests itself >>>>>>>>> as >>>>>>>>> a coarser surface (as you describe it, the triangles look bigger >>>>>>>>> because you can actually see them). I've sort of know about this >>>>>>>>> problem for a while, but I'm not sure I know yet a good way to >>>>>>>>> address >>>>>>>>> it. I've tried, for example, to extend the segmented regions by a >>>>>>>>> small number of voxels when masking the map, however this looks even >>>>>>>>> worse (it sometimes looks like little fragments coming out of the >>>>>>>>> surface). As long as you know why this happes (let me know if it's >>>>>>>>> still not clear, and I'll try to explain more), I hope at least it >>>>>>>>> seems reasonable. If you have any ideas on how to address it, please >>>>>>>>> let me know! Meanwhile, here are some things you might try to get >>>>>>>>> around this issue: >>>>>>>>> >>>>>>>>> 1) filter the masked map - use the Volume Data / Volume Filter tool >>>>>>>>> - >>>>>>>>> this will remove some signal from your map, but it will make the >>>>>>>>> boundaries smoother as well >>>>>>>>> >>>>>>>>> 2) if you're mainly concerned about illustrating the segmentation >>>>>>>>> results, re-segment the masked map, and use the segmented region for >>>>>>>>> illustration - the segmented region is always smooth as you might >>>>>>>>> have >>>>>>>>> noticed... >>>>>>>>> >>>>>>>>> I hope this helps, and again let me know if you have any ideas... >>>>>>>>> >>>>>>>>> Greg >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> On Tue, May 17, 2011 at 6:51 PM, Ernesto >>>>>>>>> Arias >>>>>>>>> wrote: >>>>>>>>>> Dear Greg, >>>>>>>>>> >>>>>>>>>> My name is Ernesto and I'm a postdoc in James Berger's lab at UC >>>>>>>>>> Berkeley. >>>>>>>>>> I'm using segment 1.6 built in chimera 1.5.3 and is working >>>>>>>>>> remarkably >>>>>>>>>> well. >>>>>>>>>> I have a question and I'd be grateful if you could answer it. >>>>>>>>>> I want to save in individual mrc files the segmented regions of my >>>>>>>>>> map, >>>>>>>>>> but >>>>>>>>>> when I do it and open the volume of the subregion region it seems >>>>>>>>>> like >>>>>>>>>> the >>>>>>>>>> triangle size is bigger than in the segmentation and in the >>>>>>>>>> original >>>>>>>>>> volume. >>>>>>>>>> I tryed to save the segmented volumes using the "File->save" >>>>>>>>>> options >>>>>>>>>> of >>>>>>>>>> segger as well as "Regions->Mask map with selected", but I get the >>>>>>>>>> same >>>>>>>>>> results. >>>>>>>>>> I don't know if I'm explaining myself clear enough, so I attach two >>>>>>>>>> pictures >>>>>>>>>> to try to illustrate what is happening. >>>>>>>>>> Do you know how can I save segmented regions without this loss of >>>>>>>>>> quality? >>>>>>>>>> >>>>>>>>>> Thanks very much for you help, >>>>>>>>>> Sincerely, >>>>>>>>>> Ernesto. >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>> >> >> > Thanks, Tom. That helped a lot. However, is there anyway to smooth out the masked edge? I end up with chopped voxels (looks like stair-steps), rather than getting an interpolated smooth surface at the edge. This is true whether I am masking directly, or the inverted view. > > Kelly > > On Mon, 16 May 2011 12:18:01 -0700 > Tom Goddard wrote: >> Hi Kelly, >> >> There is no command to position the volume eraser sphere using typed coordinates. >> >> If you want to erase a spherical region centered on the center of a virus map use the shape and mask commands: >> >> shape sphere radius 120 center 0,0,0 coord #0 color blue >> mask #0 #1 invert true >> >> The first command makes a spherical surface of radius 120 Angstroms at center 0,0,0 (Angstroms) in the map #0 coordinate frame colored blue. The second command copies the region of map #0 outside the sphere #1, making a new volume data set. >> >> The main trouble here is figuring out the coordinates of the center of virus map. The virus map origin is set in the Volume dialog Coordinates panel where you specify the grid index for position (0,0,0). In the above example I've got the map origin set to the center of the virus (EMDB 1058, grid index 87 for a size 175 map, base index is 0). You can use >> >> shape sphere radius 120 center #0 color blue >> >> which puts the center at the center of the bounding box of the displayed surface for map #0. But that doesn't in general give you the exact center of symmetry. So it is better to find the exact grid point that is the center of symmetry used when the map was calculated. >> >> Tom >> >>> Hi, >>> >>> I would like to place the origin of the eraser to correspond with the >>> center of my map but haven't found a way to define its position based on >>> coordinates, only by moving it with the mouse. Is there a line command >>> or other menu option that allows me to set the position more precisely? >>> >>> Thanks, >>> Kelly From jeffhu7 at gmail.com Sat Jun 4 18:58:37 2011 From: jeffhu7 at gmail.com (Jeffrey Hu) Date: Sat, 4 Jun 2011 18:58:37 -0700 Subject: [Chimera-users] coordinate rotation measuring Message-ID: Hi, I'm currently working on a gp140 model and have docked coordinates for 2 different conformations. I am trying to measure the rotation between the docked coordinates using the method in the EM-fit tutorial and i had a few questions. How does the "measure rotation #1 #3 showslab true" command measure the rotation? How does it determine the axis of rotation? Is it possible for me to create my own axis? Is there any way to increase the size of the slabs (they are too small visually)? -Thanks! -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Mon Jun 6 12:10:15 2011 From: goddard at sonic.net (Tom Goddard) Date: Mon, 06 Jun 2011 12:10:15 -0700 Subject: [Chimera-users] coordinate rotation measuring In-Reply-To: References: Message-ID: <4DED2617.4000200@sonic.net> Hi Jeffrey, The "measure rotation" command determines the rotation between the coordinate frames of two models that have been moved relative to one another. A rigid motion involves a rotation and a translation. The rotation axis direction and angle is uniquely determined (for rotation angles > 0) but the axis could go through any point in space. Using axes that go through different points just changes the translation needed to achieve the rigid motion. There is a point you can choose the rotation axis to go through such that the translation needed is only parallel the rotation axis. Basically the rigid motion consists of a rotation about this axis, and a translation parallel to that axis. That is the rotation axis placement given by "measure rotation". It does not allow you to place the axis wherever you want. There is currently no option in the measure rotation command to make the slab display larger. You can edit a Python file chimera/share/MatchDomains/__init__.py changing the lines near the end e = 2 # Factor for enlarging square dz = chimera.cross(axis, sq1) * .05 # Thickness vector to say e = 4 dz = chimera.cross(axis, sq1) * .1 to make the slabs bigger. I'll add a feature request to improve the measure rotation command to include slab size options. Tom > Hi, > I'm currently working on a gp140 model and have docked coordinates for > 2 different conformations. I am trying to measure the rotation between > the docked coordinates using the method in the EM-fit tutorial and i > had a few questions. > How does the "measure rotation #1 #3 showslab true" command measure > the rotation? How does it determine the axis of rotation? Is it > possible for me to create my own axis? Is there any way to increase > the size of the slabs (they are too small visually)? > > -Thanks! > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Mon Jun 6 14:18:19 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 6 Jun 2011 14:18:19 -0700 Subject: [Chimera-users] coordinate rotation measuring In-Reply-To: References: Message-ID: <9E46964A-A144-4E02-A14B-2021FE07FD5B@cgl.ucsf.edu> Hi Jeffrey, As an alternative: Chimera also allows defining planes and axes from whatever sets of atoms you like, and making measurements that involve these objects. I don't know how well it applies to your situation, but you could define two planes from corresponding sets of atoms in the two structures, then get the angle between those planes. This can be done with the "Axes/Planes/Centroids" tool (under Tools.... Structure Analysis), or in scripts with the commands "define" and "angle". I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jun 4, 2011, at 6:58 PM, Jeffrey Hu wrote: > Hi, > I'm currently working on a gp140 model and have docked coordinates for 2 different conformations. I am trying to measure the rotation between the docked coordinates using the method in the EM-fit tutorial and i had a few questions. > How does the "measure rotation #1 #3 showslab true" command measure the rotation? How does it determine the axis of rotation? Is it possible for me to create my own axis? Is there any way to increase the size of the slabs (they are too small visually)? > > -Thanks! From matthewd at bcm.edu Mon Jun 6 15:37:47 2011 From: matthewd at bcm.edu (Dougherty, Matthew T) Date: Mon, 6 Jun 2011 17:37:47 -0500 Subject: [Chimera-users] mac default directory Message-ID: <5A4EB281C1666D43919DEEA432B505334AE4D7A1A0@EXCMSMBX03.ad.bcm.edu> Hi- Where is the default directory for movie images on the mac? thanks, Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine From goddard at sonic.net Mon Jun 6 15:59:18 2011 From: goddard at sonic.net (Tom Goddard) Date: Mon, 06 Jun 2011 15:59:18 -0700 Subject: [Chimera-users] mac default directory In-Reply-To: <5A4EB281C1666D43919DEEA432B505334AE4D7A1A0@EXCMSMBX03.ad.bcm.edu> References: <5A4EB281C1666D43919DEEA432B505334AE4D7A1A0@EXCMSMBX03.ad.bcm.edu> Message-ID: <4DED5BC6.7080405@sonic.net> Hi Matt, Chimera puts movie frame images in a system temporary directory obtained from the Python tempfile.gettempdir() routine. If you record a movie with the Chimera "movie encode" command you can see the actual ffmpeg command used to do the encoding in the Chimera reply log (Favorites / Reply Log). Here's an example /usr/local/src/staff/goddard/daily-cocoa64/install/Chimera.app/Contents/Resources/bin/ffmpeg -r 25 -i /var/folders/+g/+gO21g+SFqCxNgLVgIvElk+++TM/-Tmp-/chimovie_hqMi-%05d.ppm -y -f mov -b 2000kb -qscale 8 /Users/goddard/Desktop/test.mov I see that it had the temporary files on my Mac in /var/folders/+g/+gO21g+SFqCxNgLVgIvElk+++TM/-Tmp-/ Checking the Python documentation for gettempdir() I see it looks at the TMPDIR environment variable. On my Mac that is indeed set to this hideous path. Here is the Python documentation for gettempdir() if you need to dig further http://docs.python.org/library/tempfile.html You can set the directory to store the images in the "movie record" command using the "directory" option. http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/movie.html#record-options Tom Dougherty, Matthew T wrote: > Hi- > > Where is the default directory for movie images on the mac? > > thanks, > > > Matthew Dougherty > National Center for Macromolecular Imaging > Baylor College of Medicine > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From gtzotzos at me.com Tue Jun 7 10:12:16 2011 From: gtzotzos at me.com (George Tzotzos) Date: Tue, 07 Jun 2011 19:12:16 +0200 Subject: [Chimera-users] Contacts Message-ID: Hi everybody, I'm trying to analyse AMBER trajectories of protein/ligand complexes. The objective of my exercise is to find out contacts/interactions between the ligand and the receptor in the course of the trajectory. Is there a way of doing this DIRECTLY in Chimera? Or one has to first perform clustering of structures and then work out clashes/contacts on the representative structures that are dumped from the trajectory. Best regards George From meng at cgl.ucsf.edu Tue Jun 7 10:53:40 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 7 Jun 2011 10:53:40 -0700 Subject: [Chimera-users] Contacts In-Reply-To: References: Message-ID: <09B11580-3BDD-4E18-8BC1-354583ADBFA0@cgl.ucsf.edu> Hi George, It can be done directly, although that may generate more data than you really want. First, show your trajectory in Chimera - start MD Movie (under Tools... MD/Ensemble analysis), then enter the file types and file locations. The MD Movie tool lets you play back your trajectory and do a bunch of other stuff, such as running commands at each step. The commands "findhbond" and/or "findclash" could be run for each frame -- these are the command-line implementations of the FindHBond and Find Clashes/Contacts tools. Depending on the command options you use, all the info could be sent to the Reply Log, or written to a different text file for each frame. Before plunging into running the commands at each frame, you would try them out on the Command Line (show the command line using the Chimera Favorites menu) to figure out what options to use. Here are their man pages: Then, choose Per-Frame... Define Script from the MD Movie menu, and enter a Chimera command script containing the desired command(s). The "trajectory and ensemble analysis" tutorial includes using MD Movie and per-frame scripting, and here is a related chimera-users post: All the data for each frame may be more than you want. You might ultimately decide only to run the commands for representative frames. MD Movie can also do clustering: I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jun 7, 2011, at 10:12 AM, George Tzotzos wrote: > Hi everybody, > I'm trying to analyse AMBER trajectories of protein/ligand complexes. The objective of my exercise is to find out contacts/interactions between the ligand and the receptor in the course of the trajectory. > > Is there a way of doing this DIRECTLY in Chimera? Or one has to first perform clustering of structures and then work out clashes/contacts on the representative structures that are dumped from the trajectory. > > Best regards > George From glennm at ucsc.edu Tue Jun 7 14:30:10 2011 From: glennm at ucsc.edu (Glenn Millhauser) Date: Tue, 7 Jun 2011 14:30:10 -0700 Subject: [Chimera-users] creating a peptide bond between two fragments Message-ID: Hi Folks, I am trying to add a four amino acid segment to the N-terminus of a protein in the pdb. I can generate the four residue stretch and move its C-term close to the N-term of the structured protein. I can then select the C' and N atoms, which are about 1.0 Angstrom apart. At that point, I am stuck. Not sure how to add a bond and then create a proper structure. I've played around with Join Models, but no luck. Without a peptide bond recognized by Chimera, ribbons are discontinuous. Any ideas? Many thanks, glenn Glenn L. Millhauser Department of Chemistry & Biochemistry UC Santa Cruz Santa Cruz, CA 95064 831 459 2176 voice 831 566 3337 cell 831 459 2935 fax 831 824 4645 google voice glennm at ucsc.edu http://chemistry.ucsc.edu/~glennm http://www.chemistry.ucsc.edu/faculty/millhauser.html -------------- next part -------------- An HTML attachment was scrubbed... URL: From tstravers at gmail.com Tue Jun 7 19:07:24 2011 From: tstravers at gmail.com (Tim Travers) Date: Tue, 7 Jun 2011 22:07:24 -0400 Subject: [Chimera-users] creating a peptide bond between two fragments In-Reply-To: References: Message-ID: Hi Glenn, You can combine the segments in Chimera into one PDB. What I usually do is go to Favorites->Model Panel (which lists all the segments open in your current session), then there is a button on the right labeled 'copy/combine'. You would want the combine functionality. Check the following for the Model Panel window: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html Alternatively, there's a command-line version of 'combine' (which I haven't used yet); details here: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html Just to add, I would recommend minimizing the structure after combining the segments. This can be done in Chimera with Tools->Structure Editing->Minimize Structure. Also, besides checking the distance between the C and N atoms, you would want to make sure they are in the trans configuration for peptide bonds. In my limited experience, the minimization doesn't always fix peptide bonds that start in the cis configuration. Hope this helps, Tim On Tue, Jun 7, 2011 at 5:30 PM, Glenn Millhauser wrote: > Hi Folks, > I am trying to add a four amino acid segment to the N-terminus of a > protein in the pdb. I can generate the four residue stretch and move its > C-term close to the N-term of the structured protein. I can then select the > C' and N atoms, which are about 1.0 Angstrom apart. At that point, I am > stuck. Not sure how to add a bond and then create a proper structure. I've > played around with Join Models, but no luck. Without a peptide bond > recognized by Chimera, ribbons are discontinuous. Any ideas? > Many thanks, > glenn > > > Glenn L. Millhauser > Department of Chemistry & Biochemistry > UC Santa Cruz > Santa Cruz, CA 95064 > 831 459 2176 voice > 831 566 3337 cell > 831 459 2935 fax > 831 824 4645 google voice > > glennm at ucsc.edu > > http://chemistry.ucsc.edu/~glennm > http://www.chemistry.ucsc.edu/faculty/millhauser.html > > > > > > > > > > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Tue Jun 7 20:16:42 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 7 Jun 2011 20:16:42 -0700 Subject: [Chimera-users] creating a peptide bond between two fragments In-Reply-To: References: Message-ID: <8C3F698A-3844-4349-8A36-00795AC3794D@cgl.ucsf.edu> Hi Glenn, It may be tricky because Join Models requires some overlap of the input structures -- not spatially, as it will move the models for you, but an extra atom from each model that will be eliminated as it is replaced by the other model. It is done that way so you there are fewer geometrical parameters for the user to specify -- only one torsion and one bond length. Here's what I did to attach 1zik chain A to the end of 1gcn chain A. First some setup commands (same stuff could be done with menus and dialogs): open 1gcn open 1zik # display all atoms display # get rid of waters and 1zik chain B just to simplify system delete solvent delete :.b # hide ribbon ~ribbon rlabel For replacement by Join Models, we need an -OXT at the C-term of 1gcn and at least one hydrogen on the N-term of 1zik. Generally if these are missing, they can be added with AddH, or the corresponding command: addh 1gcn already had an OXT on Thr29, but addh was needed to put hydrogens on the terminal N of 1zik Arg1. For Join Models, I select one of those N-term hydrogens of 1zik and the OXT of 1gcn (could also be done with the mouse, Ctrl-click on one and Shift-Ctrl-click on the other): select #1:1.a at h1#0:29.a at oxt Then start Build Structure (under Tools... Structure Editing) and go to Join Models tab. It already has 180 as the torsion angle for the peptide bond that will be created, CA-C-N-CA, so I go ahead and click Apply. Now the whole thing is a joined single model, but there is still an extra hydrogen on the former N-terminal nitrogen of 1zik (since that nitrogen used to be tetrahedral but should now be a planar amide). Remove those incorrectly placed hydrogens. You could select them with the mouse and use command "del sel" or delete by name as in this command: delete :1.a at h2,h3 If you run addh again, it will correctly place a single amide hydrogen on that nitrogen: addh Verify that you get a single continuous ribbon: ribbon # refresh residue labels ~rlabel rlabel I see the numbering may be somewhat unexpected: the whole 1gcn part got negative numbers. We hope to make peptide joining less tricky in the future. Yet another complication is that if you are lacking an OXT, but addh does not add it, it is because Chimera knows that residue is not the "real" C-terminus because it is looking at the SEQRES information in the input file. In that case, you could try removing the SEQRES information from the PDB file before opening it in Chimera and running addh. I hope this helps (rather than discourages!), Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jun 7, 2011, at 2:30 PM, Glenn Millhauser wrote: > Hi Folks, > I am trying to add a four amino acid segment to the N-terminus of a protein in the pdb. I can generate the four residue stretch and move its C-term close to the N-term of the structured protein. I can then select the C' and N atoms, which are about 1.0 Angstrom apart. At that point, I am stuck. Not sure how to add a bond and then create a proper structure. I've played around with Join Models, but no luck. Without a peptide bond recognized by Chimera, ribbons are discontinuous. Any ideas? > Many thanks, > glenn > From glennm at ucsc.edu Tue Jun 7 21:19:30 2011 From: glennm at ucsc.edu (Glenn Millhauser) Date: Tue, 7 Jun 2011 21:19:30 -0700 Subject: [Chimera-users] creating a peptide bond between two fragments In-Reply-To: <8C3F698A-3844-4349-8A36-00795AC3794D@cgl.ucsf.edu> References: <8C3F698A-3844-4349-8A36-00795AC3794D@cgl.ucsf.edu> Message-ID: Thank you Elaine and Tim -- much appreciated. I will give this a try. One more question -- as opposed to linking two fragments, is it possible (and perhaps easier) to build residues one at a time on to the N-term of a protein from the pdb? all the best, glenn On Jun 7, 2011, at 8:16 PM, Elaine Meng wrote: > Hi Glenn, > It may be tricky because Join Models requires some overlap of the input structures -- not spatially, as it will move the models for you, but an extra atom from each model that will be eliminated as it is replaced by the other model. It is done that way so you there are fewer geometrical parameters for the user to specify -- only one torsion and one bond length. > > Here's what I did to attach 1zik chain A to the end of 1gcn chain A. First some setup commands (same stuff could be done with menus and dialogs): > > open 1gcn > open 1zik > # display all atoms > display > # get rid of waters and 1zik chain B just to simplify system > delete solvent > delete :.b > # hide ribbon > ~ribbon > rlabel > > For replacement by Join Models, we need an -OXT at the C-term of 1gcn and at least one hydrogen on the N-term of 1zik. Generally if these are missing, they can be added with AddH, or the corresponding command: > > addh > > 1gcn already had an OXT on Thr29, but addh was needed to put hydrogens on the terminal N of 1zik Arg1. For Join Models, I select one of those N-term hydrogens of 1zik and the OXT of 1gcn (could also be done with the mouse, Ctrl-click on one and Shift-Ctrl-click on the other): > > select #1:1.a at h1#0:29.a at oxt > > Then start Build Structure (under Tools... Structure Editing) and go to Join Models tab. It already has 180 as the torsion angle for the peptide bond that will be created, CA-C-N-CA, so I go ahead and click Apply. > > Now the whole thing is a joined single model, but there is still an extra hydrogen on the former N-terminal nitrogen of 1zik (since that nitrogen used to be tetrahedral but should now be a planar amide). Remove those incorrectly placed hydrogens. You could select them with the mouse and use command "del sel" or delete by name as in this command: > > delete :1.a at h2,h3 > > If you run addh again, it will correctly place a single amide hydrogen on that nitrogen: > > addh > > Verify that you get a single continuous ribbon: > > ribbon > # refresh residue labels > ~rlabel > rlabel > > I see the numbering may be somewhat unexpected: the whole 1gcn part got negative numbers. We hope to make peptide joining less tricky in the future. > > Yet another complication is that if you are lacking an OXT, but addh does not add it, it is because Chimera knows that residue is not the "real" C-terminus because it is looking at the SEQRES information in the input file. In that case, you could try removing the SEQRES information from the PDB file before opening it in Chimera and running addh. > > I hope this helps (rather than discourages!), > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > > On Jun 7, 2011, at 2:30 PM, Glenn Millhauser wrote: > >> Hi Folks, >> I am trying to add a four amino acid segment to the N-terminus of a protein in the pdb. I can generate the four residue stretch and move its C-term close to the N-term of the structured protein. I can then select the C' and N atoms, which are about 1.0 Angstrom apart. At that point, I am stuck. Not sure how to add a bond and then create a proper structure. I've played around with Join Models, but no luck. Without a peptide bond recognized by Chimera, ribbons are discontinuous. Any ideas? >> Many thanks, >> glenn >> > Glenn Millhauser Department of Chemistry & Biochemistry UC Santa Cruz Santa Cruz, CA 95064 831 459 2176 voice 831 459 2935 fax 831 566 3337 cell 831 824 4645 google voice glennm at ucsc.edu http://chemistry.ucsc.edu/~glennm From meng at cgl.ucsf.edu Wed Jun 8 09:12:22 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 8 Jun 2011 09:12:22 -0700 Subject: [Chimera-users] creating a peptide bond between two fragments In-Reply-To: References: <8C3F698A-3844-4349-8A36-00795AC3794D@cgl.ucsf.edu> Message-ID: <173D696B-41BE-4EB6-B685-E5619717DA7A@cgl.ucsf.edu> Hi Glenn, If you were building out from the C-term, the "addaa" command would probably be the easiest approach in Chimera. However, for putting residues on the N-term or for joining two experimentally determined structures, Join Models (part of Build Structure) is generally the way to go. Start Structure (another part of Build Structure) allows creating peptides with specified phi,psi angles. The alternative presented by Tim is positioning the models "manually" and then combining them into a single model with Chimera, then adding a bond. Personally, I usually find it too difficult to position the models correctly and would rather let Join Models take care of that part. Minimization has limited power in correcting the result. However, if the two structures have several atoms' overlap (say a few redundant residues), you could use the "match" command to superimpose the overlapping parts, then delete the redundant atoms, then combine into a single model and add the bond. That works pretty well if the match atoms are in approximately the same conformation. I've used that approach before we had Join Models, for example to splice an NMR-determined peptide structure on the end of an X-ray structure in which those residues were not resolved. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jun 7, 2011, at 9:19 PM, Glenn Millhauser wrote: > Thank you Elaine and Tim -- much appreciated. I will give this a try. One more question -- as opposed to linking two fragments, is it possible (and perhaps easier) to build residues one at a time on to the N-term of a protein from the pdb? > all the best, > glenn > > > On Jun 7, 2011, at 8:16 PM, Elaine Meng wrote: > >> Hi Glenn, >> It may be tricky because Join Models requires some overlap of the input structures -- not spatially, as it will move the models for you, but an extra atom from each model that will be eliminated as it is replaced by the other model. It is done that way so you there are fewer geometrical parameters for the user to specify -- only one torsion and one bond length. >> >> Here's what I did to attach 1zik chain A to the end of 1gcn chain A. First some setup commands (same stuff could be done with menus and dialogs): >> >> open 1gcn >> open 1zik >> # display all atoms >> display >> # get rid of waters and 1zik chain B just to simplify system >> delete solvent >> delete :.b >> # hide ribbon >> ~ribbon >> rlabel >> >> For replacement by Join Models, we need an -OXT at the C-term of 1gcn and at least one hydrogen on the N-term of 1zik. Generally if these are missing, they can be added with AddH, or the corresponding command: >> >> addh >> >> 1gcn already had an OXT on Thr29, but addh was needed to put hydrogens on the terminal N of 1zik Arg1. For Join Models, I select one of those N-term hydrogens of 1zik and the OXT of 1gcn (could also be done with the mouse, Ctrl-click on one and Shift-Ctrl-click on the other): >> >> select #1:1.a at h1#0:29.a at oxt >> >> Then start Build Structure (under Tools... Structure Editing) and go to Join Models tab. It already has 180 as the torsion angle for the peptide bond that will be created, CA-C-N-CA, so I go ahead and click Apply. >> >> Now the whole thing is a joined single model, but there is still an extra hydrogen on the former N-terminal nitrogen of 1zik (since that nitrogen used to be tetrahedral but should now be a planar amide). Remove those incorrectly placed hydrogens. You could select them with the mouse and use command "del sel" or delete by name as in this command: >> >> delete :1.a at h2,h3 >> >> If you run addh again, it will correctly place a single amide hydrogen on that nitrogen: >> >> addh >> >> Verify that you get a single continuous ribbon: >> >> ribbon >> # refresh residue labels >> ~rlabel >> rlabel >> >> I see the numbering may be somewhat unexpected: the whole 1gcn part got negative numbers. We hope to make peptide joining less tricky in the future. >> >> Yet another complication is that if you are lacking an OXT, but addh does not add it, it is because Chimera knows that residue is not the "real" C-terminus because it is looking at the SEQRES information in the input file. In that case, you could try removing the SEQRES information from the PDB file before opening it in Chimera and running addh. >> >> I hope this helps (rather than discourages!), >> Elaine >> ----- >> Elaine C. Meng, Ph.D. >> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >> >> >> On Jun 7, 2011, at 2:30 PM, Glenn Millhauser wrote: >> >>> Hi Folks, >>> I am trying to add a four amino acid segment to the N-terminus of a protein in the pdb. I can generate the four residue stretch and move its C-term close to the N-term of the structured protein. I can then select the C' and N atoms, which are about 1.0 Angstrom apart. At that point, I am stuck. Not sure how to add a bond and then create a proper structure. I've played around with Join Models, but no luck. Without a peptide bond recognized by Chimera, ribbons are discontinuous. Any ideas? >>> Many thanks, >>> glenn >>> >> > > > > Glenn Millhauser > Department of Chemistry & Biochemistry > UC Santa Cruz > Santa Cruz, CA 95064 > > 831 459 2176 voice > 831 459 2935 fax > 831 566 3337 cell > 831 824 4645 google voice > > glennm at ucsc.edu > > http://chemistry.ucsc.edu/~glennm > > > > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From glennm at ucsc.edu Wed Jun 8 21:05:54 2011 From: glennm at ucsc.edu (Glenn Millhauser) Date: Wed, 8 Jun 2011 21:05:54 -0700 Subject: [Chimera-users] creating a peptide bond between two fragments In-Reply-To: <173D696B-41BE-4EB6-B685-E5619717DA7A@cgl.ucsf.edu> References: <8C3F698A-3844-4349-8A36-00795AC3794D@cgl.ucsf.edu> <173D696B-41BE-4EB6-B685-E5619717DA7A@cgl.ucsf.edu> Message-ID: Terrific -- many thanks, Elaine. That does help. all the best, glenn On Jun 8, 2011, at 9:12 AM, Elaine Meng wrote: > Hi Glenn, > If you were building out from the C-term, the "addaa" command would probably be the easiest approach in Chimera. > > > However, for putting residues on the N-term or for joining two experimentally determined structures, Join Models (part of Build Structure) is generally the way to go. Start Structure (another part of Build Structure) allows creating peptides with specified phi,psi angles. > > > The alternative presented by Tim is positioning the models "manually" and then combining them into a single model with Chimera, then adding a bond. Personally, I usually find it too difficult to position the models correctly and would rather let Join Models take care of that part. Minimization has limited power in correcting the result. However, if the two structures have several atoms' overlap (say a few redundant residues), you could use the "match" command to superimpose the overlapping parts, then delete the redundant atoms, then combine into a single model and add the bond. That works pretty well if the match atoms are in approximately the same conformation. I've used that approach before we had Join Models, for example to splice an NMR-determined peptide structure on the end of an X-ray structure in which those residues were not resolved. > > I hope this helps, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > > On Jun 7, 2011, at 9:19 PM, Glenn Millhauser wrote: > >> Thank you Elaine and Tim -- much appreciated. I will give this a try. One more question -- as opposed to linking two fragments, is it possible (and perhaps easier) to build residues one at a time on to the N-term of a protein from the pdb? >> all the best, >> glenn >> >> >> On Jun 7, 2011, at 8:16 PM, Elaine Meng wrote: >> >>> Hi Glenn, >>> It may be tricky because Join Models requires some overlap of the input structures -- not spatially, as it will move the models for you, but an extra atom from each model that will be eliminated as it is replaced by the other model. It is done that way so you there are fewer geometrical parameters for the user to specify -- only one torsion and one bond length. >>> >>> Here's what I did to attach 1zik chain A to the end of 1gcn chain A. First some setup commands (same stuff could be done with menus and dialogs): >>> >>> open 1gcn >>> open 1zik >>> # display all atoms >>> display >>> # get rid of waters and 1zik chain B just to simplify system >>> delete solvent >>> delete :.b >>> # hide ribbon >>> ~ribbon >>> rlabel >>> >>> For replacement by Join Models, we need an -OXT at the C-term of 1gcn and at least one hydrogen on the N-term of 1zik. Generally if these are missing, they can be added with AddH, or the corresponding command: >>> >>> addh >>> >>> 1gcn already had an OXT on Thr29, but addh was needed to put hydrogens on the terminal N of 1zik Arg1. For Join Models, I select one of those N-term hydrogens of 1zik and the OXT of 1gcn (could also be done with the mouse, Ctrl-click on one and Shift-Ctrl-click on the other): >>> >>> select #1:1.a at h1#0:29.a at oxt >>> >>> Then start Build Structure (under Tools... Structure Editing) and go to Join Models tab. It already has 180 as the torsion angle for the peptide bond that will be created, CA-C-N-CA, so I go ahead and click Apply. >>> >>> Now the whole thing is a joined single model, but there is still an extra hydrogen on the former N-terminal nitrogen of 1zik (since that nitrogen used to be tetrahedral but should now be a planar amide). Remove those incorrectly placed hydrogens. You could select them with the mouse and use command "del sel" or delete by name as in this command: >>> >>> delete :1.a at h2,h3 >>> >>> If you run addh again, it will correctly place a single amide hydrogen on that nitrogen: >>> >>> addh >>> >>> Verify that you get a single continuous ribbon: >>> >>> ribbon >>> # refresh residue labels >>> ~rlabel >>> rlabel >>> >>> I see the numbering may be somewhat unexpected: the whole 1gcn part got negative numbers. We hope to make peptide joining less tricky in the future. >>> >>> Yet another complication is that if you are lacking an OXT, but addh does not add it, it is because Chimera knows that residue is not the "real" C-terminus because it is looking at the SEQRES information in the input file. In that case, you could try removing the SEQRES information from the PDB file before opening it in Chimera and running addh. >>> >>> I hope this helps (rather than discourages!), >>> Elaine >>> ----- >>> Elaine C. Meng, Ph.D. >>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >>> Department of Pharmaceutical Chemistry >>> University of California, San Francisco >>> >>> >>> >>> On Jun 7, 2011, at 2:30 PM, Glenn Millhauser wrote: >>> >>>> Hi Folks, >>>> I am trying to add a four amino acid segment to the N-terminus of a protein in the pdb. I can generate the four residue stretch and move its C-term close to the N-term of the structured protein. I can then select the C' and N atoms, which are about 1.0 Angstrom apart. At that point, I am stuck. Not sure how to add a bond and then create a proper structure. I've played around with Join Models, but no luck. Without a peptide bond recognized by Chimera, ribbons are discontinuous. Any ideas? >>>> Many thanks, >>>> glenn >>>> >>> >> >> >> >> Glenn Millhauser >> Department of Chemistry & Biochemistry >> UC Santa Cruz >> Santa Cruz, CA 95064 >> >> 831 459 2176 voice >> 831 459 2935 fax >> 831 566 3337 cell >> 831 824 4645 google voice >> >> glennm at ucsc.edu >> >> http://chemistry.ucsc.edu/~glennm >> >> >> >> >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > Glenn Millhauser Department of Chemistry & Biochemistry UC Santa Cruz Santa Cruz, CA 95064 831 459 2176 voice 831 459 2935 fax 831 566 3337 cell 831 824 4645 google voice glennm at ucsc.edu http://chemistry.ucsc.edu/~glennm From meng at cgl.ucsf.edu Thu Jun 9 13:30:22 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 9 Jun 2011 13:30:22 -0700 Subject: [Chimera-users] [chimera-dev] Protofibril model In-Reply-To: <201106091913.p59JDJbS022053@fafnir.cs.unc.edu> References: <201106091913.p59JDJbS022053@fafnir.cs.unc.edu> Message-ID: <865D94CF-7BB4-4C33-952D-5B6178EAFB1A@cgl.ucsf.edu> Dear Lihong and others, The Multiscale Models tool in Chimera is meant for this purpose --- it shows low-resolution surfaces, which are often preferred for large complexes. In Chimera I tried opening 1ei3, then started Multiscale Models (in menu under Tools... Higher-Order Structure), then clicked the "Make models" button at the bottom of the multiscale dialog. This shows the structure with low-resolution surfaces and automatically uses different colors for the different chains. You can adjust the colors, surface resolution, etc. in the dialog. Click the dialog's Help button to see its manual page. There is also a copy here: I also tried it with 1m1j, which also worked fine on my computer. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jun 9, 2011, at 12:13 PM, Russell M. Taylor II wrote: > Dear Lihong, > I am glad to hear that Chimera let you start down this path. > I'm CCing the Chimera developer mailing list in case they know of a better solution. > You can also join the chimera users list at http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users/index.html and then post a query there. > > The following is a somewhat convoluted path to get where you want to go. Hopefully someone on one of the above mailing lists will know a better one. If you need to go down this path, we should probably set a time for us to sit down together and go through this. > > Download MGLTools from http://mgltools.scripps.edu/downloads. I ran the Windows installer. > This launched the Python Molecule Viewer. > Select Compute/Coarse Molecular Surface. Kept the default parameters. This produced a surface that was near the outside of the molecule. > Clicked to turn off the red dot under the CPK label so that we only see the surface. > Selected File/Save/VRML 2.0 (.wrl) file. Also saved STL file. > > I was able to load the resulting .wrl file back into Chimera. This should provide you with a simplified model. You should be able to adjust the parameters for the coarse saving to get different model quality. > > I attach the resulting coarse model (inside a Zip file) to this email. > Russ > > [Things below I tried that didn't work] > > (Fine surface) > Select File/Read Molecule. Opened 1EI3.pdb (when I used 1M1J.pdb, it crashed trying to make the surface). > Compute/Molecular Surface/Compute Molecular Surface. Used the default parameters (other parameters caused it to crash). This produced a fine molecular surface. This could be used directly or simplified. > > VMD uses a program called MSMS, but can't run it. When I go to the MSMS home page, it eventually redirects me to MGLTools from Scripps. > > NOPE: > > You can load the PDB file into the VMD program (File/New, select the file name and click Load on the Molecule File Browser). Then select Graphics/Representations from the VMD Main menu. Then pull down Drawing Method and select Surf. Turn off the "Apply Changes Automatically" control and then set the Probe Radius to 4.0 and click Apply. > To turn off the little axes display, select Display/Axes/Off > To save the resulting geometry, select File/Render from the main menu. Pull down "Render using" and select Wavefront. Change the .obj file name to one that is useful to you (I named id protofibril.obj). Click the "Start Rendering" button. > > Open Blender (available from blender.org). Press delete to get rid of the cube that is created by default. > Select File/Import/Wavefront to load the model. Pick the file name and then click "Import a Wavefront OBJ" > > At 10:18 AM 6/7/2011, lihong huang wrote: >> Dear Dr. Taylor, >> >> I am postdoc working in Dr. Susan Lord's lab. According to your suggestion, we set up the protofibril model using UCSF Chimera program which is very nice. Now we want to move on to make small fiber model, however, the program run very slowly when we add more fibrinogen molecules. We are thinking if we could make the fibrinogen molecule lose more details, maybe the program could run easily. Do you know which program could do this? We just want to show the basic shape of fibrinogen, no needs to show very detailed part, such as alpha, beta and gamma chains. Thanks a lot for your help. >> >> Lihong Huang, >> Postdco >> Pathology and lab medicine > > --- > Russell M. Taylor II, Ph.D. taylorr at cs.unc.edu > CB #3175, Sitterson Hall www.cs.unc.edu/~taylorr > University of North Carolina, Voice: (919) 962-1701 > Chapel Hill, NC 27599-3175 FAX: (919) 962-1799 _______________________________________________ > Chimera-dev mailing list > Chimera-dev at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev From goddard at sonic.net Thu Jun 9 16:19:50 2011 From: goddard at sonic.net (Tom Goddard) Date: Thu, 09 Jun 2011 16:19:50 -0700 Subject: [Chimera-users] [chimera-dev] Protofibril model In-Reply-To: <865D94CF-7BB4-4C33-952D-5B6178EAFB1A@cgl.ucsf.edu> References: <201106091913.p59JDJbS022053@fafnir.cs.unc.edu> <865D94CF-7BB4-4C33-952D-5B6178EAFB1A@cgl.ucsf.edu> Message-ID: <4DF15516.9070104@sonic.net> Hi Lihong, The sym command in Chimera can also make copies of molecules and display them as surfaces. I've attached an image where I made 5 copies of fibrinogen 1ei3 into a filament with the following commands: open 1ei3 sym #0 group t,5,280 axis 1,0,.4 coord #0 surf true The spacing of the copies is 280 Angstroms along direction 1,0,.4 and the copies are shown as surfaces. This makes a model whose style can be changed with the multiscale dialog and I changed surface resolution to 3 Angstroms and showed one copy as ribbon. I tried 500 copies and Chimera had no trouble with it -- took a few seconds to create and then rotated at several frames per second. Here's an actin filament network that was made by putting REMARK 350 BIOMT matrices in a PDB file of an actin monomer and also the ARP2/3 junction complex. http://www.cgl.ucsf.edu/chimera/ImageGallery/entries/actin/actin.html The matrices were generated by a script to make a branching tree structure. http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/sym.html Tom > Dear Lihong and others, > The Multiscale Models tool in Chimera is meant for this purpose --- it shows low-resolution surfaces, which are often preferred for large complexes. > > In Chimera I tried opening 1ei3, then started Multiscale Models (in menu under Tools... Higher-Order Structure), then clicked the "Make models" button at the bottom of the multiscale dialog. This shows the structure with low-resolution surfaces and automatically uses different colors for the different chains. You can adjust the colors, surface resolution, etc. in the dialog. Click the dialog's Help button to see its manual page. There is also a copy here: > > > I also tried it with 1m1j, which also worked fine on my computer. > > I hope this helps, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Jun 9, 2011, at 12:13 PM, Russell M. Taylor II wrote: > >> Dear Lihong, >> I am glad to hear that Chimera let you start down this path. >> I'm CCing the Chimera developer mailing list in case they know of a better solution. >> You can also join the chimera users list at http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users/index.html and then post a query there. >> >> The following is a somewhat convoluted path to get where you want to go. Hopefully someone on one of the above mailing lists will know a better one. If you need to go down this path, we should probably set a time for us to sit down together and go through this. >> >> Download MGLTools from http://mgltools.scripps.edu/downloads. I ran the Windows installer. >> This launched the Python Molecule Viewer. >> Select Compute/Coarse Molecular Surface. Kept the default parameters. This produced a surface that was near the outside of the molecule. >> Clicked to turn off the red dot under the CPK label so that we only see the surface. >> Selected File/Save/VRML 2.0 (.wrl) file. Also saved STL file. >> >> I was able to load the resulting .wrl file back into Chimera. This should provide you with a simplified model. You should be able to adjust the parameters for the coarse saving to get different model quality. >> >> I attach the resulting coarse model (inside a Zip file) to this email. >> Russ >> >> [Things below I tried that didn't work] >> >> (Fine surface) >> Select File/Read Molecule. Opened 1EI3.pdb (when I used 1M1J.pdb, it crashed trying to make the surface). >> Compute/Molecular Surface/Compute Molecular Surface. Used the default parameters (other parameters caused it to crash). This produced a fine molecular surface. This could be used directly or simplified. >> >> VMD uses a program called MSMS, but can't run it. When I go to the MSMS home page, it eventually redirects me to MGLTools from Scripps. >> >> NOPE: >> >> You can load the PDB file into the VMD program (File/New, select the file name and click Load on the Molecule File Browser). Then select Graphics/Representations from the VMD Main menu. Then pull down Drawing Method and select Surf. Turn off the "Apply Changes Automatically" control and then set the Probe Radius to 4.0 and click Apply. >> To turn off the little axes display, select Display/Axes/Off >> To save the resulting geometry, select File/Render from the main menu. Pull down "Render using" and select Wavefront. Change the .obj file name to one that is useful to you (I named id protofibril.obj). Click the "Start Rendering" button. >> >> Open Blender (available from blender.org). Press delete to get rid of the cube that is created by default. >> Select File/Import/Wavefront to load the model. Pick the file name and then click "Import a Wavefront OBJ" >> >> At 10:18 AM 6/7/2011, lihong huang wrote: >>> Dear Dr. Taylor, >>> >>> I am postdoc working in Dr. Susan Lord's lab. According to your suggestion, we set up the protofibril model using UCSF Chimera program which is very nice. Now we want to move on to make small fiber model, however, the program run very slowly when we add more fibrinogen molecules. We are thinking if we could make the fibrinogen molecule lose more details, maybe the program could run easily. Do you know which program could do this? We just want to show the basic shape of fibrinogen, no needs to show very detailed part, such as alpha, beta and gamma chains. Thanks a lot for your help. >>> >>> Lihong Huang, >>> Postdco >>> Pathology and lab medicine >> --- >> Russell M. Taylor II, Ph.D. taylorr at cs.unc.edu >> CB #3175, Sitterson Hall www.cs.unc.edu/~taylorr >> University of North Carolina, Voice: (919) 962-1701 >> Chapel Hill, NC 27599-3175 FAX: (919) 962-1799_______________________________________________ >> Chimera-dev mailing list >> Chimera-dev at cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > -------------- next part -------------- A non-text attachment was scrubbed... Name: 1ei3.jpg Type: image/jpeg Size: 40646 bytes Desc: not available URL: From jchinu2014 at gmail.com Fri Jun 10 18:26:12 2011 From: jchinu2014 at gmail.com (chinmaya joshi) Date: Fri, 10 Jun 2011 18:26:12 -0700 Subject: [Chimera-users] help Message-ID: Hello, I want to write a script in python to open a set of images in chimera set a viewpoint(rotate, translate,etc). and make a movie out of them all through command line for my project. Can someone please let me know how it can be done. I am new to python. Can anyone tell me any good links for these? The documentation on chimera ucsf is a bit confusing. Thanks. Chinmaya -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Fri Jun 10 18:42:54 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 10 Jun 2011 18:42:54 -0700 Subject: [Chimera-users] help In-Reply-To: References: Message-ID: <99037B5F-0ECB-4665-9B75-303F404EC242@cgl.ucsf.edu> Hi Chinmaya, Before you start scripting, the first thing to consider is whether Chimera can do what you want. Have you tried doing what you want to show in the movie, but while using Chimera interactively? From your description, I am concerned that Chimera may not read your input format. The input types are generally 3D data files, not images. The one exception is that an image stack can be used as a "volume data" input format. Here is information on what formats Chimera can read: If you think Chimera can do what you want, here is information on making movies, ...including commands for rotation and translation, etc. ...and example scripts ...however, these examples are Chimera command scripts, not python scripts. I think python scripts would be more difficult to make than Chimera command scripts, and you would only start working with python if (A) Chimera can do what you want or nearly so, but (B) there are no Chimera commands for those things. After you figure out what you want to do by using Chimera interactively, then figure out the commands for those actions, then put them into a script. The last step would be to add movie recording commands to that script. I don't know python, so I can't say any more about using that approach. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jun 10, 2011, at 6:26 PM, chinmaya joshi wrote: > Hello, > I want to write a script in python to open a set of images in chimera set a viewpoint(rotate, translate,etc). and make a movie out of them all through command line for my project. > > Can someone please let me know how it can be done. > > I am new to python. > > Can anyone tell me any good links for these? > > The documentation on chimera ucsf is a bit confusing. > Thanks. > Chinmaya From jchinu2014 at gmail.com Sat Jun 11 12:34:00 2011 From: jchinu2014 at gmail.com (chinmaya joshi) Date: Sat, 11 Jun 2011 15:34:00 -0400 Subject: [Chimera-users] help In-Reply-To: <99037B5F-0ECB-4665-9B75-303F404EC242@cgl.ucsf.edu> References: <99037B5F-0ECB-4665-9B75-303F404EC242@cgl.ucsf.edu> Message-ID: Hello Elaine, Thanks a lot for your mail. I am working on the points you have suggested. However I am a bit confused whether my input files will work in chimera or not? Herewith I am attaching a sample example of the dataset which I will be taking as the input, perform some viewpoint operation on it and then make a movie. Can you please let me know whether this can be done in chimera or not? If yes, can it be done in a python script file? Regards, Chinmaya Joshi On Fri, Jun 10, 2011 at 9:42 PM, Elaine Meng wrote: > Hi Chinmaya, > Before you start scripting, the first thing to consider is whether Chimera > can do what you want. Have you tried doing what you want to show in the > movie, but while using Chimera interactively? From your description, I am > concerned that Chimera may not read your input format. The input types are > generally 3D data files, not images. The one exception is that an image > stack can be used as a "volume data" input format. Here is information on > what formats Chimera can read: > > > If you think Chimera can do what you want, here is information on making > movies, > > > ...including commands for rotation and translation, etc. > > > > ...and example scripts > > > ...however, these examples are Chimera command scripts, not python scripts. > I think python scripts would be more difficult to make than Chimera command > scripts, and you would only start working with python if (A) Chimera can do > what you want or nearly so, but (B) there are no Chimera commands for those > things. After you figure out what you want to do by using Chimera > interactively, then figure out the commands for those actions, then put them > into a script. The last step would be to add movie recording commands to > that script. > > I don't know python, so I can't say any more about using that approach. > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Jun 10, 2011, at 6:26 PM, chinmaya joshi wrote: > > > Hello, > > I want to write a script in python to open a set of images in chimera set > a viewpoint(rotate, translate,etc). and make a movie out of them all through > command line for my project. > > > > Can someone please let me know how it can be done. > > > > I am new to python. > > > > Can anyone tell me any good links for these? > > > > The documentation on chimera ucsf is a bit confusing. > > Thanks. > > Chinmaya > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: pointcloud.csv Type: text/csv Size: 16777 bytes Desc: not available URL: From meng at cgl.ucsf.edu Sat Jun 11 13:42:25 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Sat, 11 Jun 2011 13:42:25 -0700 Subject: [Chimera-users] help In-Reply-To: References: <99037B5F-0ECB-4665-9B75-303F404EC242@cgl.ucsf.edu> Message-ID: Hi Chinmaya, The way to see if Chimera opens your file is to either (A) look at the list of file types in the link I sent in the previous message, or (B) start Chimera, and try using File... Open in the menu. However, no: Chimera does not read a ".csv" file. You never said what your file is supposed to contain, but from the name and contents of the file it appears to be x,y,z coordinates of a bunch of dots. If you just want to display this as a bunch of dots or spheres in Chimera, you could convert this file (write a script to do it in any language you like) to the simple "BILD" text format described here: Then the "BILD" file (name it something.bild) can be opened in Chimera to display the dots or spheres. As I mentioned earlier I do not know python, and I don't recommend it in this case. Using python would require some knowledge of Chimera code. Instead use a Chimera command script. Just start Chimera, open the BILD file, show the Chimera command line (choose from the Favorites menu), try typing in commands. Figure out the movement commands you want, then put the commands and movie-recording commands in text file to make the Chimera script. Command "roll" does rotation, "move" does translation, "scale" does scaling, "movie" does the movie stuff. The script might be as simple as: movie record roll y 1 360; wait wait 10 movie stop movie encode mformat mov output /MyPath/mymovie.mov ... but you would need to look at the command documentation to see what options you want. There are links to that documentation and to example Chimera command scripts in my previous message. Elaine On Jun 11, 2011, at 12:34 PM, chinmaya joshi wrote: > Hello Elaine, > > Thanks a lot for your mail. I am working on the points you have suggested. However I am a bit confused whether my input files will work in chimera or not? > Herewith I am attaching a sample example of the dataset which I will be taking as the input, perform some viewpoint operation on it and then make a movie. > Can you please let me know whether this can be done in chimera or not? > If yes, can it be done in a python script file? > > Regards, > Chinmaya Joshi > > On Fri, Jun 10, 2011 at 9:42 PM, Elaine Meng wrote: > Hi Chinmaya, > Before you start scripting, the first thing to consider is whether Chimera can do what you want. Have you tried doing what you want to show in the movie, but while using Chimera interactively? From your description, I am concerned that Chimera may not read your input format. The input types are generally 3D data files, not images. The one exception is that an image stack can be used as a "volume data" input format. Here is information on what formats Chimera can read: > > > If you think Chimera can do what you want, here is information on making movies, > > > ...including commands for rotation and translation, etc. > > > ...and example scripts > > > ...however, these examples are Chimera command scripts, not python scripts. I think python scripts would be more difficult to make than Chimera command scripts, and you would only start working with python if (A) Chimera can do what you want or nearly so, but (B) there are no Chimera commands for those things. After you figure out what you want to do by using Chimera interactively, then figure out the commands for those actions, then put them into a script. The last step would be to add movie recording commands to that script. > > I don't know python, so I can't say any more about using that approach. > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Jun 10, 2011, at 6:26 PM, chinmaya joshi wrote: > > > Hello, > > I want to write a script in python to open a set of images in chimera set a viewpoint(rotate, translate,etc). and make a movie out of them all through command line for my project. > > > > Can someone please let me know how it can be done. > > > > I am new to python. > > > > Can anyone tell me any good links for these? > > > > The documentation on chimera ucsf is a bit confusing. > > Thanks. > > Chinmaya > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From jchinu2014 at gmail.com Sat Jun 11 15:24:29 2011 From: jchinu2014 at gmail.com (chinmaya joshi) Date: Sat, 11 Jun 2011 18:24:29 -0400 Subject: [Chimera-users] help In-Reply-To: References: <99037B5F-0ECB-4665-9B75-303F404EC242@cgl.ucsf.edu> Message-ID: Hey Elaine, Thanks for the mail. Just open the file in notepad and save it as .xyz (dont need to do that I am attaching the file here now) Then I have just opened this .xyz file in chimera and chimera loads the desired image(attached: open with notepad or any text editor)(I have also attached the output image of chimera) Now my question is that How do I use the script calle xyzmap.py on the following link http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts for opening the above file from the command line. what should I replace the 'xyz_path' and the 'xyz_list' in the xyzmap.py code with? Regards, Chinmaya On Sat, Jun 11, 2011 at 4:42 PM, Elaine Meng wrote: > Hi Chinmaya, > The way to see if Chimera opens your file is to either > (A) look at the list of file types in the link I sent in the previous > message, or > (B) start Chimera, and try using File... Open in the menu. > > However, no: Chimera does not read a ".csv" file. You never said what > your file is supposed to contain, but from the name and contents of the file > it appears to be x,y,z coordinates of a bunch of dots. If you just want to > display this as a bunch of dots or spheres in Chimera, you could convert > this file (write a script to do it in any language you like) to the simple > "BILD" text format described here: > > > Then the "BILD" file (name it something.bild) can be opened in Chimera to > display the dots or spheres. > > As I mentioned earlier I do not know python, and I don't recommend it in > this case. Using python would require some knowledge of Chimera code. > Instead use a Chimera command script. > > Just start Chimera, open the BILD file, show the Chimera command line > (choose from the Favorites menu), try typing in commands. Figure out the > movement commands you want, then put the commands and movie-recording > commands in text file to make the Chimera script. Command "roll" does > rotation, "move" does translation, "scale" does scaling, "movie" does the > movie stuff. The script might be as simple as: > > movie record > roll y 1 360; wait > wait 10 > movie stop > movie encode mformat mov output /MyPath/mymovie.mov > > ... but you would need to look at the command documentation to see what > options you want. There are links to that documentation and to example > Chimera command scripts in my previous message. > Elaine > > On Jun 11, 2011, at 12:34 PM, chinmaya joshi wrote: > > > Hello Elaine, > > > > Thanks a lot for your mail. I am working on the points you have > suggested. However I am a bit confused whether my input files will work in > chimera or not? > > Herewith I am attaching a sample example of the dataset which I will be > taking as the input, perform some viewpoint operation on it and then make a > movie. > > Can you please let me know whether this can be done in chimera or not? > > If yes, can it be done in a python script file? > > > > Regards, > > Chinmaya Joshi > > > > On Fri, Jun 10, 2011 at 9:42 PM, Elaine Meng wrote: > > Hi Chinmaya, > > Before you start scripting, the first thing to consider is whether > Chimera can do what you want. Have you tried doing what you want to show in > the movie, but while using Chimera interactively? From your description, I > am concerned that Chimera may not read your input format. The input types > are generally 3D data files, not images. The one exception is that an image > stack can be used as a "volume data" input format. Here is information on > what formats Chimera can read: > > > > > > If you think Chimera can do what you want, here is information on making > movies, > > > > > > ...including commands for rotation and translation, etc. > > < > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html#moviecommands> > > > > ...and example scripts > > > > > > ...however, these examples are Chimera command scripts, not python > scripts. I think python scripts would be more difficult to make than Chimera > command scripts, and you would only start working with python if (A) Chimera > can do what you want or nearly so, but (B) there are no Chimera commands for > those things. After you figure out what you want to do by using Chimera > interactively, then figure out the commands for those actions, then put them > into a script. The last step would be to add movie recording commands to > that script. > > > > I don't know python, so I can't say any more about using that approach. > > > > I hope this helps, > > Elaine > > ----- > > Elaine C. Meng, Ph.D. > > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > > Department of Pharmaceutical Chemistry > > University of California, San Francisco > > > > On Jun 10, 2011, at 6:26 PM, chinmaya joshi wrote: > > > > > Hello, > > > I want to write a script in python to open a set of images in chimera > set a viewpoint(rotate, translate,etc). and make a movie out of them all > through command line for my project. > > > > > > Can someone please let me know how it can be done. > > > > > > I am new to python. > > > > > > Can anyone tell me any good links for these? > > > > > > The documentation on chimera ucsf is a bit confusing. > > > Thanks. > > > Chinmaya > > > > > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users at cgl.ucsf.edu > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: trial5.xyz Type: chemical/x-pdb Size: 18321 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image_stickman2.png Type: image/png Size: 7901 bytes Desc: not available URL: From meng at cgl.ucsf.edu Sun Jun 12 10:05:13 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Sun, 12 Jun 2011 10:05:13 -0700 Subject: [Chimera-users] help In-Reply-To: References: <99037B5F-0ECB-4665-9B75-303F404EC242@cgl.ucsf.edu> Message-ID: <34708863-C809-4F8D-B40E-BE81DA993D2D@cgl.ucsf.edu> Hi Chinmaya, Forget the script, just use the Chimera "molmap" command. That python script may have been written before we had the command. Now that you already figured out an input format and opened it in Chimera, you only need to show the command line (from Favorites menu in Chimera) and enter one "molmap" command, something like molmap #0 15 where the first number is the model number of the points and the second number is a resolution, related to Gaussian width. You may wish to use a different resolution, and there are other options, see I would have mentioned "molmap" earlier if you had said you wanted to make a map from your points. Elaine On Jun 11, 2011, at 3:24 PM, chinmaya joshi wrote: > Hey Elaine, > > Thanks for the mail. > > Just open the file in notepad and save it as .xyz (dont need to do that I am attaching the file here now) > Then I have just opened this .xyz file in chimera and chimera loads the desired image(attached: open with notepad or any text editor)(I have also attached the output image of chimera) > > Now my question is that > How do I use the script calle xyzmap.py on the following link http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts > for opening the above file from the command line. > what should I replace the 'xyz_path' and the 'xyz_list' in the xyzmap.py code with? > > Regards, > Chinmaya > On Sat, Jun 11, 2011 at 4:42 PM, Elaine Meng wrote: > Hi Chinmaya, > The way to see if Chimera opens your file is to either > (A) look at the list of file types in the link I sent in the previous message, or > (B) start Chimera, and try using File... Open in the menu. > > However, no: Chimera does not read a ".csv" file. You never said what your file is supposed to contain, but from the name and contents of the file it appears to be x,y,z coordinates of a bunch of dots. If you just want to display this as a bunch of dots or spheres in Chimera, you could convert this file (write a script to do it in any language you like) to the simple "BILD" text format described here: > > > Then the "BILD" file (name it something.bild) can be opened in Chimera to display the dots or spheres. > > As I mentioned earlier I do not know python, and I don't recommend it in this case. Using python would require some knowledge of Chimera code. Instead use a Chimera command script. > > Just start Chimera, open the BILD file, show the Chimera command line (choose from the Favorites menu), try typing in commands. Figure out the movement commands you want, then put the commands and movie-recording commands in text file to make the Chimera script. Command "roll" does rotation, "move" does translation, "scale" does scaling, "movie" does the movie stuff. The script might be as simple as: > > movie record > roll y 1 360; wait > wait 10 > movie stop > movie encode mformat mov output /MyPath/mymovie.mov > > ... but you would need to look at the command documentation to see what options you want. There are links to that documentation and to example Chimera command scripts in my previous message. > Elaine > > On Jun 11, 2011, at 12:34 PM, chinmaya joshi wrote: > > > Hello Elaine, > > > > Thanks a lot for your mail. I am working on the points you have suggested. However I am a bit confused whether my input files will work in chimera or not? > > Herewith I am attaching a sample example of the dataset which I will be taking as the input, perform some viewpoint operation on it and then make a movie. > > Can you please let me know whether this can be done in chimera or not? > > If yes, can it be done in a python script file? > > > > Regards, > > Chinmaya Joshi > > > > On Fri, Jun 10, 2011 at 9:42 PM, Elaine Meng wrote: > > Hi Chinmaya, > > Before you start scripting, the first thing to consider is whether Chimera can do what you want. Have you tried doing what you want to show in the movie, but while using Chimera interactively? From your description, I am concerned that Chimera may not read your input format. The input types are generally 3D data files, not images. The one exception is that an image stack can be used as a "volume data" input format. Here is information on what formats Chimera can read: > > > > > > If you think Chimera can do what you want, here is information on making movies, > > > > > > ...including commands for rotation and translation, etc. > > > > > > ...and example scripts > > > > > > ...however, these examples are Chimera command scripts, not python scripts. I think python scripts would be more difficult to make than Chimera command scripts, and you would only start working with python if (A) Chimera can do what you want or nearly so, but (B) there are no Chimera commands for those things. After you figure out what you want to do by using Chimera interactively, then figure out the commands for those actions, then put them into a script. The last step would be to add movie recording commands to that script. > > > > I don't know python, so I can't say any more about using that approach. > > > > I hope this helps, > > Elaine > > ----- > > Elaine C. Meng, Ph.D. > > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > > Department of Pharmaceutical Chemistry > > University of California, San Francisco > > > > On Jun 10, 2011, at 6:26 PM, chinmaya joshi wrote: > > > > > Hello, > > > I want to write a script in python to open a set of images in chimera set a viewpoint(rotate, translate,etc). and make a movie out of them all through command line for my project. > > > > > > Can someone please let me know how it can be done. > > > > > > I am new to python. > > > > > > Can anyone tell me any good links for these? > > > > > > The documentation on chimera ucsf is a bit confusing. > > > Thanks. > > > Chinmaya > > > > > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users at cgl.ucsf.edu > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From jchinu2014 at gmail.com Sun Jun 12 13:09:20 2011 From: jchinu2014 at gmail.com (chinmaya joshi) Date: Sun, 12 Jun 2011 16:09:20 -0400 Subject: [Chimera-users] help In-Reply-To: <34708863-C809-4F8D-B40E-BE81DA993D2D@cgl.ucsf.edu> References: <99037B5F-0ECB-4665-9B75-303F404EC242@cgl.ucsf.edu> <34708863-C809-4F8D-B40E-BE81DA993D2D@cgl.ucsf.edu> Message-ID: Dear Elaine, Thanks a lot for the molmap command. I want to map the x,y,z co-ordinates and the intensity of each pixel. Regards, Chinmaya On Sun, Jun 12, 2011 at 1:05 PM, Elaine Meng wrote: > Hi Chinmaya, > Forget the script, just use the Chimera "molmap" command. That python > script may have been written before we had the command. Now that you > already figured out an input format and opened it in Chimera, you only need > to show the command line (from Favorites menu in Chimera) and enter one > "molmap" command, something like > > molmap #0 15 > > where the first number is the model number of the points and the second > number is a resolution, related to Gaussian width. You may wish to use a > different resolution, and there are other options, see > > > I would have mentioned "molmap" earlier if you had said you wanted to make > a map from your points. > Elaine > > On Jun 11, 2011, at 3:24 PM, chinmaya joshi wrote: > > > Hey Elaine, > > > > Thanks for the mail. > > > > Just open the file in notepad and save it as .xyz (dont need to do that I > am attaching the file here now) > > Then I have just opened this .xyz file in chimera and chimera loads the > desired image(attached: open with notepad or any text editor)(I have also > attached the output image of chimera) > > > > Now my question is that > > How do I use the script calle xyzmap.py on the following link > http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts > > for opening the above file from the command line. > > what should I replace the 'xyz_path' and the 'xyz_list' in the xyzmap.py > code with? > > > > Regards, > > Chinmaya > > On Sat, Jun 11, 2011 at 4:42 PM, Elaine Meng wrote: > > Hi Chinmaya, > > The way to see if Chimera opens your file is to either > > (A) look at the list of file types in the link I sent in the previous > message, or > > (B) start Chimera, and try using File... Open in the menu. > > > > However, no: Chimera does not read a ".csv" file. You never said what > your file is supposed to contain, but from the name and contents of the file > it appears to be x,y,z coordinates of a bunch of dots. If you just want to > display this as a bunch of dots or spheres in Chimera, you could convert > this file (write a script to do it in any language you like) to the simple > "BILD" text format described here: > > > > > > Then the "BILD" file (name it something.bild) can be opened in Chimera to > display the dots or spheres. > > > > As I mentioned earlier I do not know python, and I don't recommend it in > this case. Using python would require some knowledge of Chimera code. > Instead use a Chimera command script. > > > > Just start Chimera, open the BILD file, show the Chimera command line > (choose from the Favorites menu), try typing in commands. Figure out the > movement commands you want, then put the commands and movie-recording > commands in text file to make the Chimera script. Command "roll" does > rotation, "move" does translation, "scale" does scaling, "movie" does the > movie stuff. The script might be as simple as: > > > > movie record > > roll y 1 360; wait > > wait 10 > > movie stop > > movie encode mformat mov output /MyPath/mymovie.mov > > > > ... but you would need to look at the command documentation to see what > options you want. There are links to that documentation and to example > Chimera command scripts in my previous message. > > Elaine > > > > On Jun 11, 2011, at 12:34 PM, chinmaya joshi wrote: > > > > > Hello Elaine, > > > > > > Thanks a lot for your mail. I am working on the points you have > suggested. However I am a bit confused whether my input files will work in > chimera or not? > > > Herewith I am attaching a sample example of the dataset which I will > be taking as the input, perform some viewpoint operation on it and then make > a movie. > > > Can you please let me know whether this can be done in chimera or not? > > > If yes, can it be done in a python script file? > > > > > > Regards, > > > Chinmaya Joshi > > > > > > On Fri, Jun 10, 2011 at 9:42 PM, Elaine Meng > wrote: > > > Hi Chinmaya, > > > Before you start scripting, the first thing to consider is whether > Chimera can do what you want. Have you tried doing what you want to show in > the movie, but while using Chimera interactively? From your description, I > am concerned that Chimera may not read your input format. The input types > are generally 3D data files, not images. The one exception is that an image > stack can be used as a "volume data" input format. Here is information on > what formats Chimera can read: > > > > > > > > > If you think Chimera can do what you want, here is information on > making movies, > > > > > > > > > ...including commands for rotation and translation, etc. > > > < > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html#moviecommands> > > > > > > ...and example scripts > > > > > > > > > ...however, these examples are Chimera command scripts, not python > scripts. I think python scripts would be more difficult to make than Chimera > command scripts, and you would only start working with python if (A) Chimera > can do what you want or nearly so, but (B) there are no Chimera commands for > those things. After you figure out what you want to do by using Chimera > interactively, then figure out the commands for those actions, then put them > into a script. The last step would be to add movie recording commands to > that script. > > > > > > I don't know python, so I can't say any more about using that approach. > > > > > > I hope this helps, > > > Elaine > > > ----- > > > Elaine C. Meng, Ph.D. > > > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > > > Department of Pharmaceutical Chemistry > > > University of California, San Francisco > > > > > > On Jun 10, 2011, at 6:26 PM, chinmaya joshi wrote: > > > > > > > Hello, > > > > I want to write a script in python to open a set of images in chimera > set a viewpoint(rotate, translate,etc). and make a movie out of them all > through command line for my project. > > > > > > > > Can someone please let me know how it can be done. > > > > > > > > I am new to python. > > > > > > > > Can anyone tell me any good links for these? > > > > > > > > The documentation on chimera ucsf is a bit confusing. > > > > Thanks. > > > > Chinmaya > > > > > > > > > _______________________________________________ > > > Chimera-users mailing list > > > Chimera-users at cgl.ucsf.edu > > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > > > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users at cgl.ucsf.edu > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jchinu2014 at gmail.com Mon Jun 13 07:05:33 2011 From: jchinu2014 at gmail.com (chinmaya joshi) Date: Mon, 13 Jun 2011 10:05:33 -0400 Subject: [Chimera-users] help In-Reply-To: References: <99037B5F-0ECB-4665-9B75-303F404EC242@cgl.ucsf.edu> <34708863-C809-4F8D-B40E-BE81DA993D2D@cgl.ucsf.edu> Message-ID: Hello Elaine, Can you please help in how to map this data (confidence map) in the following attachment. It has a fourth dimension which is the confidence. You can open the attachment with notepad. Regards, Chinmaya On Sun, Jun 12, 2011 at 4:09 PM, chinmaya joshi wrote: > Dear Elaine, > > > Thanks a lot for the molmap command. > > I want to map the x,y,z co-ordinates and the intensity of each pixel. > > Regards, > Chinmaya > On Sun, Jun 12, 2011 at 1:05 PM, Elaine Meng wrote: > >> Hi Chinmaya, >> Forget the script, just use the Chimera "molmap" command. That python >> script may have been written before we had the command. Now that you >> already figured out an input format and opened it in Chimera, you only need >> to show the command line (from Favorites menu in Chimera) and enter one >> "molmap" command, something like >> >> molmap #0 15 >> >> where the first number is the model number of the points and the second >> number is a resolution, related to Gaussian width. You may wish to use a >> different resolution, and there are other options, see >> >> >> I would have mentioned "molmap" earlier if you had said you wanted to make >> a map from your points. >> Elaine >> >> On Jun 11, 2011, at 3:24 PM, chinmaya joshi wrote: >> >> > Hey Elaine, >> > >> > Thanks for the mail. >> > >> > Just open the file in notepad and save it as .xyz (dont need to do that >> I am attaching the file here now) >> > Then I have just opened this .xyz file in chimera and chimera loads >> the desired image(attached: open with notepad or any text editor)(I have >> also attached the output image of chimera) >> > >> > Now my question is that >> > How do I use the script calle xyzmap.py on the following link >> http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts >> > for opening the above file from the command line. >> > what should I replace the 'xyz_path' and the 'xyz_list' in the xyzmap.py >> code with? >> > >> > Regards, >> > Chinmaya >> > On Sat, Jun 11, 2011 at 4:42 PM, Elaine Meng wrote: >> > Hi Chinmaya, >> > The way to see if Chimera opens your file is to either >> > (A) look at the list of file types in the link I sent in the previous >> message, or >> > (B) start Chimera, and try using File... Open in the menu. >> > >> > However, no: Chimera does not read a ".csv" file. You never said what >> your file is supposed to contain, but from the name and contents of the file >> it appears to be x,y,z coordinates of a bunch of dots. If you just want to >> display this as a bunch of dots or spheres in Chimera, you could convert >> this file (write a script to do it in any language you like) to the simple >> "BILD" text format described here: >> > >> > >> > Then the "BILD" file (name it something.bild) can be opened in Chimera >> to display the dots or spheres. >> > >> > As I mentioned earlier I do not know python, and I don't recommend it in >> this case. Using python would require some knowledge of Chimera code. >> Instead use a Chimera command script. >> > >> > Just start Chimera, open the BILD file, show the Chimera command line >> (choose from the Favorites menu), try typing in commands. Figure out the >> movement commands you want, then put the commands and movie-recording >> commands in text file to make the Chimera script. Command "roll" does >> rotation, "move" does translation, "scale" does scaling, "movie" does the >> movie stuff. The script might be as simple as: >> > >> > movie record >> > roll y 1 360; wait >> > wait 10 >> > movie stop >> > movie encode mformat mov output /MyPath/mymovie.mov >> > >> > ... but you would need to look at the command documentation to see what >> options you want. There are links to that documentation and to example >> Chimera command scripts in my previous message. >> > Elaine >> > >> > On Jun 11, 2011, at 12:34 PM, chinmaya joshi wrote: >> > >> > > Hello Elaine, >> > > >> > > Thanks a lot for your mail. I am working on the points you have >> suggested. However I am a bit confused whether my input files will work in >> chimera or not? >> > > Herewith I am attaching a sample example of the dataset which I will >> be taking as the input, perform some viewpoint operation on it and then make >> a movie. >> > > Can you please let me know whether this can be done in chimera or not? >> > > If yes, can it be done in a python script file? >> > > >> > > Regards, >> > > Chinmaya Joshi >> > > >> > > On Fri, Jun 10, 2011 at 9:42 PM, Elaine Meng >> wrote: >> > > Hi Chinmaya, >> > > Before you start scripting, the first thing to consider is whether >> Chimera can do what you want. Have you tried doing what you want to show in >> the movie, but while using Chimera interactively? From your description, I >> am concerned that Chimera may not read your input format. The input types >> are generally 3D data files, not images. The one exception is that an image >> stack can be used as a "volume data" input format. Here is information on >> what formats Chimera can read: >> > > >> > > >> > > If you think Chimera can do what you want, here is information on >> making movies, >> > > >> > > >> > > ...including commands for rotation and translation, etc. >> > > < >> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html#moviecommands >> > >> > > >> > > ...and example scripts >> > > > > >> > > >> > > ...however, these examples are Chimera command scripts, not python >> scripts. I think python scripts would be more difficult to make than Chimera >> command scripts, and you would only start working with python if (A) Chimera >> can do what you want or nearly so, but (B) there are no Chimera commands for >> those things. After you figure out what you want to do by using Chimera >> interactively, then figure out the commands for those actions, then put them >> into a script. The last step would be to add movie recording commands to >> that script. >> > > >> > > I don't know python, so I can't say any more about using that >> approach. >> > > >> > > I hope this helps, >> > > Elaine >> > > ----- >> > > Elaine C. Meng, Ph.D. >> > > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >> > > Department of Pharmaceutical Chemistry >> > > University of California, San Francisco >> > > >> > > On Jun 10, 2011, at 6:26 PM, chinmaya joshi wrote: >> > > >> > > > Hello, >> > > > I want to write a script in python to open a set of images in >> chimera set a viewpoint(rotate, translate,etc). and make a movie out of them >> all through command line for my project. >> > > > >> > > > Can someone please let me know how it can be done. >> > > > >> > > > I am new to python. >> > > > >> > > > Can anyone tell me any good links for these? >> > > > >> > > > The documentation on chimera ucsf is a bit confusing. >> > > > Thanks. >> > > > Chinmaya >> > > >> > > >> > > _______________________________________________ >> > > Chimera-users mailing list >> > > Chimera-users at cgl.ucsf.edu >> > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > >> > >> > >> _______________________________________________ >> > Chimera-users mailing list >> > Chimera-users at cgl.ucsf.edu >> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jchinu2014 at gmail.com Mon Jun 13 07:06:03 2011 From: jchinu2014 at gmail.com (chinmaya joshi) Date: Mon, 13 Jun 2011 10:06:03 -0400 Subject: [Chimera-users] help In-Reply-To: References: <99037B5F-0ECB-4665-9B75-303F404EC242@cgl.ucsf.edu> <34708863-C809-4F8D-B40E-BE81DA993D2D@cgl.ucsf.edu> Message-ID: Dear Elaine, Thanks a lot for the molmap command. I want to map the x,y,z co-ordinates and the intensity of each pixel. Regards, Chinmaya On Mon, Jun 13, 2011 at 10:05 AM, chinmaya joshi wrote: > Hello Elaine, > > Can you please help in how to map this data (confidence map) in the > following attachment. > It has a fourth dimension which is the confidence. > You can open the attachment with notepad. > > Regards, > Chinmaya > > > > On Sun, Jun 12, 2011 at 4:09 PM, chinmaya joshi wrote: > >> Dear Elaine, >> >> >> Thanks a lot for the molmap command. >> >> I want to map the x,y,z co-ordinates and the intensity of each pixel. >> >> Regards, >> Chinmaya >> On Sun, Jun 12, 2011 at 1:05 PM, Elaine Meng wrote: >> >>> Hi Chinmaya, >>> Forget the script, just use the Chimera "molmap" command. That python >>> script may have been written before we had the command. Now that you >>> already figured out an input format and opened it in Chimera, you only need >>> to show the command line (from Favorites menu in Chimera) and enter one >>> "molmap" command, something like >>> >>> molmap #0 15 >>> >>> where the first number is the model number of the points and the second >>> number is a resolution, related to Gaussian width. You may wish to use a >>> different resolution, and there are other options, see >>> >>> >>> I would have mentioned "molmap" earlier if you had said you wanted to >>> make a map from your points. >>> Elaine >>> >>> On Jun 11, 2011, at 3:24 PM, chinmaya joshi wrote: >>> >>> > Hey Elaine, >>> > >>> > Thanks for the mail. >>> > >>> > Just open the file in notepad and save it as .xyz (dont need to do that >>> I am attaching the file here now) >>> > Then I have just opened this .xyz file in chimera and chimera loads >>> the desired image(attached: open with notepad or any text editor)(I have >>> also attached the output image of chimera) >>> > >>> > Now my question is that >>> > How do I use the script calle xyzmap.py on the following link >>> http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts >>> > for opening the above file from the command line. >>> > what should I replace the 'xyz_path' and the 'xyz_list' in the >>> xyzmap.py code with? >>> > >>> > Regards, >>> > Chinmaya >>> > On Sat, Jun 11, 2011 at 4:42 PM, Elaine Meng >>> wrote: >>> > Hi Chinmaya, >>> > The way to see if Chimera opens your file is to either >>> > (A) look at the list of file types in the link I sent in the previous >>> message, or >>> > (B) start Chimera, and try using File... Open in the menu. >>> > >>> > However, no: Chimera does not read a ".csv" file. You never said what >>> your file is supposed to contain, but from the name and contents of the file >>> it appears to be x,y,z coordinates of a bunch of dots. If you just want to >>> display this as a bunch of dots or spheres in Chimera, you could convert >>> this file (write a script to do it in any language you like) to the simple >>> "BILD" text format described here: >>> > >>> > >>> > Then the "BILD" file (name it something.bild) can be opened in Chimera >>> to display the dots or spheres. >>> > >>> > As I mentioned earlier I do not know python, and I don't recommend it >>> in this case. Using python would require some knowledge of Chimera code. >>> Instead use a Chimera command script. >>> > >>> > Just start Chimera, open the BILD file, show the Chimera command line >>> (choose from the Favorites menu), try typing in commands. Figure out the >>> movement commands you want, then put the commands and movie-recording >>> commands in text file to make the Chimera script. Command "roll" does >>> rotation, "move" does translation, "scale" does scaling, "movie" does the >>> movie stuff. The script might be as simple as: >>> > >>> > movie record >>> > roll y 1 360; wait >>> > wait 10 >>> > movie stop >>> > movie encode mformat mov output /MyPath/mymovie.mov >>> > >>> > ... but you would need to look at the command documentation to see what >>> options you want. There are links to that documentation and to example >>> Chimera command scripts in my previous message. >>> > Elaine >>> > >>> > On Jun 11, 2011, at 12:34 PM, chinmaya joshi wrote: >>> > >>> > > Hello Elaine, >>> > > >>> > > Thanks a lot for your mail. I am working on the points you have >>> suggested. However I am a bit confused whether my input files will work in >>> chimera or not? >>> > > Herewith I am attaching a sample example of the dataset which I will >>> be taking as the input, perform some viewpoint operation on it and then make >>> a movie. >>> > > Can you please let me know whether this can be done in chimera or >>> not? >>> > > If yes, can it be done in a python script file? >>> > > >>> > > Regards, >>> > > Chinmaya Joshi >>> > > >>> > > On Fri, Jun 10, 2011 at 9:42 PM, Elaine Meng >>> wrote: >>> > > Hi Chinmaya, >>> > > Before you start scripting, the first thing to consider is whether >>> Chimera can do what you want. Have you tried doing what you want to show in >>> the movie, but while using Chimera interactively? From your description, I >>> am concerned that Chimera may not read your input format. The input types >>> are generally 3D data files, not images. The one exception is that an image >>> stack can be used as a "volume data" input format. Here is information on >>> what formats Chimera can read: >>> > > >>> > > >>> > > If you think Chimera can do what you want, here is information on >>> making movies, >>> > > >>> > > >>> > > ...including commands for rotation and translation, etc. >>> > > < >>> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html#moviecommands >>> > >>> > > >>> > > ...and example scripts >>> > > < >>> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html#examples> >>> > > >>> > > ...however, these examples are Chimera command scripts, not python >>> scripts. I think python scripts would be more difficult to make than Chimera >>> command scripts, and you would only start working with python if (A) Chimera >>> can do what you want or nearly so, but (B) there are no Chimera commands for >>> those things. After you figure out what you want to do by using Chimera >>> interactively, then figure out the commands for those actions, then put them >>> into a script. The last step would be to add movie recording commands to >>> that script. >>> > > >>> > > I don't know python, so I can't say any more about using that >>> approach. >>> > > >>> > > I hope this helps, >>> > > Elaine >>> > > ----- >>> > > Elaine C. Meng, Ph.D. >>> > > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >>> > > Department of Pharmaceutical Chemistry >>> > > University of California, San Francisco >>> > > >>> > > On Jun 10, 2011, at 6:26 PM, chinmaya joshi wrote: >>> > > >>> > > > Hello, >>> > > > I want to write a script in python to open a set of images in >>> chimera set a viewpoint(rotate, translate,etc). and make a movie out of them >>> all through command line for my project. >>> > > > >>> > > > Can someone please let me know how it can be done. >>> > > > >>> > > > I am new to python. >>> > > > >>> > > > Can anyone tell me any good links for these? >>> > > > >>> > > > The documentation on chimera ucsf is a bit confusing. >>> > > > Thanks. >>> > > > Chinmaya >>> > > >>> > > >>> > > _______________________________________________ >>> > > Chimera-users mailing list >>> > > Chimera-users at cgl.ucsf.edu >>> > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> > >>> > >>> > >>> _______________________________________________ >>> > Chimera-users mailing list >>> > Chimera-users at cgl.ucsf.edu >>> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: confidencecloud4.csv Type: text/csv Size: 875872 bytes Desc: not available URL: From meng at cgl.ucsf.edu Mon Jun 13 09:44:34 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 13 Jun 2011 09:44:34 -0700 Subject: [Chimera-users] showing points and confidence values In-Reply-To: References: <99037B5F-0ECB-4665-9B75-303F404EC242@cgl.ucsf.edu> <34708863-C809-4F8D-B40E-BE81DA993D2D@cgl.ucsf.edu> Message-ID: Dear Chinmaya, Please describe the whole picture of what you want to do: How do you expect to display the points? (spread out into Gaussians of density, or as dots or spheres? something else?) How do you expect to show the confidence values (with colors? or making the spheres different sizes? something else?) Are there other things you wanted to do with the display besides rotate, translate, make a movie? It is impossible to answer well when you only ask about one step at a time. Sometimes a good way to do one step is not compatible with the next step. Thanks Elaine On Jun 13, 2011, at 7:06 AM, chinmaya joshi wrote: > > Dear Elaine, > > > Thanks a lot for the molmap command. > > I want to map the x,y,z co-ordinates and the intensity of each pixel. > > Regards, > Chinmaya > On Mon, Jun 13, 2011 at 10:05 AM, chinmaya joshi wrote: > Hello Elaine, > > Can you please help in how to map this data (confidence map) in the following attachment. > It has a fourth dimension which is the confidence. > You can open the attachment with notepad. > > Regards, > Chinmaya > > > > On Sun, Jun 12, 2011 at 4:09 PM, chinmaya joshi wrote: > Dear Elaine, > > > Thanks a lot for the molmap command. > > I want to map the x,y,z co-ordinates and the intensity of each pixel. > > Regards, > Chinmaya > On Sun, Jun 12, 2011 at 1:05 PM, Elaine Meng wrote: > Hi Chinmaya, > Forget the script, just use the Chimera "molmap" command. That python script may have been written before we had the command. Now that you already figured out an input format and opened it in Chimera, you only need to show the command line (from Favorites menu in Chimera) and enter one "molmap" command, something like > > molmap #0 15 > > where the first number is the model number of the points and the second number is a resolution, related to Gaussian width. You may wish to use a different resolution, and there are other options, see > > > I would have mentioned "molmap" earlier if you had said you wanted to make a map from your points. > Elaine > > On Jun 11, 2011, at 3:24 PM, chinmaya joshi wrote: > > > Hey Elaine, > > > > Thanks for the mail. > > > > Just open the file in notepad and save it as .xyz (dont need to do that I am attaching the file here now) > > Then I have just opened this .xyz file in chimera and chimera loads the desired image(attached: open with notepad or any text editor)(I have also attached the output image of chimera) > > > > Now my question is that > > How do I use the script calle xyzmap.py on the following link http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts > > for opening the above file from the command line. > > what should I replace the 'xyz_path' and the 'xyz_list' in the xyzmap.py code with? > > > > Regards, > > Chinmaya > > On Sat, Jun 11, 2011 at 4:42 PM, Elaine Meng wrote: > > Hi Chinmaya, > > The way to see if Chimera opens your file is to either > > (A) look at the list of file types in the link I sent in the previous message, or > > (B) start Chimera, and try using File... Open in the menu. > > > > However, no: Chimera does not read a ".csv" file. You never said what your file is supposed to contain, but from the name and contents of the file it appears to be x,y,z coordinates of a bunch of dots. If you just want to display this as a bunch of dots or spheres in Chimera, you could convert this file (write a script to do it in any language you like) to the simple "BILD" text format described here: > > > > > > Then the "BILD" file (name it something.bild) can be opened in Chimera to display the dots or spheres. > > > > As I mentioned earlier I do not know python, and I don't recommend it in this case. Using python would require some knowledge of Chimera code. Instead use a Chimera command script. > > > > Just start Chimera, open the BILD file, show the Chimera command line (choose from the Favorites menu), try typing in commands. Figure out the movement commands you want, then put the commands and movie-recording commands in text file to make the Chimera script. Command "roll" does rotation, "move" does translation, "scale" does scaling, "movie" does the movie stuff. The script might be as simple as: > > > > movie record > > roll y 1 360; wait > > wait 10 > > movie stop > > movie encode mformat mov output /MyPath/mymovie.mov > > > > ... but you would need to look at the command documentation to see what options you want. There are links to that documentation and to example Chimera command scripts in my previous message. > > Elaine > > > > On Jun 11, 2011, at 12:34 PM, chinmaya joshi wrote: > > > > > Hello Elaine, > > > > > > Thanks a lot for your mail. I am working on the points you have suggested. However I am a bit confused whether my input files will work in chimera or not? > > > Herewith I am attaching a sample example of the dataset which I will be taking as the input, perform some viewpoint operation on it and then make a movie. > > > Can you please let me know whether this can be done in chimera or not? > > > If yes, can it be done in a python script file? > > > > > > Regards, > > > Chinmaya Joshi > > > > > > On Fri, Jun 10, 2011 at 9:42 PM, Elaine Meng wrote: > > > Hi Chinmaya, > > > Before you start scripting, the first thing to consider is whether Chimera can do what you want. Have you tried doing what you want to show in the movie, but while using Chimera interactively? From your description, I am concerned that Chimera may not read your input format. The input types are generally 3D data files, not images. The one exception is that an image stack can be used as a "volume data" input format. Here is information on what formats Chimera can read: > > > > > > > > > If you think Chimera can do what you want, here is information on making movies, > > > > > > > > > ...including commands for rotation and translation, etc. > > > > > > > > > ...and example scripts > > > > > > > > > ...however, these examples are Chimera command scripts, not python scripts. I think python scripts would be more difficult to make than Chimera command scripts, and you would only start working with python if (A) Chimera can do what you want or nearly so, but (B) there are no Chimera commands for those things. After you figure out what you want to do by using Chimera interactively, then figure out the commands for those actions, then put them into a script. The last step would be to add movie recording commands to that script. > > > > > > I don't know python, so I can't say any more about using that approach. > > > > > > I hope this helps, > > > Elaine > > > ----- > > > Elaine C. Meng, Ph.D. > > > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > > > Department of Pharmaceutical Chemistry > > > University of California, San Francisco > > > > > > On Jun 10, 2011, at 6:26 PM, chinmaya joshi wrote: > > > > > > > Hello, > > > > I want to write a script in python to open a set of images in chimera set a viewpoint(rotate, translate,etc). and make a movie out of them all through command line for my project. > > > > > > > > Can someone please let me know how it can be done. > > > > > > > > I am new to python. > > > > > > > > Can anyone tell me any good links for these? > > > > > > > > The documentation on chimera ucsf is a bit confusing. > > > > Thanks. > > > > Chinmaya > > > > > > > > > _______________________________________________ > > > Chimera-users mailing list > > > Chimera-users at cgl.ucsf.edu > > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users at cgl.ucsf.edu > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From darkforestzero at gmail.com Fri Jun 10 17:47:36 2011 From: darkforestzero at gmail.com (Jonathan Rodgers) Date: Fri, 10 Jun 2011 17:47:36 -0700 Subject: [Chimera-users] Chimera API question Message-ID: Hello, After looking through the Chimera documentation and examples, I couldn't find any mention of working with volumes. Is that data currently accessible through the API? Thanks, Jonathan Rodgers -------------- next part -------------- An HTML attachment was scrubbed... URL: From jpa37 at drexel.edu Sat Jun 11 13:34:48 2011 From: jpa37 at drexel.edu (Jared Adolf-Bryfogle) Date: Sat, 11 Jun 2011 16:34:48 -0400 Subject: [Chimera-users] Protein Design Message-ID: An HTML attachment was scrubbed... URL: From britta2 at stanford.edu Sat Jun 11 14:15:51 2011 From: britta2 at stanford.edu (James Ferrell) Date: Sat, 11 Jun 2011 14:15:51 -0700 Subject: [Chimera-users] Biological dimer shows up as a monomer Message-ID: I'm new to Chimera and trying to create a figure panel for a paper. I'm running Chimera on a Mac from the graphical interface. The protein is a a yeast topoisomerase II. Its PDB ID is 2RGR. If I view the protein with Cn3D I can see the whole biological unit, in which the protein is present as a symmetrical dimer (with some DNA strands too). If I view it with Chimera I see a protein monomer. The problem is I want to illustrate a particular intermolecular salt bridge, which is present in the dimer but isn't present in the monomer. Is there some preference to toggle to allow Chimera to display the whole biological unit? Or would I have to artificially build a dimer out of two monomer models? Thanks, Jim -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- James E. Ferrell, Jr., M.D., Ph.D. Professor and Chair of Chemical and Systems Biology Stanford University School of Medicine From pett at cgl.ucsf.edu Mon Jun 13 10:36:52 2011 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 13 Jun 2011 10:36:52 -0700 Subject: [Chimera-users] Protein Design In-Reply-To: References: Message-ID: On Jun 11, 2011, at 1:34 PM, Jared Adolf-Bryfogle wrote: > Hi All, > > I am trying to work on the design of a protein, and am unable to > figure out the correct tool to accomplish this: > > I have a protein and a region that I would like to replace with > another region. Essentially, the insert is a long motif. > (Literally making a chimeric structure). In Chimera, I can merge > the two pdb's at one terminus, however I can't seem to create the > bond at the other terminus, once the models are merged. Is this > possible? It should be. Are you saying you don't know how to add the bond, or that the attempt to add the bond fails? The simplest way to add the bond is to select the two atoms you want bonded and either type "bond sel" in Chimera's command line or use the "Adjust Bonds" tab of the Build Structure tool (in the Structure Editing category) to add the bond. If these approaches fail for you, let me know what the error was exactly and I'll try to provide more guidance. > If not, does anyone know of other programs out there that can > accomplish this, and any interest in putting it in chimera? I hope it's already there! --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Mon Jun 13 11:13:24 2011 From: goddard at sonic.net (Tom Goddard) Date: Mon, 13 Jun 2011 11:13:24 -0700 Subject: [Chimera-users] Biological dimer shows up as a monomer In-Reply-To: References: Message-ID: <4DF65344.1040607@sonic.net> Hi Jim, The 2rgr PDB file contains just the monomer atomic coordinates. You can get the dimer by opening it in Chimera then use Model Panel (Favorites menu) and press the Biological Unit button. This uses the REMARK 350 biological unit matrices in the PDB file to create the dimer. Tom > I'm new to Chimera and trying to create a figure panel for a paper. > I'm running Chimera on a Mac from the graphical interface. > > The protein is a a yeast topoisomerase II. Its PDB ID is 2RGR. > > If I view the protein with Cn3D I can see the whole biological unit, > in which the protein is present as a symmetrical dimer (with some DNA > strands too). If I view it with Chimera I see a protein monomer. The > problem is I want to illustrate a particular intermolecular salt > bridge, which is present in the dimer but isn't present in the monomer. > > Is there some preference to toggle to allow Chimera to display the > whole biological unit? Or would I have to artificially build a dimer > out of two monomer models? > > Thanks, > > Jim > -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- > James E. Ferrell, Jr., M.D., Ph.D. > Professor and Chair of Chemical and Systems Biology > Stanford University School of Medicine > > > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > From goddard at sonic.net Mon Jun 13 11:19:24 2011 From: goddard at sonic.net (Tom Goddard) Date: Mon, 13 Jun 2011 11:19:24 -0700 Subject: [Chimera-users] Chimera API question In-Reply-To: References: Message-ID: <4DF654AC.3030009@sonic.net> Hi Jonathan, All of the Chimera volume data functionality is available using the Python language. We don't have much documentation of Chimera programming interfaces, and it is especially lacking for volumes. The best starting point is probably the example Python scripts page: http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts The most important Chimera volume object Python code is in chimera/share/VolumeViewer/volume.py and chimera/share/VolumeData/griddata.py If you describe what you want to program, I can give you more specific pointers. Tom > Hello, > After looking through the Chimera documentation and examples, I > couldn't find any mention of working with volumes. Is that data > currently accessible through the API? > > Thanks, > Jonathan Rodgers > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From jchinu2014 at gmail.com Tue Jun 14 16:03:27 2011 From: jchinu2014 at gmail.com (chinmaya joshi) Date: Tue, 14 Jun 2011 16:03:27 -0700 Subject: [Chimera-users] showing points and confidence values In-Reply-To: References: <99037B5F-0ECB-4665-9B75-303F404EC242@cgl.ucsf.edu> <34708863-C809-4F8D-B40E-BE81DA993D2D@cgl.ucsf.edu> Message-ID: Dear Elaine, First of all sorry for writing only a step at a time earlier. well this is what exactly I want to do. I want to display the points as spread out gaussians of density and not simply dots or spheres. I expect to show the confidence values with different intensity/transparency. no I do not want to display anything else other than rotate, translate and making a movie out of them. Can you suggest me something? Well what exactly is the image is of a stick man being imaged with different postures as apart of the project. So I have to open the stack of such images perform these viewpoint operations and make a movie out of it. Right now the imput of image is in .xyz format so it opens the spheres. But I also want to inlude the confidence values as described above. >From a set of these images I want to make a movie. Regards, Yours Sincerely, Chinmaya Joshi On Mon, Jun 13, 2011 at 9:44 AM, Elaine Meng wrote: > Dear Chinmaya, > Please describe the whole picture of what you want to do: > > How do you expect to display the points? (spread out into Gaussians of > density, or as dots or spheres? something else?) > > How do you expect to show the confidence values (with colors? or making the > spheres different sizes? something else?) > > Are there other things you wanted to do with the display besides rotate, > translate, make a movie? > > It is impossible to answer well when you only ask about one step at a time. > Sometimes a good way to do one step is not compatible with the next step. > > Thanks > Elaine > > On Jun 13, 2011, at 7:06 AM, chinmaya joshi wrote: > > > > > Dear Elaine, > > > > > > Thanks a lot for the molmap command. > > > > I want to map the x,y,z co-ordinates and the intensity of each pixel. > > > > Regards, > > Chinmaya > > On Mon, Jun 13, 2011 at 10:05 AM, chinmaya joshi > wrote: > > Hello Elaine, > > > > Can you please help in how to map this data (confidence map) in the > following attachment. > > It has a fourth dimension which is the confidence. > > You can open the attachment with notepad. > > > > Regards, > > Chinmaya > > > > > > > > On Sun, Jun 12, 2011 at 4:09 PM, chinmaya joshi > wrote: > > Dear Elaine, > > > > > > Thanks a lot for the molmap command. > > > > I want to map the x,y,z co-ordinates and the intensity of each pixel. > > > > Regards, > > Chinmaya > > On Sun, Jun 12, 2011 at 1:05 PM, Elaine Meng wrote: > > Hi Chinmaya, > > Forget the script, just use the Chimera "molmap" command. That python > script may have been written before we had the command. Now that you > already figured out an input format and opened it in Chimera, you only need > to show the command line (from Favorites menu in Chimera) and enter one > "molmap" command, something like > > > > molmap #0 15 > > > > where the first number is the model number of the points and the second > number is a resolution, related to Gaussian width. You may wish to use a > different resolution, and there are other options, see > > > > > > I would have mentioned "molmap" earlier if you had said you wanted to > make a map from your points. > > Elaine > > > > On Jun 11, 2011, at 3:24 PM, chinmaya joshi wrote: > > > > > Hey Elaine, > > > > > > Thanks for the mail. > > > > > > Just open the file in notepad and save it as .xyz (dont need to do that > I am attaching the file here now) > > > Then I have just opened this .xyz file in chimera and chimera loads > the desired image(attached: open with notepad or any text editor)(I have > also attached the output image of chimera) > > > > > > Now my question is that > > > How do I use the script calle xyzmap.py on the following link > http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts > > > for opening the above file from the command line. > > > what should I replace the 'xyz_path' and the 'xyz_list' in the > xyzmap.py code with? > > > > > > Regards, > > > Chinmaya > > > On Sat, Jun 11, 2011 at 4:42 PM, Elaine Meng > wrote: > > > Hi Chinmaya, > > > The way to see if Chimera opens your file is to either > > > (A) look at the list of file types in the link I sent in the previous > message, or > > > (B) start Chimera, and try using File... Open in the menu. > > > > > > However, no: Chimera does not read a ".csv" file. You never said what > your file is supposed to contain, but from the name and contents of the file > it appears to be x,y,z coordinates of a bunch of dots. If you just want to > display this as a bunch of dots or spheres in Chimera, you could convert > this file (write a script to do it in any language you like) to the simple > "BILD" text format described here: > > > > > > > > > Then the "BILD" file (name it something.bild) can be opened in Chimera > to display the dots or spheres. > > > > > > As I mentioned earlier I do not know python, and I don't recommend it > in this case. Using python would require some knowledge of Chimera code. > Instead use a Chimera command script. > > > > > > Just start Chimera, open the BILD file, show the Chimera command line > (choose from the Favorites menu), try typing in commands. Figure out the > movement commands you want, then put the commands and movie-recording > commands in text file to make the Chimera script. Command "roll" does > rotation, "move" does translation, "scale" does scaling, "movie" does the > movie stuff. The script might be as simple as: > > > > > > movie record > > > roll y 1 360; wait > > > wait 10 > > > movie stop > > > movie encode mformat mov output /MyPath/mymovie.mov > > > > > > ... but you would need to look at the command documentation to see what > options you want. There are links to that documentation and to example > Chimera command scripts in my previous message. > > > Elaine > > > > > > On Jun 11, 2011, at 12:34 PM, chinmaya joshi wrote: > > > > > > > Hello Elaine, > > > > > > > > Thanks a lot for your mail. I am working on the points you have > suggested. However I am a bit confused whether my input files will work in > chimera or not? > > > > Herewith I am attaching a sample example of the dataset which I will > be taking as the input, perform some viewpoint operation on it and then make > a movie. > > > > Can you please let me know whether this can be done in chimera or > not? > > > > If yes, can it be done in a python script file? > > > > > > > > Regards, > > > > Chinmaya Joshi > > > > > > > > On Fri, Jun 10, 2011 at 9:42 PM, Elaine Meng > wrote: > > > > Hi Chinmaya, > > > > Before you start scripting, the first thing to consider is whether > Chimera can do what you want. Have you tried doing what you want to show in > the movie, but while using Chimera interactively? From your description, I > am concerned that Chimera may not read your input format. The input types > are generally 3D data files, not images. The one exception is that an image > stack can be used as a "volume data" input format. Here is information on > what formats Chimera can read: > > > > > > > > > > > > If you think Chimera can do what you want, here is information on > making movies, > > > > > > > > > > > > ...including commands for rotation and translation, etc. > > > > < > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html#moviecommands> > > > > > > > > ...and example scripts > > > > < > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html#examples> > > > > > > > > ...however, these examples are Chimera command scripts, not python > scripts. I think python scripts would be more difficult to make than Chimera > command scripts, and you would only start working with python if (A) Chimera > can do what you want or nearly so, but (B) there are no Chimera commands for > those things. After you figure out what you want to do by using Chimera > interactively, then figure out the commands for those actions, then put them > into a script. The last step would be to add movie recording commands to > that script. > > > > > > > > I don't know python, so I can't say any more about using that > approach. > > > > > > > > I hope this helps, > > > > Elaine > > > > ----- > > > > Elaine C. Meng, Ph.D. > > > > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > > > > Department of Pharmaceutical Chemistry > > > > University of California, San Francisco > > > > > > > > On Jun 10, 2011, at 6:26 PM, chinmaya joshi wrote: > > > > > > > > > Hello, > > > > > I want to write a script in python to open a set of images in > chimera set a viewpoint(rotate, translate,etc). and make a movie out of them > all through command line for my project. > > > > > > > > > > Can someone please let me know how it can be done. > > > > > > > > > > I am new to python. > > > > > > > > > > Can anyone tell me any good links for these? > > > > > > > > > > The documentation on chimera ucsf is a bit confusing. > > > > > Thanks. > > > > > Chinmaya > > > > > > > > > > > > _______________________________________________ > > > > Chimera-users mailing list > > > > Chimera-users at cgl.ucsf.edu > > > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > > > > > > > _______________________________________________ > > > Chimera-users mailing list > > > Chimera-users at cgl.ucsf.edu > > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > > > > > > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users at cgl.ucsf.edu > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at sonic.net Tue Jun 14 18:27:13 2011 From: goddard at sonic.net (Tom Goddard) Date: Tue, 14 Jun 2011 18:27:13 -0700 Subject: [Chimera-users] showing points and confidence values In-Reply-To: References: <99037B5F-0ECB-4665-9B75-303F404EC242@cgl.ucsf.edu> <34708863-C809-4F8D-B40E-BE81DA993D2D@cgl.ucsf.edu> Message-ID: <4DF80A71.9010207@sonic.net> Hi Chinmaya, I think the idea of making a 3-dimensional density map where "confidence" values correspond to intensity isn't going to make a useful visualization. If by confidence you mean how accurately the point is placed then maybe you should display each point as a sphere with the sphere radius proportional to "confidence". Chimera is for displaying atomic models where standard atom radii are used, but there are some quirky ways to change the radii to those specified in a file. One is to use the Chimera defattr command. Another approach is to rewrite your CSV file into a Chimera marker file which describes spheres with specific positions, radii and colors. All of these will require you to do some programming. Since you are trying to use a molecular visualization program for data that isn't much like a molecule you can't avoid that. We probably won't be able to do this programming for you -- too many actual molecule problems to solve! Tom > Dear Elaine, > > First of all sorry for writing only a step at a time earlier. > > well this is what exactly I want to do. > I want to display the points as spread out gaussians of density and > not simply dots or spheres. > I expect to show the confidence values with different > intensity/transparency. > no I do not want to display anything else other than rotate, translate > and making a movie out of them. > Can you suggest me something? > > Well what exactly is the image is of a stick man being imaged with > different postures as apart of the project. > So I have to open the stack of such images perform these viewpoint > operations and make a movie out of it. > Right now the imput of image is in .xyz format so it opens the spheres. > But I also want to inlude the confidence values as described above. > From a set of these images I want to make a movie. > > Regards, > Yours Sincerely, > Chinmaya Joshi > > On Mon, Jun 13, 2011 at 9:44 AM, Elaine Meng > wrote: > > Dear Chinmaya, > Please describe the whole picture of what you want to do: > > How do you expect to display the points? (spread out into > Gaussians of density, or as dots or spheres? something else?) > > How do you expect to show the confidence values (with colors? or > making the spheres different sizes? something else?) > > Are there other things you wanted to do with the display besides > rotate, translate, make a movie? > > It is impossible to answer well when you only ask about one step > at a time. Sometimes a good way to do one step is not compatible > with the next step. > > Thanks > Elaine > > On Jun 13, 2011, at 7:06 AM, chinmaya joshi wrote: > > > > > Dear Elaine, > > > > > > Thanks a lot for the molmap command. > > > > I want to map the x,y,z co-ordinates and the intensity of each pixel. > > > > Regards, > > Chinmaya > > On Mon, Jun 13, 2011 at 10:05 AM, chinmaya joshi > > wrote: > > Hello Elaine, > > > > Can you please help in how to map this data (confidence map) in > the following attachment. > > It has a fourth dimension which is the confidence. > > You can open the attachment with notepad. > > > > Regards, > > Chinmaya > > > > > > > > On Sun, Jun 12, 2011 at 4:09 PM, chinmaya joshi > > wrote: > > Dear Elaine, > > > > > > Thanks a lot for the molmap command. > > > > I want to map the x,y,z co-ordinates and the intensity of each pixel. > > > > Regards, > > Chinmaya > > On Sun, Jun 12, 2011 at 1:05 PM, Elaine Meng > wrote: > > Hi Chinmaya, > > Forget the script, just use the Chimera "molmap" command. That > python script may have been written before we had the command. > Now that you already figured out an input format and opened it in > Chimera, you only need to show the command line (from Favorites > menu in Chimera) and enter one "molmap" command, something like > > > > molmap #0 15 > > > > where the first number is the model number of the points and the > second number is a resolution, related to Gaussian width. You may > wish to use a different resolution, and there are other options, see > > > > > > I would have mentioned "molmap" earlier if you had said you > wanted to make a map from your points. > > Elaine > > > > On Jun 11, 2011, at 3:24 PM, chinmaya joshi wrote: > > > > > Hey Elaine, > > > > > > Thanks for the mail. > > > > > > Just open the file in notepad and save it as .xyz (dont need to > do that I am attaching the file here now) > > > Then I have just opened this .xyz file in chimera and chimera > loads the desired image(attached: open with notepad or any text > editor)(I have also attached the output image of chimera) > > > > > > Now my question is that > > > How do I use the script calle xyzmap.py on the following link > http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts > > > for opening the above file from the command line. > > > what should I replace the 'xyz_path' and the 'xyz_list' in the > xyzmap.py code with? > > > > > > Regards, > > > Chinmaya > > > On Sat, Jun 11, 2011 at 4:42 PM, Elaine Meng > wrote: > > > Hi Chinmaya, > > > The way to see if Chimera opens your file is to either > > > (A) look at the list of file types in the link I sent in the > previous message, or > > > (B) start Chimera, and try using File... Open in the menu. > > > > > > However, no: Chimera does not read a ".csv" file. You never > said what your file is supposed to contain, but from the name and > contents of the file it appears to be x,y,z coordinates of a bunch > of dots. If you just want to display this as a bunch of dots or > spheres in Chimera, you could convert this file (write a script to > do it in any language you like) to the simple "BILD" text format > described here: > > > > > > > > > Then the "BILD" file (name it something.bild) can be opened in > Chimera to display the dots or spheres. > > > > > > As I mentioned earlier I do not know python, and I don't > recommend it in this case. Using python would require some > knowledge of Chimera code. Instead use a Chimera command script. > > > > > > Just start Chimera, open the BILD file, show the Chimera > command line (choose from the Favorites menu), try typing in > commands. Figure out the movement commands you want, then put the > commands and movie-recording commands in text file to make the > Chimera script. Command "roll" does rotation, "move" does > translation, "scale" does scaling, "movie" does the movie stuff. > The script might be as simple as: > > > > > > movie record > > > roll y 1 360; wait > > > wait 10 > > > movie stop > > > movie encode mformat mov output /MyPath/mymovie.mov > > > > > > ... but you would need to look at the command documentation to > see what options you want. There are links to that documentation > and to example Chimera command scripts in my previous message. > > > Elaine > > > > > > On Jun 11, 2011, at 12:34 PM, chinmaya joshi wrote: > > > > > > > Hello Elaine, > > > > > > > > Thanks a lot for your mail. I am working on the points you > have suggested. However I am a bit confused whether my input files > will work in chimera or not? > > > > Herewith I am attaching a sample example of the dataset > which I will be taking as the input, perform some viewpoint > operation on it and then make a movie. > > > > Can you please let me know whether this can be done in > chimera or not? > > > > If yes, can it be done in a python script file? > > > > > > > > Regards, > > > > Chinmaya Joshi > > > > > > > > On Fri, Jun 10, 2011 at 9:42 PM, Elaine Meng > > wrote: > > > > Hi Chinmaya, > > > > Before you start scripting, the first thing to consider is > whether Chimera can do what you want. Have you tried doing what > you want to show in the movie, but while using Chimera > interactively? From your description, I am concerned that Chimera > may not read your input format. The input types are generally 3D > data files, not images. The one exception is that an image stack > can be used as a "volume data" input format. Here is information > on what formats Chimera can read: > > > > > > > > > > > > If you think Chimera can do what you want, here is > information on making movies, > > > > > > > > > > > > ...including commands for rotation and translation, etc. > > > > > > > > > > > > > ...and example scripts > > > > > > > > > > > > > ...however, these examples are Chimera command scripts, not > python scripts. I think python scripts would be more difficult to > make than Chimera command scripts, and you would only start > working with python if (A) Chimera can do what you want or nearly > so, but (B) there are no Chimera commands for those things. After > you figure out what you want to do by using Chimera interactively, > then figure out the commands for those actions, then put them into > a script. The last step would be to add movie recording commands > to that script. > > > > > > > > I don't know python, so I can't say any more about using that > approach. > > > > > > > > I hope this helps, > > > > Elaine > > > > ----- > > > > Elaine C. Meng, Ph.D. > > > > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > > > > Department of Pharmaceutical Chemistry > > > > University of California, San Francisco > > > > > > > > On Jun 10, 2011, at 6:26 PM, chinmaya joshi wrote: > > > > > > > > > Hello, > > > > > I want to write a script in python to open a set of images > in chimera set a viewpoint(rotate, translate,etc). and make a > movie out of them all through command line for my project. > > > > > > > > > > Can someone please let me know how it can be done. > > > > > > > > > > I am new to python. > > > > > > > > > > Can anyone tell me any good links for these? > > > > > > > > > > The documentation on chimera ucsf is a bit confusing. > > > > > Thanks. > > > > > Chinmaya > > > > > > > > > > > > _______________________________________________ > > > > Chimera-users mailing list > > > > Chimera-users at cgl.ucsf.edu > > > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > > > > > > > _______________________________________________ > > > Chimera-users mailing list > > > Chimera-users at cgl.ucsf.edu > > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > > > > > > > _______________________________________________ > > Chimera-users mailing list > > Chimera-users at cgl.ucsf.edu > > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From marek.maly at ujep.cz Wed Jun 15 09:37:11 2011 From: marek.maly at ujep.cz (Marek Maly) Date: Wed, 15 Jun 2011 18:37:11 +0200 Subject: [Chimera-users] Chimera movie with simulation time labels ? In-Reply-To: References: Message-ID: Hello all, Is it possible to create Chimera movie (MD trajectory animation) with simulation time labeled on the corner ? (Of course after I provide through some appropriate dialogue the time interval between two consequent frames). Thanks in advance for any hint ! Best wishes, Marek From meng at cgl.ucsf.edu Wed Jun 15 10:08:38 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 15 Jun 2011 10:08:38 -0700 Subject: [Chimera-users] Chimera movie with simulation time labels ? In-Reply-To: References: Message-ID: Hello Marek, It may be possible using per-frame scripting in MD Movie (in that tool's menu: Per-Frame... Define script). I've definitely shown frame number as a label for a trajectory, details below. The process would be something like: - figure out equation to convert frame number to time - per-frame script would use that equation and show result as a 2D label - record movie while the per-frame script is active I think it would be necessary to do it in Python, to include the equation part, but the script dialog provides a way to use frame number in the script. The only part I am concerned about is whether the equation output (simulation time) has to be converted to a character string to be used as label contents. I have definitely used this process to simply show the frame number as a label during the trajectory. That is done with a per-frame script of Chimera commands in the "Trajectory and Ensemble Analysis" tutorial, part 1: I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jun 15, 2011, at 9:37 AM, Marek Maly wrote: > Hello all, > Is it possible to create Chimera movie (MD trajectory animation) with > simulation time labeled on the corner ? (Of course after I provide through > some appropriate > dialogue the time interval between two consequent frames). > Thanks in advance for any hint ! > Best wishes, > Marek From marek.maly at ujep.cz Wed Jun 15 10:03:28 2011 From: marek.maly at ujep.cz (Marek Maly) Date: Wed, 15 Jun 2011 19:03:28 +0200 Subject: [Chimera-users] Chimera movie with simulation time labels ? In-Reply-To: References: Message-ID: Hello Elaine, thanks a lot for prompt and useful advice ! Best wishes, Marek Dne Wed, 15 Jun 2011 19:08:38 +0200 Elaine Meng napsal/-a: > Hello Marek, > It may be possible using per-frame scripting in MD Movie (in that tool's > menu: Per-Frame... Define script). I've definitely shown frame number as > a label for a trajectory, details below. > > > > > The process would be something like: > - figure out equation to convert frame number to time > - per-frame script would use that equation and show result as a 2D label > - record movie while the per-frame script is active > > I think it would be necessary to do it in Python, to include the > equation part, but the script dialog provides a way to use frame number > in the script. The only part I am concerned about is whether the > equation output (simulation time) has to be converted to a character > string to be used as label contents. > > I have definitely used this process to simply show the frame number as a > label during the trajectory. That is done with a per-frame script of > Chimera commands in the "Trajectory and Ensemble Analysis" tutorial, > part 1: > > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Jun 15, 2011, at 9:37 AM, Marek Maly wrote: > >> Hello all, >> Is it possible to create Chimera movie (MD trajectory animation) with >> simulation time labeled on the corner ? (Of course after I provide >> through >> some appropriate >> dialogue the time interval between two consequent frames). >> Thanks in advance for any hint ! >> Best wishes, >> Marek > -- Tato zpr?va byla vytvo?ena p?evratn?m po?tovn?m klientem Opery: http://www.opera.com/mail/ From pett at cgl.ucsf.edu Wed Jun 15 10:44:19 2011 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 15 Jun 2011 10:44:19 -0700 Subject: [Chimera-users] Chimera movie with simulation time labels ? In-Reply-To: References: Message-ID: <69D59B34-4985-47D5-86D1-A8498C03ECAC@cgl.ucsf.edu> To expand a little on the details, I think that outside the trajectory script you would create a 2D label for the script to work with, something like: 2dlabels create timer text "0 ns" which would create a label that can be referred to with the name "timer" in subsequent commands. Then just use the 2D Labels tool to position, color, and size the label as you like. Then your trajectory script would be something like: from chimera import runCommand runCommand("2dlabels change timer text '%.1f ns'" % (mdInfo['frame'] * 27.5)) The '%.1f' part means show a floating point number with one decimal place. You can change the label text surrounding that as appropriate. Change 27.5 to whatever conversion factor is appropriate, possibly adding an offset if your time doesn't start at zero. --Eric On Jun 15, 2011, at 10:08 AM, Elaine Meng wrote: > Hello Marek, > It may be possible using per-frame scripting in MD Movie (in that > tool's menu: Per-Frame... Define script). I've definitely shown > frame number as a label for a trajectory, details below. > > > > > > > The process would be something like: > - figure out equation to convert frame number to time > - per-frame script would use that equation and show result as a 2D > label > - record movie while the per-frame script is active > > I think it would be necessary to do it in Python, to include the > equation part, but the script dialog provides a way to use frame > number in the script. The only part I am concerned about is whether > the equation output (simulation time) has to be converted to a > character string to be used as label contents. > > I have definitely used this process to simply show the frame number > as a label during the trajectory. That is done with a per-frame > script of Chimera commands in the "Trajectory and Ensemble Analysis" > tutorial, part 1: > > > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Jun 15, 2011, at 9:37 AM, Marek Maly wrote: > >> Hello all, >> Is it possible to create Chimera movie (MD trajectory animation) with >> simulation time labeled on the corner ? (Of course after I provide >> through >> some appropriate >> dialogue the time interval between two consequent frames). >> Thanks in advance for any hint ! >> Best wishes, >> Marek > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From pett at cgl.ucsf.edu Wed Jun 15 10:50:04 2011 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 15 Jun 2011 10:50:04 -0700 Subject: [Chimera-users] Chimera movie with simulation time labels ? In-Reply-To: <69D59B34-4985-47D5-86D1-A8498C03ECAC@cgl.ucsf.edu> References: <69D59B34-4985-47D5-86D1-A8498C03ECAC@cgl.ucsf.edu> Message-ID: <04083906-2039-4F4B-8B78-51BD2749DC35@cgl.ucsf.edu> On Jun 15, 2011, at 10:44 AM, Eric Pettersen wrote: > from chimera import runCommand > runCommand("2dlabels change timer text '%.1f ns'" % (mdInfo['frame'] * > 27.5)) This was so close to being correct. :-( Since frame numbers start at 1, the last part needs to be: % ((mdInfo['frame']-1) * 27.5)) --Eric -------------- next part -------------- An HTML attachment was scrubbed... URL: From marek.maly at ujep.cz Wed Jun 15 10:42:30 2011 From: marek.maly at ujep.cz (Marek Maly) Date: Wed, 15 Jun 2011 19:42:30 +0200 Subject: [Chimera-users] Chimera movie with simulation time labels ? In-Reply-To: <69D59B34-4985-47D5-86D1-A8498C03ECAC@cgl.ucsf.edu> References: <69D59B34-4985-47D5-86D1-A8498C03ECAC@cgl.ucsf.edu> Message-ID: Dear Eric, thanks a lot for providing all the necessary details ! Best wishes, Marek Dne Wed, 15 Jun 2011 19:44:19 +0200 Eric Pettersen napsal/-a: > To expand a little on the details, I think that outside the trajectory > script you would create a 2D label for the script to work with, > something like: > > 2dlabels create timer text "0 ns" > > which would create a label that can be referred to with the name "timer" > in subsequent commands. Then just use the 2D Labels tool to position, > color, and size the label as you like. Then your trajectory script > would be something like: > > from chimera import runCommand > runCommand("2dlabels change timer text '%.1f ns'" % (mdInfo['frame'] * > 27.5)) > > The '%.1f' part means show a floating point number with one decimal > place. You can change the label text surrounding that as appropriate. > Change 27.5 to whatever conversion factor is appropriate, possibly > adding an offset if your time doesn't start at zero. > > --Eric > > On Jun 15, 2011, at 10:08 AM, Elaine Meng wrote: > >> Hello Marek, >> It may be possible using per-frame scripting in MD Movie (in that >> tool's menu: Per-Frame... Define script). I've definitely shown frame >> number as a label for a trajectory, details below. >> >> >> >> >> The process would be something like: >> - figure out equation to convert frame number to time >> - per-frame script would use that equation and show result as a 2D label >> - record movie while the per-frame script is active >> >> I think it would be necessary to do it in Python, to include the >> equation part, but the script dialog provides a way to use frame number >> in the script. The only part I am concerned about is whether the >> equation output (simulation time) has to be converted to a character >> string to be used as label contents. >> >> I have definitely used this process to simply show the frame number as >> a label during the trajectory. That is done with a per-frame script of >> Chimera commands in the "Trajectory and Ensemble Analysis" tutorial, >> part 1: >> >> >> I hope this helps, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. >> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >> On Jun 15, 2011, at 9:37 AM, Marek Maly wrote: >> >>> Hello all, >>> Is it possible to create Chimera movie (MD trajectory animation) with >>> simulation time labeled on the corner ? (Of course after I provide >>> through >>> some appropriate >>> dialogue the time interval between two consequent frames). >>> Thanks in advance for any hint ! >>> Best wishes, >>> Marek >> >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > -- Tato zpr?va byla vytvo?ena p?evratn?m po?tovn?m klientem Opery: http://www.opera.com/mail/ From marek.maly at ujep.cz Wed Jun 15 10:50:11 2011 From: marek.maly at ujep.cz (Marek Maly) Date: Wed, 15 Jun 2011 19:50:11 +0200 Subject: [Chimera-users] Chimera movie with simulation time labels ? In-Reply-To: <04083906-2039-4F4B-8B78-51BD2749DC35@cgl.ucsf.edu> References: <69D59B34-4985-47D5-86D1-A8498C03ECAC@cgl.ucsf.edu> <04083906-2039-4F4B-8B78-51BD2749DC35@cgl.ucsf.edu> Message-ID: OK, thanks a lot ! Best, Marek Dne Wed, 15 Jun 2011 19:50:04 +0200 Eric Pettersen napsal/-a: > On Jun 15, 2011, at 10:44 AM, Eric Pettersen wrote: > >> from chimera import runCommand >> runCommand("2dlabels change timer text '%.1f ns'" % (mdInfo['frame'] * >> 27.5)) > > This was so close to being correct. :-( Since frame numbers start at > 1, the last part needs to be: > > % ((mdInfo['frame']-1) * 27.5)) > > --Eric > > -- Tato zpr?va byla vytvo?ena p?evratn?m po?tovn?m klientem Opery: http://www.opera.com/mail/ From hazards at musc.edu Wed Jun 15 11:26:48 2011 From: hazards at musc.edu (Starr Hazard) Date: Wed, 15 Jun 2011 14:26:48 -0400 Subject: [Chimera-users] Chimera-1.5.3 on RHEL 5 Linux workstation does not display surface Message-ID: <4DF8F968.5080108@musc.edu> Folks, I recently upgraded my LINUX to RHEL 5 (its an old machine and RHEL 6 did not recognize my old graphics card so I settled for RHEL5). I have installed xterm (eg yum install xerm). I downloaded Chimera 1.5.3 build 33475 2011-5-24 17:23 When I read in a PDB file and then try to display a surface, the calculation finishes but the display of the surface is fragmented with only a few of the triangular surface components displayed. The issue is not confined to a particular PDB. A windows version 1.5.3 works nominally with respect to surface display. So I am wondering if I have my xterm properly installed. Can you suggest some things for me to examine? Thanks Starr From goddard at sonic.net Wed Jun 15 11:34:39 2011 From: goddard at sonic.net (Tom Goddard) Date: Wed, 15 Jun 2011 11:34:39 -0700 Subject: [Chimera-users] Chimera-1.5.3 on RHEL 5 Linux workstation does not display surface In-Reply-To: <4DF8F968.5080108@musc.edu> References: <4DF8F968.5080108@musc.edu> Message-ID: <4DF8FB3F.3030007@sonic.net> This is a graphics driver bug. Maybe you have no graphics driver installed and it is using an old buggy version of Mesa to do the 3d graphics. The best solution is to install a graphics driver from the maker of your card Nvidia or AMD/ATI. Tom > Folks, > > I recently upgraded my LINUX to RHEL 5 (its an old machine and RHEL 6 > did not recognize my old graphics card so I settled for RHEL5). I have > installed xterm (eg yum install xerm). I downloaded Chimera 1.5.3 build > 33475 2011-5-24 17:23 > > When I read in a PDB file and then try to display a surface, the > calculation finishes but the display of the surface is fragmented with > only a few of the triangular > surface components displayed. The issue is not confined to a particular PDB. > > A windows version 1.5.3 works nominally with respect to surface display. > > So I am wondering if I have my xterm properly installed. > > Can you suggest some things for me to examine? > > Thanks > > > Starr From gregc at cgl.ucsf.edu Wed Jun 15 11:51:50 2011 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Wed, 15 Jun 2011 11:51:50 -0700 Subject: [Chimera-users] Chimera-1.5.3 on RHEL 5 Linux workstation does not display surface In-Reply-To: <4DF8FB3F.3030007@sonic.net> References: <4DF8F968.5080108@musc.edu> <4DF8FB3F.3030007@sonic.net> Message-ID: <4DF8FF46.8050403@cgl.ucsf.edu> In general, you would be better off with a current desktop version of Linux, like Ubuntu or Fedora, than a server version of Linux, like RHEL. The software graphics drivers in the server editions are conservatively updated and are often buggy for 3D graphics. As Tom said, you need to install the graphics driver from the card's vendor. If you have Intel graphics, my condolences -- you can try the newest version of Linux you can find, but you would be better off replacing the laptop with one that has AMD/ATI or NVIDIA graphics, and if it's a desktop, putting in an AMD/ATI or NVIDIA graphics card. In a similar vein, if your graphics card is ancient and not recognized, then maybe it's time to spend $20-$50 for a newer card :-) Good luck, Greg On 06/15/2011 11:34 AM, Tom Goddard wrote: > This is a graphics driver bug. Maybe you have no graphics driver > installed and it is using an old buggy version of Mesa to do the 3d > graphics. The best solution is to install a graphics driver from the > maker of your card Nvidia or AMD/ATI. > > Tom > >> Folks, >> >> I recently upgraded my LINUX to RHEL 5 (its an old machine and RHEL 6 >> did not recognize my old graphics card so I settled for RHEL5). I have >> installed xterm (eg yum install xerm). I downloaded Chimera 1.5.3 build >> 33475 2011-5-24 17:23 >> >> When I read in a PDB file and then try to display a surface, the >> calculation finishes but the display of the surface is fragmented with >> only a few of the triangular >> surface components displayed. The issue is not confined to a particular PDB. >> >> A windows version 1.5.3 works nominally with respect to surface display. >> >> So I am wondering if I have my xterm properly installed. >> >> Can you suggest some things for me to examine? >> >> Thanks >> >> >> Starr > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From jchinu2014 at gmail.com Thu Jun 16 16:59:58 2011 From: jchinu2014 at gmail.com (chinmaya joshi) Date: Thu, 16 Jun 2011 19:59:58 -0400 Subject: [Chimera-users] opening image stack Message-ID: Can you help me how I can open a stack of .png images using a command line in chimera. I will have a set of images and I want to open the stack in chimera using the command line. Is there any python script for this? Waiting for replies -------------- next part -------------- An HTML attachment was scrubbed... URL: From jjm at mdc-berlin.de Fri Jun 17 02:53:24 2011 From: jjm at mdc-berlin.de (Mueller, Juergen-Joachim) Date: Fri, 17 Jun 2011 11:53:24 +0200 Subject: [Chimera-users] Inner Cavities Message-ID: <7F4F0797574B0542B3EF27994B8FBCFB015CDB8A@MDCEXCL2.mdc-berlin.net> Dear helper, I know the general pathway to get an inner cavity with CHIMERA 1.5.2 e.g. tools surface surfnet #0 MESH Apply control click on mesh (all bubbles selected) commandline:ac Sc control click on bubble of interest (select only 1 bubble) select invert (selected models) all wrong bubbles are selected action surface hide .... My problem is, there is no inner bubble detected in my molecule but there is one! There were ligands which have been removed before. What happens? Is there a probe sphere too large? Where can it set smaller? Thank you for help, Juergen -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Fri Jun 17 10:01:22 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 17 Jun 2011 10:01:22 -0700 Subject: [Chimera-users] Inner Cavities In-Reply-To: <7F4F0797574B0542B3EF27994B8FBCFB015CDB8A@MDCEXCL2.mdc-berlin.net> References: <7F4F0797574B0542B3EF27994B8FBCFB015CDB8A@MDCEXCL2.mdc-berlin.net> Message-ID: <00849BD9-6D1A-423C-A6B3-ACE3251F0877@cgl.ucsf.edu> Dear Juergen, I would use a regular molecular surface instead of the surfnet surface. Surfnet has parameters you can play with, but personally I find it more difficult to control the outcome than with the molecular surface. If your structure is in the CASTp database, you could just fetch results including all the precalculated cavity volumes and surface areas, into Chimera. Chimera uses the regular molecular surface to display the CASTp results, but also lists them in a convenient table. For example, use File... Fetch by ID, enter a PDB ID in the CASTp fetch area -- I know 2gbp is in that database, but you could try your own PDB IDs of interest. The advantage of the CASTp approach is that even if the pockets are not closed, it figures out boundaries between the pocket and the outside space and can report pocket volumes. Or, if your structure isn't in CASTp and/or you just want to explore the bubbles yourself, you could use a similar process as you described, but with a molecular surface instead of a Surfnet surface. For example: open 2gbp surf color white,s surftransp 75 ~disp ~ribbon ... then Ctrl-click to select the whole surface, then click the green magnifying glass at the bottom right of the Chimera window to open the Selection Inspector. In that dialog, inspect "MSMS surface": (a) change "one transparent layer" to false ... now you can see inside bubbles (b) if you don't see the one you expect, you can also change "probe radius" in that dialog Once you see there is a bubble of interest, you can use command "ac Sc" and continue as you said. The molecular surface can also be shown as mesh, but I think it is easier to see the bubbles with transparency. One problem is that the molecular surface calculation may fail numerically with certain sets of parameters. In that case you could try different combinations of molecular surface probe radius and vertex density. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jun 17, 2011, at 2:53 AM, Mueller, Juergen-Joachim wrote: > Dear helper, > > I know the general pathway to get an inner cavity with CHIMERA 1.5.2 > e.g. > tools surface surfnet #0 MESH Apply > control click on mesh (all bubbles selected) > commandline:ac Sc > control click on bubble of interest (select only 1 bubble) > select invert (selected models) all wrong bubbles are selected > action surface hide > .... > > My problem is, there is no inner bubble detected in my molecule but there is one! > There were ligands which have been removed before. > What happens? Is there a probe sphere too large? Where can it set smaller? > Thank you for help, > Juergen From stkachev at cellsignal.com Fri Jun 17 13:49:55 2011 From: stkachev at cellsignal.com (Sasha Tkachev) Date: Fri, 17 Jun 2011 13:49:55 -0700 (PDT) Subject: [Chimera-users] custom residue label Message-ID: <201106172049.p5HKnt032025581@guanine.cgl.ucsf.edu> How to programmatically set a residue label to an arbitrary text, e.g. to say something like: rlabel :656.E "Lys-57" What happens in some structures, like for instance 1U35 structure that contains H3 proteins, is that residue numbers in a PDB file is different from residue number of the sequence. In this particular example Lys57 of H3 on chain E maps to PDB residue number 656. So if I use default labeling I am getting wrong results... From Simon.Sham at USU.Edu Fri Jun 17 14:11:17 2011 From: Simon.Sham at USU.Edu (Simon Sham) Date: Fri, 17 Jun 2011 21:11:17 +0000 Subject: [Chimera-users] Sequence aligment Message-ID: <7EDE6B59B687D44FB317A960F906CD163028254A@mb03.aggies.usu.edu> Hi, Is it possible that to do a sequence alignment in Chimera given only a text file with 2 protein amino acid sequences? I have the pdb files but there are some missing amino acids in them. Thanks for your help. Simon -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Fri Jun 17 14:20:24 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 17 Jun 2011 14:20:24 -0700 Subject: [Chimera-users] custom residue label In-Reply-To: <201106172049.p5HKnt032025581@guanine.cgl.ucsf.edu> References: <201106172049.p5HKnt032025581@guanine.cgl.ucsf.edu> Message-ID: Hi Sasha, If "programatically" includes Chimera commands, you could use a command something like: setattr r label "Lys-57" :656.e Non-programatically, it can also be done by selecting the residue and then using the menu (Actions... Label... residue... custom). I don't know python, so if that is what you meant, somebody else will have to answer. However, you might just want to edit the PDB file in the first place to avoid the bother. You could text-edit it "manually" or use one of these handy PDB-editing web servers: I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jun 17, 2011, at 1:49 PM, Sasha Tkachev wrote: > How to programmatically set a residue label to an arbitrary text, e.g. > to say something like: > > rlabel :656.E "Lys-57" > > What happens in some structures, like for instance 1U35 structure that > contains H3 proteins, is that residue numbers in a PDB file is > different from residue number of the sequence. In this particular > example Lys57 of H3 on chain E maps to PDB residue number 656. So if I > use default labeling I am getting wrong results... > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From meng at cgl.ucsf.edu Fri Jun 17 14:38:37 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 17 Jun 2011 14:38:37 -0700 Subject: [Chimera-users] Sequence aligment In-Reply-To: <7EDE6B59B687D44FB317A960F906CD163028254A@mb03.aggies.usu.edu> References: <7EDE6B59B687D44FB317A960F906CD163028254A@mb03.aggies.usu.edu> Message-ID: <29199EED-04CE-4721-80FF-F006A9D19A13@cgl.ucsf.edu> Hi Simon, Although Chimera certainly isn't a sequence-aligning machine (intended more for integrated sequence-structure work), it can be done without too much trouble if the sequences are fairly easy to align. Chimera doesn't read non-aligned multisequence files, so the approach would be to put one sequence in a Fasta file, open that in Chimera, then use Multalign Viewer's (the tool that is showing the sequence) Edit menu to add the other sequence to create a pairwise alignment. Note that Chimera will use the SEQRES information, if present, in a PDB file. Thus if you used Sequence (in Favorites menu) to show the sequence for a chain in your PDB structure, it may include residues for which coordinates are missing. If all the residues are included in the SEQRES but for only one structure, you could show it with Sequence to get the first sequence and then proceed as above. If all the residues are included in the SEQRES info for both your structures, you could just use the Matchmaker tool (under Tools... Structure Comparison) or matchmaker command with the "show alignment" option to give you the pairwise sequence alignment. If the sequences are not easy to align, i.e. quite dissimilar, the alignment with default parameters might not be good enough. You may need to delete the second sequence (see Multalign Viewer's Edit menu), and re-add after changing parameters, or if you had used the Matchmaker approach, delete the whole alignment and try matchmaker again with different alignment parameters. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jun 17, 2011, at 2:11 PM, Simon Sham wrote: > Hi, > Is it possible that to do a sequence alignment in Chimera given only a text file with 2 protein amino acid sequences? I have the pdb files but there are some missing amino acids in them. > Thanks for your help. > Simon > From meng at cgl.ucsf.edu Fri Jun 17 17:22:31 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 17 Jun 2011 17:22:31 -0700 Subject: [Chimera-users] opening image stack In-Reply-To: References: Message-ID: <30826D21-FE12-4365-AF06-7768AD9E6509@cgl.ucsf.edu> Hi Chinmaya, If you are using the Chimera command line, you want Chimera commands, not python. Here is how to use the "open" command, see the part about local files, However, based on our earlier correspondence, I somewhat doubt you have a PNG stack. Just having multiple PNG files does not mean that they are a stack. An image stack is generally produced by some instrument (say a microscope) and consists of 2D images that when opened together and slightly displaced from one another along the third dimension, create a single 3D map or object. Elaine On Jun 16, 2011, at 4:59 PM, chinmaya joshi wrote: > Can you help me how I can open a stack of .png images using a command line in chimera. > I will have a set of images and I want to open the stack in chimera using the command line. > Is there any python script for this? > > Waiting for replies From jjm at mdc-berlin.de Mon Jun 20 03:12:46 2011 From: jjm at mdc-berlin.de (Mueller, Juergen-Joachim) Date: Mon, 20 Jun 2011 12:12:46 +0200 Subject: [Chimera-users] Inner Cavities References: <7F4F0797574B0542B3EF27994B8FBCFB015CDB8A@MDCEXCL2.mdc-berlin.net> <00849BD9-6D1A-423C-A6B3-ACE3251F0877@cgl.ucsf.edu> Message-ID: <7F4F0797574B0542B3EF27994B8FBCFB015CDB8D@MDCEXCL2.mdc-berlin.net> Dear Elaine, thank you, I have choosen the CASTp-variant because the inner bubble could not be selected from the surface (tunnel to the surface exists). Greetings, Juergen -----Urspr?ngliche Nachricht----- Von: Elaine Meng [mailto:meng at cgl.ucsf.edu] Gesendet: Fr 17.06.2011 19:01 An: Mueller, Juergen-Joachim Cc: chimera-users at cgl.ucsf.edu Betreff: Re: [Chimera-users] Inner Cavities Dear Juergen, I would use a regular molecular surface instead of the surfnet surface. Surfnet has parameters you can play with, but personally I find it more difficult to control the outcome than with the molecular surface. If your structure is in the CASTp database, you could just fetch results including all the precalculated cavity volumes and surface areas, into Chimera. Chimera uses the regular molecular surface to display the CASTp results, but also lists them in a convenient table. For example, use File... Fetch by ID, enter a PDB ID in the CASTp fetch area -- I know 2gbp is in that database, but you could try your own PDB IDs of interest. The advantage of the CASTp approach is that even if the pockets are not closed, it figures out boundaries between the pocket and the outside space and can report pocket volumes. Or, if your structure isn't in CASTp and/or you just want to explore the bubbles yourself, you could use a similar process as you described, but with a molecular surface instead of a Surfnet surface. For example: open 2gbp surf color white,s surftransp 75 ~disp ~ribbon ... then Ctrl-click to select the whole surface, then click the green magnifying glass at the bottom right of the Chimera window to open the Selection Inspector. In that dialog, inspect "MSMS surface": (a) change "one transparent layer" to false ... now you can see inside bubbles (b) if you don't see the one you expect, you can also change "probe radius" in that dialog Once you see there is a bubble of interest, you can use command "ac Sc" and continue as you said. The molecular surface can also be shown as mesh, but I think it is easier to see the bubbles with transparency. One problem is that the molecular surface calculation may fail numerically with certain sets of parameters. In that case you could try different combinations of molecular surface probe radius and vertex density. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jun 17, 2011, at 2:53 AM, Mueller, Juergen-Joachim wrote: > Dear helper, > > I know the general pathway to get an inner cavity with CHIMERA 1.5.2 > e.g. > tools surface surfnet #0 MESH Apply > control click on mesh (all bubbles selected) > commandline:ac Sc > control click on bubble of interest (select only 1 bubble) > select invert (selected models) all wrong bubbles are selected > action surface hide > .... > > My problem is, there is no inner bubble detected in my molecule but there is one! > There were ligands which have been removed before. > What happens? Is there a probe sphere too large? Where can it set smaller? > Thank you for help, > Juergen -------------- next part -------------- A non-text attachment was scrubbed... Name: winmail.dat Type: application/ms-tnef Size: 4355 bytes Desc: not available URL: From gtzotzos at me.com Mon Jun 20 08:03:07 2011 From: gtzotzos at me.com (George Tzotzos) Date: Mon, 20 Jun 2011 17:03:07 +0200 Subject: [Chimera-users] Manual placement of ligand into the receptor binding site Message-ID: Hi everybody, I'm trying to simulated ligand binding by molecular dynamics. I'd like to place a ligand into the binding site of a receptor molecule downloaded from the Protein Data Bank. The ligand has not been co-crystalised with the protein and its coordinates do not match those of the protein. Is there a way that I can achieve a coordinate "translation" manually by using Chimera? Thanks in advance for any suggestions Regards George From menetret at gmail.com Mon Jun 20 08:35:19 2011 From: menetret at gmail.com (Jean-Francois Menetret) Date: Mon, 20 Jun 2011 17:35:19 +0200 Subject: [Chimera-users] Segmentation fault Message-ID: Hello, I have installed chimera (chimera-alpha-linux_x86_64.bin) on my Ubuntu laptop. The session crashes with segmentation fault without apparent reasons (30% memory usage; 0% swap) and even when doing nothing ... How can I debug this situation ? Jean-Francois -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Mon Jun 20 08:39:26 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 20 Jun 2011 08:39:26 -0700 Subject: [Chimera-users] Manual placement of ligand into the receptor binding site In-Reply-To: References: Message-ID: <9B0F595B-62A9-4E1B-BB9A-AD9D25DDE4DB@cgl.ucsf.edu> Hi George, You can move one structure interactively with the mouse while the other is frozen in place ("deactivated for motion"). Model activation/deactivation can be controlled with the "A" or "Active" checkboxes in the Model Panel (this tool is under Favorites), or the checkboxes under the Command Line, or with the select command. Or, if you are using motion commands (move, turn, etc.) instead of the mouse, there are command options to move only certain models instead of everything. However, that would require knowing the desired rotation or translation quantity and direction. It is more likely you will be using the mouse. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jun 20, 2011, at 8:03 AM, George Tzotzos wrote: > Hi everybody, > I'm trying to simulated ligand binding by molecular dynamics. I'd like to place a ligand into the binding site of a receptor molecule downloaded from the Protein Data Bank. > The ligand has not been co-crystalised with the protein and its coordinates do not match those of the protein. Is there a way that I can achieve a coordinate "translation" manually by using Chimera? > Thanks in advance for any suggestions > Regards > George From gregc at cgl.ucsf.edu Mon Jun 20 08:57:01 2011 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Mon, 20 Jun 2011 08:57:01 -0700 Subject: [Chimera-users] Segmentation fault In-Reply-To: References: Message-ID: <4DFF6DCD.4030601@cgl.ucsf.edu> On 6/20/2011 8:35 AM, Jean-Francois Menetret wrote: > Hello, > I have installed chimera (chimera-alpha-linux_x86_64.bin) on my Ubuntu > laptop. > The session crashes with segmentation fault without apparent reasons > (30% memory usage; 0% swap) and even when doing nothing ... > How can I debug this situation ? > Jean-Francois Usually odd crashes are caused by a faulty graphics driver. So if you have an AMD/ATI or NVIDIA graphics card, you should install the proprietary drivers, they are more robust than the open-source ones and faster too. If you have Intel graphics, then you might be out of luck depending on which model you have, but in general, you want the newest version of the driver you can get which means the more recent desktop Linux you can get -- the Intel driver is under very active development right now. If you use chimera's Help / Report a Bug dialog to report this as a bug, that will tell me about the hardware in your system and which version of Ubuntu you have and then I'll be able to help you better. HTH, Greg -------------- next part -------------- An HTML attachment was scrubbed... URL: From stkachev at cellsignal.com Mon Jun 20 08:26:04 2011 From: stkachev at cellsignal.com (Sasha Tkachev) Date: Mon, 20 Jun 2011 11:26:04 -0400 Subject: [Chimera-users] custom residue label In-Reply-To: References: <201106172049.p5HKnt032025581@guanine.cgl.ucsf.edu> Message-ID: <244D9F19-FF94-4342-9F5B-3D588A814FF7@cellsignal.com> Hi Elaine, Yes it definitely helps, thanks! Sasha. On Jun 17, 2011, at 5:20 PM, Elaine Meng wrote: > Hi Sasha, > If "programatically" includes Chimera commands, you could use a > command something like: > > setattr r label "Lys-57" :656.e > > Non-programatically, it can also be done by selecting the residue > and then using the menu (Actions... Label... residue... custom). > > I don't know python, so if that is what you meant, somebody else > will have to answer. > > However, you might just want to edit the PDB file in the first place > to avoid the bother. You could text-edit it "manually" or use one > of these handy PDB-editing web servers: > > > > > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Jun 17, 2011, at 1:49 PM, Sasha Tkachev wrote: > >> How to programmatically set a residue label to an arbitrary text, >> e.g. >> to say something like: >> >> rlabel :656.E "Lys-57" >> >> What happens in some structures, like for instance 1U35 structure >> that >> contains H3 proteins, is that residue numbers in a PDB file is >> different from residue number of the sequence. In this particular >> example Lys57 of H3 on chain E maps to PDB residue number 656. So >> if I >> use default labeling I am getting wrong results... >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From rlwoltz at ucdavis.edu Tue Jun 21 11:44:37 2011 From: rlwoltz at ucdavis.edu (Ryan Woltz) Date: Tue, 21 Jun 2011 11:44:37 -0700 Subject: [Chimera-users] computer advice Message-ID: Dear Chimera, We are looking at getting a new computer for our lab to used for only modeling. We are planning using chimera, pymol, and dock 6.4 as primary programs for this. What specifications i.e. graphic cards, ram, do you recommend us getting? Thank you, Ryan Woltz UC Davis Cardiology -------------- next part -------------- An HTML attachment was scrubbed... URL: From gregc at cgl.ucsf.edu Tue Jun 21 17:02:10 2011 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Tue, 21 Jun 2011 17:02:10 -0700 Subject: [Chimera-users] computer advice In-Reply-To: References: Message-ID: <4E013102.9080200@cgl.ucsf.edu> On 06/21/2011 11:44 AM, Ryan Woltz wrote: > Dear Chimera, > > We are looking at getting a new computer for our lab to > used for only modeling. We are planning using chimera, pymol, and > dock 6.4 as primary programs for this. What specifications i.e. > graphic cards, ram, do you recommend us getting? > > Thank you, > > Ryan Woltz > UC Davis Cardiology It depends on how big your data is, how you want to visualize it, and your budget. All of the programs would benefit from faster CPUs and more RAM, and the visualization programs benefit from faster graphics. Dock can run in parallel, so the more CPUs the better. Chimera gets more benefit from faster individual CPUs, but is starting to use some parallelized code. Don't know about pymol. So, if you can do your docking on a computational cluster, then I'd suggest just getting a quad-core computer. Take a look at the chimera benchmark results, http://plato.cgl.ucsf.edu/trac/chimera/wiki/benchmarks, for an idea of the relative performance of graphics cards. The benchmark results are submitted by chimera users (using Tools / Utilities / Benchmark, please submit your results too), so the coverage of graphics cards is spotty. Another good source of relative graphics card performance is Tom's Hardware's, http://www.tomshardware.com/, "Best Graphics Cards For the Money" articles. The last page has a "Graphics Card Hierarchy Chart" -- note that the best performing cards are the most power hungry and the hottest. If you want to display 3D stereo graphics with chimera, you'll need a workstation graphics card, a NVidia Quadro or AMD/ATI FirePro, instead of a consumer card (AMD/ATI Radeon, NVIDIA GeForce) and a suitable display. Stay away from Intel integrated graphics. Graphics on Linux is typically slightly faster with identical hardware than Apple Mac OS X or Microsoft Windows, but that should not be a major consideration. HTH, Greg From meng at cgl.ucsf.edu Thu Jun 23 09:23:31 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 23 Jun 2011 09:23:31 -0700 Subject: [Chimera-users] Drug-Metal Complexation Modeling In-Reply-To: <4E02F53A0200008500034342@dbngwia1.ukzn.ac.za> References: <4E02F53A0200008500034342@dbngwia1.ukzn.ac.za> Message-ID: <1B8524D8-18D6-4B0B-BBAE-6AFF00246059@cgl.ucsf.edu> Hello Mickey, Chimera has a "Metal Geometry" tool for assessing the coordination geometry within metal complexes, for example, identifying a protein complexation site as octahedral vs. pentagonal bipyramidal. It is intended for use with existing coordinates, such as from crystallography or output by other computational methods. Chimera does not include QM calculations, and would not replace the programs you mention if you are primarily interested in generating the coordinates in the first place. You can build structures with Chimera, but optimization is rather limited to only a few metals, and those that are handled are treated as point-charge VDW spheres (only minimization, no MD, and no QM to incorporate orbital directionality). It could be useful modifying existing metal complex structures, and as mentioned above, analyzing those structures output from other programs. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jun 22, 2011, at 11:11 PM, Mickey Branham wrote: > Dr. Meng > Our group is interested in drug-metal complexation modeling. We have ongoing MM and MD studies using Gaussian or COSMO, with mixed results. Before we embark on a new voyage into Chimera can you tell us its capacity for elucidating drug-metal complexes e.g. tetracycline-M+2. > > Cheers > Mickey > > Michael Lee Branham, PhD. > University of KwaZulu-Natal > School of Pharmacy and Pharmacology > Durban, South Africa > > Please find our Email Disclaimer here-->: http://www.ukzn.ac.za/disclaimer > From mkthomps at ncsu.edu Wed Jun 22 20:44:54 2011 From: mkthomps at ncsu.edu (Matthew Thompson) Date: Wed, 22 Jun 2011 23:44:54 -0400 Subject: [Chimera-users] Water Ice Structures Message-ID: I am looking for the crystal structures of "normal" ice (Ih), ice(VI), and ice(VII). I have found the .cif file for ice(VI), but I can't seem to get it to load properly into Chimera. I am really only familiar with using pdb's in Chimera. These would be used in a presentation given this coming weekend at the National School for Neutron and X-ray Scattering. Any help in this would be greatly appreciated Thanks Matt _ Matthew K. Thompson, PhD North Carolina State University Raleigh, NC 27695 Office: 919-515-2105 Cell: 919-455-1775 From meng at cgl.ucsf.edu Thu Jun 23 09:43:44 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 23 Jun 2011 09:43:44 -0700 Subject: [Chimera-users] Water Ice Structures In-Reply-To: References: Message-ID: <317AA586-B468-4371-B490-829329945A0B@cgl.ucsf.edu> Hi Matt, We can't really tell what is going on without that file. Is it proprietary? You could send it to just me and I would keep it amongst the developers here. However, by googling I see there is an ice(VI) CIF available from this page, and I was able to open it in Chimera, but only three dots appear and I get the following errors in the Reply Log. If that is the same file you used and the same result, let us know. MMLIB:WARNING] GetSpaceGroup('P 42/n m c') not found [MMLIB:WARNING] monomer description not found in zipfile for 'GLOBAL' [MMLIB:WARNING] monomer description not found for 'global' [MMLIB:WARNING] monomer description not found in zipfile for 'GLOBAL' [MMLIB:WARNING] monomer description not found for 'global' [MMLIB:WARNING] read_atoms: no geom_bond section found [MMLIB:WARNING] read_atoms: no geom_angle section found [MMLIB:WARNING] monomer description not found in zipfile for 'GLOBAL' [MMLIB:WARNING] monomer description not found for 'global' AMS_DATA.cif opened The CIF reader was developed mainly for mmCIF from the PDB and does not cover the universe of CIF possibilities. It may be a current limitation as opposed to a bug, but we would need to know which file you used. Besides sending email to chimera-users, another approach is to use "Help... Report a Bug" in the Chimera menu and include a description of steps needed to reproduce the problem, attach any file needed to reproduce the problem, and include your email address if you wish feedback. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jun 22, 2011, at 8:44 PM, Matthew Thompson wrote: > I am looking for the crystal structures of "normal" ice (Ih), ice(VI), > and ice(VII). I have found the .cif file for ice(VI), but I can't > seem to get it to load properly into Chimera. I am really only > familiar with using pdb's in Chimera. These would be used in a > presentation given this coming weekend at the National School for > Neutron and X-ray Scattering. Any help in this would be greatly > appreciated > > Thanks > Matt > _ > Matthew K. Thompson, PhD > North Carolina State University > Raleigh, NC 27695 > Office: 919-515-2105 > Cell: 919-455-1775 From meng at cgl.ucsf.edu Thu Jun 23 10:06:13 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 23 Jun 2011 10:06:13 -0700 Subject: [Chimera-users] Water Ice Structures In-Reply-To: <317AA586-B468-4371-B490-829329945A0B@cgl.ucsf.edu> References: <317AA586-B468-4371-B490-829329945A0B@cgl.ucsf.edu> Message-ID: <25B858A4-AB52-4E6C-8423-9F323C5CD805@cgl.ucsf.edu> Then again, that CIF file really only has three atoms in it, named Wat1 Wat2 Wat3, so perhaps Chimera has done all it can to show it! Besides which file is used, it is unclear what you meant by not loading properly. Elaine On Jun 23, 2011, at 9:43 AM, Elaine Meng wrote: > Hi Matt, > We can't really tell what is going on without that file. Is it proprietary? You could send it to just me and I would keep it amongst the developers here. However, by googling I see there is an ice(VI) CIF available from this page, > > > and I was able to open it in Chimera, but only three dots appear and I get the following errors in the Reply Log. If that is the same file you used and the same result, let us know. > > MMLIB:WARNING] GetSpaceGroup('P 42/n m c') not found > [MMLIB:WARNING] monomer description not found in zipfile for 'GLOBAL' > [MMLIB:WARNING] monomer description not found for 'global' > [MMLIB:WARNING] monomer description not found in zipfile for 'GLOBAL' > [MMLIB:WARNING] monomer description not found for 'global' > [MMLIB:WARNING] read_atoms: no geom_bond section found > [MMLIB:WARNING] read_atoms: no geom_angle section found > [MMLIB:WARNING] monomer description not found in zipfile for 'GLOBAL' > [MMLIB:WARNING] monomer description not found for 'global' > AMS_DATA.cif opened > > The CIF reader was developed mainly for mmCIF from the PDB and does not cover the universe of CIF possibilities. It may be a current limitation as opposed to a bug, but we would need to know which file you used. > > Besides sending email to chimera-users, another approach is to use "Help... Report a Bug" in the Chimera menu and include a description of steps needed to reproduce the problem, attach any file needed to reproduce the problem, and include your email address if you wish feedback. > Best, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Jun 22, 2011, at 8:44 PM, Matthew Thompson wrote: > >> I am looking for the crystal structures of "normal" ice (Ih), ice(VI), >> and ice(VII). I have found the .cif file for ice(VI), but I can't >> seem to get it to load properly into Chimera. I am really only >> familiar with using pdb's in Chimera. These would be used in a >> presentation given this coming weekend at the National School for >> Neutron and X-ray Scattering. Any help in this would be greatly >> appreciated >> >> Thanks >> Matt >> _ >> Matthew K. Thompson, PhD >> North Carolina State University >> Raleigh, NC 27695 >> Office: 919-515-2105 >> Cell: 919-455-1775 > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From meng at cgl.ucsf.edu Thu Jun 23 10:28:27 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 23 Jun 2011 10:28:27 -0700 Subject: [Chimera-users] Water Ice Structures In-Reply-To: <25B858A4-AB52-4E6C-8423-9F323C5CD805@cgl.ucsf.edu> References: <317AA586-B468-4371-B490-829329945A0B@cgl.ucsf.edu> <25B858A4-AB52-4E6C-8423-9F323C5CD805@cgl.ucsf.edu> Message-ID: Hi Matt, Actually, that AMS website might have the forms you need, except I don't see ice VII. After I opened the ice VI cif file, I used Unit Cell (under Tools... Higher-Order Structure in the Chimera menu) to "make copies" and "show outline" which gives the appearance below. I had also showed atom-name labels (Chimera menu "Actions... Labels... name"). Reading symmetry information from CIF files is a new feature available only in Chimera 1.6 (daily build download), so if you see any problems with that let us know. At least for this ice VI structure, the relationship of the 3 atoms in the original structure (white) to the unit cell outline box looks the same as in the Jmol view at that website. I hope this helps, Elaine -------------- next part -------------- A non-text attachment was scrubbed... Name: iceVIunitcell.png Type: image/png Size: 39897 bytes Desc: not available URL: -------------- next part -------------- On Jun 23, 2011, at 10:06 AM, Elaine Meng wrote: > Then again, that CIF file really only has three atoms in it, named Wat1 Wat2 Wat3, so perhaps Chimera has done all it can to show it! Besides which file is used, it is unclear what you meant by not loading properly. > Elaine > > On Jun 23, 2011, at 9:43 AM, Elaine Meng wrote: > >> Hi Matt, >> We can't really tell what is going on without that file. Is it proprietary? You could send it to just me and I would keep it amongst the developers here. However, by googling I see there is an ice(VI) CIF available from this page, >> >> >> and I was able to open it in Chimera, but only three dots appear and I get the following errors in the Reply Log. If that is the same file you used and the same result, let us know. >> >> MMLIB:WARNING] GetSpaceGroup('P 42/n m c') not found >> [MMLIB:WARNING] monomer description not found in zipfile for 'GLOBAL' >> [MMLIB:WARNING] monomer description not found for 'global' >> [MMLIB:WARNING] monomer description not found in zipfile for 'GLOBAL' >> [MMLIB:WARNING] monomer description not found for 'global' >> [MMLIB:WARNING] read_atoms: no geom_bond section found >> [MMLIB:WARNING] read_atoms: no geom_angle section found >> [MMLIB:WARNING] monomer description not found in zipfile for 'GLOBAL' >> [MMLIB:WARNING] monomer description not found for 'global' >> AMS_DATA.cif opened >> >> The CIF reader was developed mainly for mmCIF from the PDB and does not cover the universe of CIF possibilities. It may be a current limitation as opposed to a bug, but we would need to know which file you used. >> >> Besides sending email to chimera-users, another approach is to use "Help... Report a Bug" in the Chimera menu and include a description of steps needed to reproduce the problem, attach any file needed to reproduce the problem, and include your email address if you wish feedback. >> Best, >> Elaine >> ---------- >> Elaine C. Meng, Ph.D. >> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >> On Jun 22, 2011, at 8:44 PM, Matthew Thompson wrote: >> >>> I am looking for the crystal structures of "normal" ice (Ih), ice(VI), >>> and ice(VII). I have found the .cif file for ice(VI), but I can't >>> seem to get it to load properly into Chimera. I am really only >>> familiar with using pdb's in Chimera. These would be used in a >>> presentation given this coming weekend at the National School for >>> Neutron and X-ray Scattering. Any help in this would be greatly >>> appreciated >>> >>> Thanks >>> Matt >>> _ >>> Matthew K. Thompson, PhD >>> North Carolina State University >>> Raleigh, NC 27695 >>> Office: 919-515-2105 >>> Cell: 919-455-1775 >> From mkthomps at ncsu.edu Thu Jun 23 11:35:55 2011 From: mkthomps at ncsu.edu (Matthew Thompson) Date: Thu, 23 Jun 2011 14:35:55 -0400 Subject: [Chimera-users] Water Ice Structures In-Reply-To: References: <317AA586-B468-4371-B490-829329945A0B@cgl.ucsf.edu> <25B858A4-AB52-4E6C-8423-9F323C5CD805@cgl.ucsf.edu> Message-ID: Hi Elaine, Thanks for helping me. I've attached the file I used. It is the cif file for Ice (VI). The higher-order analysis did not work for me. Matt On Thu, Jun 23, 2011 at 1:28 PM, Elaine Meng wrote: > Hi Matt, > Actually, that AMS website might have the forms you need, except I don't see ice VII. ?After I opened the ice VI cif file, I used Unit Cell (under Tools... Higher-Order Structure in the Chimera menu) to "make copies" and "show outline" which gives the appearance below. ?I had also showed atom-name labels (Chimera menu "Actions... Labels... name"). > > Reading symmetry information from CIF files is a new feature available only in Chimera 1.6 (daily build download), > > so if you see any problems with that let us know. ?At least for this ice VI structure, the relationship of the 3 atoms in the original structure (white) to the unit cell outline box looks the same as in the Jmol view at that website. > > I hope this helps, > Elaine > > > > > > On Jun 23, 2011, at 10:06 AM, Elaine Meng wrote: > >> Then again, that CIF file really only has three atoms in it, named Wat1 Wat2 Wat3, so perhaps Chimera has done all it can to show it! ? Besides which file is used, it is unclear what you meant by not loading properly. >> Elaine >> >> On Jun 23, 2011, at 9:43 AM, Elaine Meng wrote: >> >>> Hi Matt, >>> We can't really tell what is going on without that file. ?Is it proprietary? ?You could send it to just me and I would keep it amongst the developers here. ?However, by googling I see there is an ice(VI) CIF available from this page, >>> >>> >>> and I was able to open it in Chimera, but only three dots appear and I get the following errors in the Reply Log. ?If that is the same file you used and the same result, let us know. >>> >>> MMLIB:WARNING] GetSpaceGroup('P 42/n m c') not found >>> [MMLIB:WARNING] monomer description not found in zipfile for 'GLOBAL' >>> [MMLIB:WARNING] monomer description not found for 'global' >>> [MMLIB:WARNING] monomer description not found in zipfile for 'GLOBAL' >>> [MMLIB:WARNING] monomer description not found for 'global' >>> [MMLIB:WARNING] read_atoms: no geom_bond section found >>> [MMLIB:WARNING] read_atoms: no geom_angle section found >>> [MMLIB:WARNING] monomer description not found in zipfile for 'GLOBAL' >>> [MMLIB:WARNING] monomer description not found for 'global' >>> AMS_DATA.cif opened >>> >>> The CIF reader was developed mainly for mmCIF from the PDB and does not cover the universe of CIF possibilities. ?It may be a current limitation as opposed to a bug, but we would need to know which file you used. >>> >>> Besides sending email to chimera-users, another approach is to use "Help... Report a Bug" in the Chimera menu and include a description of steps needed to reproduce the problem, attach any file needed to reproduce the problem, and include your email address if you wish feedback. >>> Best, >>> Elaine >>> ---------- >>> Elaine C. Meng, Ph.D. >>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >>> Department of Pharmaceutical Chemistry >>> University of California, San Francisco >>> >>> On Jun 22, 2011, at 8:44 PM, Matthew Thompson wrote: >>> >>>> I am looking for the crystal structures of "normal" ice (Ih), ice(VI), >>>> and ice(VII). ?I have found the .cif file for ice(VI), but I can't >>>> seem to get it to load properly into Chimera. ?I am really only >>>> familiar with using pdb's in Chimera. ?These would be used in a >>>> presentation given this coming weekend at the National School for >>>> Neutron and X-ray Scattering. ?Any help in this would be greatly >>>> appreciated >>>> >>>> Thanks >>>> Matt >>>> _ >>>> Matthew K. Thompson, PhD >>>> North Carolina State University >>>> Raleigh, NC 27695 >>>> Office: 919-515-2105 >>>> Cell: 919-455-1775 >>> > > > -------------- next part -------------- A non-text attachment was scrubbed... Name: EntryWithCollCode31868.cif Type: application/octet-stream Size: 2592 bytes Desc: not available URL: From meng at cgl.ucsf.edu Thu Jun 23 12:12:36 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 23 Jun 2011 12:12:36 -0700 Subject: [Chimera-users] Water Ice Structures In-Reply-To: References: <317AA586-B468-4371-B490-829329945A0B@cgl.ucsf.edu> <25B858A4-AB52-4E6C-8423-9F323C5CD805@cgl.ucsf.edu> Message-ID: Could you clarify what "did not work for me" means? Also, as mentioned you would need to get Chimera version 1.6 (a recent daily build) for the CIF symmetry information to be read and applied by Unit Cell. "Help... About UCSF Chimera" in the menu will show you which version you have. I opened it and Unit Cell did make copies. However, I suspect something may be amiss because several copies seem to be overlapping, but I really don't know much about how it is supposed to look -- so it would be useful for you to be more descriptive. Are you comparing what you see with a picture in some book or article that shows what it is supposed to look like, or how it looks in some other program? Finally, if it is wrong I don't know if it is an error in the file or an error by Chimera. Thanks Elaine On Jun 23, 2011, at 11:35 AM, Matthew Thompson wrote: > Hi Elaine, > > Thanks for helping me. I've attached the file I used. It is the cif > file for Ice (VI). The higher-order analysis did not work for me. > > Matt > > > On Thu, Jun 23, 2011 at 1:28 PM, Elaine Meng wrote: >> Hi Matt, >> Actually, that AMS website might have the forms you need, except I don't see ice VII. After I opened the ice VI cif file, I used Unit Cell (under Tools... Higher-Order Structure in the Chimera menu) to "make copies" and "show outline" which gives the appearance below. I had also showed atom-name labels (Chimera menu "Actions... Labels... name"). >> >> Reading symmetry information from CIF files is a new feature available only in Chimera 1.6 (daily build download), >> >> so if you see any problems with that let us know. At least for this ice VI structure, the relationship of the 3 atoms in the original structure (white) to the unit cell outline box looks the same as in the Jmol view at that website. >> >> I hope this helps, >> Elaine >> >> >> >> >> >> On Jun 23, 2011, at 10:06 AM, Elaine Meng wrote: >> >>> Then again, that CIF file really only has three atoms in it, named Wat1 Wat2 Wat3, so perhaps Chimera has done all it can to show it! Besides which file is used, it is unclear what you meant by not loading properly. >>> Elaine >>> >>> On Jun 23, 2011, at 9:43 AM, Elaine Meng wrote: >>> >>>> Hi Matt, >>>> We can't really tell what is going on without that file. Is it proprietary? You could send it to just me and I would keep it amongst the developers here. However, by googling I see there is an ice(VI) CIF available from this page, >>>> >>>> >>>> and I was able to open it in Chimera, but only three dots appear and I get the following errors in the Reply Log. If that is the same file you used and the same result, let us know. >>>> >>>> MMLIB:WARNING] GetSpaceGroup('P 42/n m c') not found >>>> [MMLIB:WARNING] monomer description not found in zipfile for 'GLOBAL' >>>> [MMLIB:WARNING] monomer description not found for 'global' >>>> [MMLIB:WARNING] monomer description not found in zipfile for 'GLOBAL' >>>> [MMLIB:WARNING] monomer description not found for 'global' >>>> [MMLIB:WARNING] read_atoms: no geom_bond section found >>>> [MMLIB:WARNING] read_atoms: no geom_angle section found >>>> [MMLIB:WARNING] monomer description not found in zipfile for 'GLOBAL' >>>> [MMLIB:WARNING] monomer description not found for 'global' >>>> AMS_DATA.cif opened >>>> >>>> The CIF reader was developed mainly for mmCIF from the PDB and does not cover the universe of CIF possibilities. It may be a current limitation as opposed to a bug, but we would need to know which file you used. >>>> >>>> Besides sending email to chimera-users, another approach is to use "Help... Report a Bug" in the Chimera menu and include a description of steps needed to reproduce the problem, attach any file needed to reproduce the problem, and include your email address if you wish feedback. >>>> Best, >>>> Elaine >>>> ---------- >>>> Elaine C. Meng, Ph.D. >>>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >>>> Department of Pharmaceutical Chemistry >>>> University of California, San Francisco >>>> >>>> On Jun 22, 2011, at 8:44 PM, Matthew Thompson wrote: >>>> >>>>> I am looking for the crystal structures of "normal" ice (Ih), ice(VI), >>>>> and ice(VII). I have found the .cif file for ice(VI), but I can't >>>>> seem to get it to load properly into Chimera. I am really only >>>>> familiar with using pdb's in Chimera. These would be used in a >>>>> presentation given this coming weekend at the National School for >>>>> Neutron and X-ray Scattering. Any help in this would be greatly >>>>> appreciated >>>>> >>>>> Thanks >>>>> Matt >>>>> _ >>>>> Matthew K. Thompson, PhD >>>>> North Carolina State University >>>>> Raleigh, NC 27695 >>>>> Office: 919-515-2105 >>>>> Cell: 919-455-1775 >>>> >> >> >> > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From goddard at sonic.net Thu Jun 23 17:55:30 2011 From: goddard at sonic.net (Tom Goddard) Date: Thu, 23 Jun 2011 17:55:30 -0700 Subject: [Chimera-users] Water Ice Structures In-Reply-To: References: <317AA586-B468-4371-B490-829329945A0B@cgl.ucsf.edu> <25B858A4-AB52-4E6C-8423-9F323C5CD805@cgl.ucsf.edu> Message-ID: <4E03E082.1090407@sonic.net> Hi Matthew, Thanks for sending your file. It allowed me to figure out an error in Chimera parsing of CIF crystal symmetry. Chimera was using symmetries expressed in fractional unit cell coordinates when it thought they were real space coordinates. I've fixed that and the Unit Cell dialog in tonight's daily build will give a more sensible result for CIF files. I've attached a picture of your CIF file which I think is ice VII, not ice VI as you said. This shows 2 by 2 by 2 unit cells. I turned of the "pack molecules in unit cell" option and used the fixed code. It still looks weird with 4 hydrogens coming of each oxygen. I believe this is because their are several possible orientations for each water -- the water orientations are disordered with half occupancy at each hydrogen position, as described in this reference http://www.ncbi.nlm.nih.gov/pmc/articles/PMC300465/pdf/pnas00186-0123.pdf "One can also assume that the proton positions are disordered, in the same sense as they are in ice I or ice Ic ("cubicice").1,8 The structure is therefore described statisticaly as follows: spacegroup Pn3m(O_h^4),a= 3.30A,O in 2 (a) (000, 1/2 1/2 1/2),1/2 H in8(e) (xxx, etc.), with x ~ 0.17." Reading about CIF and small-molecule crystals I found that the symmetries can place atoms exactly on top of each other. In your file I get 24 oxygens at every position and 6 hydrogens at every position. What I read said these duplicates should be eliminated, but Chimera does not do this. In protein crystals the symmetry operators never give the same position. This will need some future fix when I understand it better. Tom > Hi Elaine, > > Thanks for helping me. I've attached the file I used. It is the cif > file for Ice (VI). The higher-order analysis did not work for me. > > Matt > > > On Thu, Jun 23, 2011 at 1:28 PM, Elaine Meng wrote: >> Hi Matt, >> Actually, that AMS website might have the forms you need, except I don't see ice VII. After I opened the ice VI cif file, I used Unit Cell (under Tools... Higher-Order Structure in the Chimera menu) to "make copies" and "show outline" which gives the appearance below. I had also showed atom-name labels (Chimera menu "Actions... Labels... name"). >> >> Reading symmetry information from CIF files is a new feature available only in Chimera 1.6 (daily build download), >> >> so if you see any problems with that let us know. At least for this ice VI structure, the relationship of the 3 atoms in the original structure (white) to the unit cell outline box looks the same as in the Jmol view at that website. >> >> I hope this helps, >> Elaine >> >> >> >> >> >> On Jun 23, 2011, at 10:06 AM, Elaine Meng wrote: >> >>> Then again, that CIF file really only has three atoms in it, named Wat1 Wat2 Wat3, so perhaps Chimera has done all it can to show it! Besides which file is used, it is unclear what you meant by not loading properly. >>> Elaine >>> >>> On Jun 23, 2011, at 9:43 AM, Elaine Meng wrote: >>> >>>> Hi Matt, >>>> We can't really tell what is going on without that file. Is it proprietary? You could send it to just me and I would keep it amongst the developers here. However, by googling I see there is an ice(VI) CIF available from this page, >>>> >>>> >>>> and I was able to open it in Chimera, but only three dots appear and I get the following errors in the Reply Log. If that is the same file you used and the same result, let us know. >>>> >>>> MMLIB:WARNING] GetSpaceGroup('P 42/n m c') not found >>>> [MMLIB:WARNING] monomer description not found in zipfile for 'GLOBAL' >>>> [MMLIB:WARNING] monomer description not found for 'global' >>>> [MMLIB:WARNING] monomer description not found in zipfile for 'GLOBAL' >>>> [MMLIB:WARNING] monomer description not found for 'global' >>>> [MMLIB:WARNING] read_atoms: no geom_bond section found >>>> [MMLIB:WARNING] read_atoms: no geom_angle section found >>>> [MMLIB:WARNING] monomer description not found in zipfile for 'GLOBAL' >>>> [MMLIB:WARNING] monomer description not found for 'global' >>>> AMS_DATA.cif opened >>>> >>>> The CIF reader was developed mainly for mmCIF from the PDB and does not cover the universe of CIF possibilities. It may be a current limitation as opposed to a bug, but we would need to know which file you used. >>>> >>>> Besides sending email to chimera-users, another approach is to use "Help... Report a Bug" in the Chimera menu and include a description of steps needed to reproduce the problem, attach any file needed to reproduce the problem, and include your email address if you wish feedback. >>>> Best, >>>> Elaine >>>> ---------- >>>> Elaine C. Meng, Ph.D. >>>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >>>> Department of Pharmaceutical Chemistry >>>> University of California, San Francisco >>>> >>>> On Jun 22, 2011, at 8:44 PM, Matthew Thompson wrote: >>>> >>>>> I am looking for the crystal structures of "normal" ice (Ih), ice(VI), >>>>> and ice(VII). I have found the .cif file for ice(VI), but I can't >>>>> seem to get it to load properly into Chimera. I am really only >>>>> familiar with using pdb's in Chimera. These would be used in a >>>>> presentation given this coming weekend at the National School for >>>>> Neutron and X-ray Scattering. Any help in this would be greatly >>>>> appreciated >>>>> >>>>> Thanks >>>>> Matt >>>>> _ >>>>> Matthew K. Thompson, PhD >>>>> North Carolina State University >>>>> Raleigh, NC 27695 >>>>> Office: 919-515-2105 >>>>> Cell: 919-455-1775 >> >> >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ice_vii.jpg Type: image/jpeg Size: 47491 bytes Desc: not available URL: From damien.lariviere at mines-douai.fr Thu Jun 23 23:34:15 2011 From: damien.lariviere at mines-douai.fr (Damien LARIVIERE) Date: Fri, 24 Jun 2011 08:34:15 +0200 (CEST) Subject: [Chimera-users] pdb to xml Message-ID: <2129935932.6025.1308897255375.JavaMail.root@obelix.interne.emd> Dear all, WritePDB enables to save a displayed structure in the pdb format. Is there a way to save the structure into the PDBML format? If not, do you know a (simple) way to do that? Many thanks Damien From ursula at salilab.org Fri Jun 24 13:34:59 2011 From: ursula at salilab.org (Ursula Pieper) Date: Fri, 24 Jun 2011 13:34:59 -0700 Subject: [Chimera-users] Water Ice Structures In-Reply-To: <4E03E082.1090407@sonic.net> References: <317AA586-B468-4371-B490-829329945A0B@cgl.ucsf.edu> <25B858A4-AB52-4E6C-8423-9F323C5CD805@cgl.ucsf.edu> <4E03E082.1090407@sonic.net> Message-ID: There might be a problem with the particular cif file. If an atom gets "multiplied" by the crystallographic symmetry (meaning it is on a "special position"), the occupancy factor in the cif file should be accordingly low, because only a fraction of the atom lies in the asymmetric unit, with the "whole" atom generated by the crystallographic symmetry. So, I think the cif files from that site look strange (occupancy factors not adjusted to crystallographic symmetry). Atoms on special positions actually do occur occasionally in protein structures, most often for water molecules or heteroatoms. When an atom sits on a symmetry element such as a two-fold axis, the occupancy factor will by 0.5 (for a two-fold axis) to make up for the symmetry generated part. Ursula On Thu, Jun 23, 2011 at 5:55 PM, Tom Goddard wrote: > ** > Hi Matthew, > > Thanks for sending your file. It allowed me to figure out an error in > Chimera parsing of CIF crystal symmetry. Chimera was using symmetries > expressed in fractional unit cell coordinates when it thought they were real > space coordinates. I've fixed that and the Unit Cell dialog in tonight's > daily build will give a more sensible result for CIF files. > > I've attached a picture of your CIF file which I think is ice VII, not > ice VI as you said. This shows 2 by 2 by 2 unit cells. I turned of the > "pack molecules in unit cell" option and used the fixed code. It still > looks weird with 4 hydrogens coming of each oxygen. I believe this is > because their are several possible orientations for each water -- the water > orientations are disordered with half occupancy at each hydrogen position, > as described in this reference > > http://www.ncbi.nlm.nih.gov/pmc/articles/PMC300465/pdf/pnas00186-0123.pdf > > "One can also assume that the proton positions are disordered, in the same > sense as they are in ice I or ice Ic ("cubicice").1,8 The structure is > therefore described statisticaly as follows: spacegroup Pn3m(O_h^4),a= > 3.30A,O in 2 (a) (000, 1/2 1/2 1/2),1/2 H in8(e) (xxx, etc.), with x ~ > 0.17." > > Reading about CIF and small-molecule crystals I found that the symmetries > can place atoms exactly on top of each other. In your file I get 24 oxygens > at every position and 6 hydrogens at every position. What I read said these > duplicates should be eliminated, but Chimera does not do this. In protein > crystals the symmetry operators never give the same position. This will > need some future fix when I understand it better. > > Tom > > > > Hi Elaine, > > Thanks for helping me. I've attached the file I used. It is the cif > file for Ice (VI). The higher-order analysis did not work for me. > > Matt > > > On Thu, Jun 23, 2011 at 1:28 PM, Elaine Meng wrote: > > Hi Matt, > Actually, that AMS website might have the forms you need, except I don't see ice VII. After I opened the ice VI cif file, I used Unit Cell (under Tools... Higher-Order Structure in the Chimera menu) to "make copies" and "show outline" which gives the appearance below. I had also showed atom-name labels (Chimera menu "Actions... Labels... name"). > > Reading symmetry information from CIF files is a new feature available only in Chimera 1.6 (daily build download), > so if you see any problems with that let us know. At least for this ice VI structure, the relationship of the 3 atoms in the original structure (white) to the unit cell outline box looks the same as in the Jmol view at that website. > > I hope this helps, > Elaine > > > > > > On Jun 23, 2011, at 10:06 AM, Elaine Meng wrote: > > > Then again, that CIF file really only has three atoms in it, named Wat1 Wat2 Wat3, so perhaps Chimera has done all it can to show it! Besides which file is used, it is unclear what you meant by not loading properly. > Elaine > > On Jun 23, 2011, at 9:43 AM, Elaine Meng wrote: > > > Hi Matt, > We can't really tell what is going on without that file. Is it proprietary? You could send it to just me and I would keep it amongst the developers here. However, by googling I see there is an ice(VI) CIF available from this page, > > and I was able to open it in Chimera, but only three dots appear and I get the following errors in the Reply Log. If that is the same file you used and the same result, let us know. > > MMLIB:WARNING] GetSpaceGroup('P 42/n m c') not found > [MMLIB:WARNING] monomer description not found in zipfile for 'GLOBAL' > [MMLIB:WARNING] monomer description not found for 'global' > [MMLIB:WARNING] monomer description not found in zipfile for 'GLOBAL' > [MMLIB:WARNING] monomer description not found for 'global' > [MMLIB:WARNING] read_atoms: no geom_bond section found > [MMLIB:WARNING] read_atoms: no geom_angle section found > [MMLIB:WARNING] monomer description not found in zipfile for 'GLOBAL' > [MMLIB:WARNING] monomer description not found for 'global' > AMS_DATA.cif opened > > The CIF reader was developed mainly for mmCIF from the PDB and does not cover the universe of CIF possibilities. It may be a current limitation as opposed to a bug, but we would need to know which file you used. > > Besides sending email to chimera-users, another approach is to use "Help... Report a Bug" in the Chimera menu and include a description of steps needed to reproduce the problem, attach any file needed to reproduce the problem, and include your email address if you wish feedback. > Best, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Jun 22, 2011, at 8:44 PM, Matthew Thompson wrote: > > > I am looking for the crystal structures of "normal" ice (Ih), ice(VI), > and ice(VII). I have found the .cif file for ice(VI), but I can't > seem to get it to load properly into Chimera. I am really only > familiar with using pdb's in Chimera. These would be used in a > presentation given this coming weekend at the National School for > Neutron and X-ray Scattering. Any help in this would be greatly > appreciated > > Thanks > Matt > _ > Matthew K. Thompson, PhD > North Carolina State University > Raleigh, NC 27695 > Office: 919-515-2105 > Cell: 919-455-1775 > > > _______________________________________________ > Chimera-users mailing listChimera-users at cgl.ucsf.eduhttp://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Fri Jun 24 15:43:09 2011 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Fri, 24 Jun 2011 15:43:09 -0700 Subject: [Chimera-users] pdb to xml In-Reply-To: <2129935932.6025.1308897255375.JavaMail.root@obelix.interne.emd> References: <2129935932.6025.1308897255375.JavaMail.root@obelix.interne.emd> Message-ID: <026D5CC7-D1FB-49DB-A974-1819BC98DB3A@cgl.ucsf.edu> Hi Damien, There seems to be very few tools that output PDBML, and Chimera unfortunately is no exception. :-( It doesn't even seem to be a format that OpenBabel can output. The only tool that my googling uncovered is 3DNA. It can apparently write PDBML, though I don't think it can handle non-nucleic acid structures [the documentation for 3DNA leaves a little to be desired so I could be wrong about that limitation]. I hope you get lucky and find something that writes it! --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Jun 23, 2011, at 11:34 PM, Damien LARIVIERE wrote: > Dear all, > > WritePDB enables to save a displayed structure in the pdb format. > > Is there a way to save the structure into the PDBML format? > > If not, do you know a (simple) way to do that? > > Many thanks > > Damien > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From mmccully at uw.edu Fri Jun 24 16:12:31 2011 From: mmccully at uw.edu (Michelle E. McCully) Date: Fri, 24 Jun 2011 16:12:31 -0700 Subject: [Chimera-users] Capping a clipped sphere representation Message-ID: Hi, I would like to create an image of a protein shown in van der Waals spheres with a clipped surface. I'd like each individual sphere/atom to be capped and colored the same color as the atom. Is this possible? I can show the protein in spheres and clip it using the side view dialog, but the clipped spheres show up as shells instead of solid balls. I also have found directions for capping and coloring surfaces, but I don't see a way to make the clipped surface colored by atom. It seems that building my protein out of sphere shapes and clipping that would give me the desired effect, but I was hoping there was something easier and built-in that I'm missing. Thanks for your help, Michelle -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Fri Jun 24 18:50:28 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 24 Jun 2011 18:50:28 -0700 Subject: [Chimera-users] Capping a clipped sphere representation In-Reply-To: References: Message-ID: <8D72891D-FB87-449B-BFE7-960A8B296C30@cgl.ucsf.edu> Hi Michelle, Sorry, Chimera doesn't have capping of atomic representations or ribbons. However, you can achieve something similar to the "sliced spheres" by: (a) showing a molecular surface (b) clipping and capping that surface (capping occurs by default) (c) coloring the molecular surface to match the atoms (this occurs by default) (d) the nonobvious step: coloring the cap to match the atoms too, using Color Zone See the picture here to get some idea if this will meet your needs: It sounds like you figured out (a)-(c). Then open Color Zone (under Tools... Volume Data), select the protein atoms (for example, command "sel protein"), click "Color" on the Color Zone tool to color the MSMS surface (which includes the cap). Radius values >2.5 should all be fine, the closest atom is used. However, at this point the coloring may look jagged. You could use a finer triangulation of both the molecular surface and the surface cap to make the former smoother, and get rid of jagged coloring edges in both. There are several ways of increasing the vertex density of a molecular surface, but the easiest to describe in email is this command: setattr s density 5 ... where the default density is 2. You could try different numbers, being aware that finer triangulations (higher density values) use more memory and may make rotating the structure slower. To get a finer triangulation of the cap, start Surface Capping, for example by clicking the "Surface capping..." button in the side view, and increase the "Mesh subdivision factor," say to 3. Several of these steps are also covered in the "B-factor coloring" image tutorial. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jun 24, 2011, at 4:12 PM, Michelle E. McCully wrote: > Hi, > I would like to create an image of a protein shown in van der Waals spheres with a clipped surface. I'd like each individual sphere/atom to be capped and colored the same color as the atom. Is this possible? > > I can show the protein in spheres and clip it using the side view dialog, but the clipped spheres show up as shells instead of solid balls. I also have found directions for capping and coloring surfaces, but I don't see a way to make the clipped surface colored by atom. It seems that building my protein out of sphere shapes and clipping that would give me the desired effect, but I was hoping there was something easier and built-in that I'm missing. > > Thanks for your help, > Michelle From pett at cgl.ucsf.edu Sun Jun 26 17:56:20 2011 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Sun, 26 Jun 2011 17:56:20 -0700 Subject: [Chimera-users] Capping a clipped sphere representation In-Reply-To: <8D72891D-FB87-449B-BFE7-960A8B296C30@cgl.ucsf.edu> References: <8D72891D-FB87-449B-BFE7-960A8B296C30@cgl.ucsf.edu> Message-ID: Hi Michelle, If you're willing to use an image that is just atom spheres, i.e. no surfaces, volumes, BILD objects, etc. then you can use the "conic" command: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/conic.html It will produce an image like the one I've attached. --Eric Eric Pettersen UCSF Computer Graphics Lab -------------- next part -------------- A non-text attachment was scrubbed... Name: conic.png Type: image/png Size: 843798 bytes Desc: not available URL: -------------- next part -------------- On Jun 24, 2011, at 6:50 PM, Elaine Meng wrote: > Hi Michelle, > Sorry, Chimera doesn't have capping of atomic representations or > ribbons. However, you can achieve something similar to the "sliced > spheres" by: > > (a) showing a molecular surface > (b) clipping and capping that surface (capping occurs by default) > (c) coloring the molecular surface to match the atoms (this occurs > by default) > (d) the nonobvious step: coloring the cap to match the atoms too, > using Color Zone > > See the picture here to get some idea if this will meet your needs: > > > > It sounds like you figured out (a)-(c). Then open Color Zone (under > Tools... Volume Data), select the protein atoms (for example, > command "sel protein"), click "Color" on the Color Zone tool to > color the MSMS surface (which includes the cap). Radius values >2.5 > should all be fine, the closest atom is used. > > However, at this point the coloring may look jagged. You could use a > finer triangulation of both the molecular surface and the surface > cap to make the former smoother, and get rid of jagged coloring > edges in both. > > There are several ways of increasing the vertex density of a > molecular surface, but the easiest to describe in email is this > command: > setattr s density 5 > ... where the default density is 2. You could try different > numbers, being aware that finer triangulations (higher density > values) use more memory and may make rotating the structure slower. > > To get a finer triangulation of the cap, start Surface Capping, for > example by clicking the "Surface capping..." button in the side > view, and increase the "Mesh subdivision factor," say to 3. > > Several of these steps are also covered in the "B-factor coloring" > image tutorial. > > > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Jun 24, 2011, at 4:12 PM, Michelle E. McCully wrote: > >> Hi, >> I would like to create an image of a protein shown in van der Waals >> spheres with a clipped surface. I'd like each individual sphere/ >> atom to be capped and colored the same color as the atom. Is this >> possible? >> >> I can show the protein in spheres and clip it using the side view >> dialog, but the clipped spheres show up as shells instead of solid >> balls. I also have found directions for capping and coloring >> surfaces, but I don't see a way to make the clipped surface colored >> by atom. It seems that building my protein out of sphere shapes >> and clipping that would give me the desired effect, but I was >> hoping there was something easier and built-in that I'm missing. >> >> Thanks for your help, >> Michelle > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users From wjallen at vt.edu Mon Jun 27 08:02:56 2011 From: wjallen at vt.edu (William Joseph Allen) Date: Mon, 27 Jun 2011 11:02:56 -0400 Subject: [Chimera-users] Stereo vision with Quadro 600 Message-ID: <4E089BA0.2050206@vt.edu> Hello Chimera Users, I am trying to view molecules in sequential stereo in Chimera (v 1.5.3). When I choose Camera -> Sequential Stereo, I get an error that says: "Unable to turn on stereo viewing (Unable to find hardware support / couldn't choose pixel format / Couldn't configure tool widget)". Here is a little bit of the background: The machine is a new Dell desktop running 64-bit Windows 7. I installed a Quadro 600 graphic cards, and I am using the Nvidia 3D vision wireless glasses kit. The version of the Nvidia driver is 275.36, which I believe is the latest version. I should also note that I was able to successfully configure VMD and MOE to work in Stereo with set up described, so I know that 3D should work, I just can't get it to work in Chimera. Previous messages in the mailing archive seem to indicate that the specific type of graphics card or the version of the driver is usually the problem. From what I have read, the Quadro 600 should be compatible. I guess my only concern is the version of the driver. It seems there was some bugs in the 197.x, 258.x, and 259.x versions of the driver, and 266.45 was reported to work. I have version 275.36, should I be worried about a bug or is there something else I missed? Than you for your help, William Allen From gregc at cgl.ucsf.edu Mon Jun 27 10:42:43 2011 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Mon, 27 Jun 2011 10:42:43 -0700 Subject: [Chimera-users] Stereo vision with Quadro 600 In-Reply-To: <4E089BA0.2050206@vt.edu> References: <4E089BA0.2050206@vt.edu> Message-ID: <4E08C113.5040706@cgl.ucsf.edu> It's should be a driver configuration issue. There are two different 3D graphics APIs on Windows, Direct3D and OpenGL, and most Windows applications use the former and Chimera uses the latter (because it works on Linux and Mac OS X too). To configure OpenGL stereo in the Quadro driver on Windows, bring up the NVIDIA Control Panel, navigate to 3D Settings, then Manage 3D Settings. And in those options, set "Stereo - Enable" to on, and "Stereo - Display mode" to the appropriate type of stereo, in your case, my guess would be "On-board DIN connector (with NVIDIA 3D Vision)". HTH, Greg On 06/27/2011 08:02 AM, William Joseph Allen wrote: > Hello Chimera Users, > > I am trying to view molecules in sequential stereo in Chimera (v 1.5.3). When I > choose Camera -> Sequential Stereo, I get an error that says: "Unable to turn on > stereo viewing (Unable to find hardware support / couldn't choose pixel format / > Couldn't configure tool widget)". > > Here is a little bit of the background: > > The machine is a new Dell desktop running 64-bit Windows 7. I installed a Quadro > 600 graphic cards, and I am using the Nvidia 3D vision wireless glasses kit. The > version of the Nvidia driver is 275.36, which I believe is the latest version. I > should also note that I was able to successfully configure VMD and MOE to work > in Stereo with set up described, so I know that 3D should work, I just can't get > it to work in Chimera. > > Previous messages in the mailing archive seem to indicate that the specific type > of graphics card or the version of the driver is usually the problem. From what > I have read, the Quadro 600 should be compatible. I guess my only concern is the > version of the driver. It seems there was some bugs in the 197.x, 258.x, and > 259.x versions of the driver, and 266.45 was reported to work. I have version > 275.36, should I be worried about a bug or is there something else I missed? > > Than you for your help, > > William Allen From gtzotzos at me.com Mon Jun 27 11:25:26 2011 From: gtzotzos at me.com (George Tzotzos) Date: Mon, 27 Jun 2011 20:25:26 +0200 Subject: [Chimera-users] Select Message-ID: <53375F42-6A86-4072-9E14-F698FC553E69@me.com> Can anyone provide some help. I'm trying to select two specific oxygen atoms in different residues (98 and 142). The command select :142 at O1 :98 at O1 selects only 1 atom (that of residue 142). I tried select :98 at O1 only. The output is "selection" cleared. I'm rather puzzled. Any help would be greatly appreciated Regards George -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Mon Jun 27 11:33:34 2011 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 27 Jun 2011 11:33:34 -0700 Subject: [Chimera-users] Select In-Reply-To: <53375F42-6A86-4072-9E14-F698FC553E69@me.com> References: <53375F42-6A86-4072-9E14-F698FC553E69@me.com> Message-ID: <8D1D1371-C6AF-4768-91CD-4212C2D40A5A@cgl.ucsf.edu> On Jun 27, 2011, at 11:25 AM, George Tzotzos wrote: > Can anyone provide some help. > > I'm trying to select two specific oxygen atoms in different residues > (98 and 142). > > The command select :142 at O1 :98 at O1 selects only 1 atom (that of > residue 142). > > I tried select :98 at O1 only. The output is "selection" cleared. > > I'm rather puzzled. Any help would be greatly appreciated Hi George, Chimera either believes there is no residue 98 in your structure, or that there is no atom named "O1" in that residue. Try this: select :98 Does anything get selected? If that does select a residue, then do this: label sel Is there an "O1" among the atoms that get labeled? --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From wjallen at vt.edu Mon Jun 27 12:34:01 2011 From: wjallen at vt.edu (William Joseph Allen) Date: Mon, 27 Jun 2011 15:34:01 -0400 Subject: [Chimera-users] Stereo vision with Quadro 600 In-Reply-To: <4E08C113.5040706@cgl.ucsf.edu> References: <4E089BA0.2050206@vt.edu> <4E08C113.5040706@cgl.ucsf.edu> Message-ID: <4E08DB29.6070502@vt.edu> Hi Greg, Thank you very much for your quick reply. I had actually already changed those settings in the Nvidia control panel. They are as follows: Stereo - Enable: 'On' Stereo - Display mode: 'Generic active stereo (with NVIDIA 3D vision)' The display mode you mentioned in your reply was not an option in my Nvidia control panel. Although, this is the only setting that really makes sense for what I am doing, and I tried most of the other settings without success. I also tried toggling some of the other features in a non-random way, but without success. These two settings, however, are the changes that made stereo in VMD and MOE start working (both of which use OpenGL). But, for whatever reason, Chimera still gives those previously mentioned errors when I try to turn on stereo. If it helps, the monitor is an Asus 120 Hz LCD display connected by a dual-link DVI cable directly to the graphics card. No DIN connector is involved. Thanks again, William Allen On 6/27/11 1:42 PM, Greg Couch wrote: > It's should be a driver configuration issue. There are two different 3D > graphics APIs on Windows, Direct3D and OpenGL, and most Windows applications > use the former and Chimera uses the latter (because it works on Linux and Mac > OS X too). To configure OpenGL stereo in the Quadro driver on Windows, bring > up the NVIDIA Control Panel, navigate to 3D Settings, then Manage 3D > Settings. And in those options, set "Stereo - Enable" to on, and "Stereo - > Display mode" to the appropriate type of stereo, in your case, my guess would > be "On-board DIN connector (with NVIDIA 3D Vision)". > > HTH, > > Greg > > On 06/27/2011 08:02 AM, William Joseph Allen wrote: >> Hello Chimera Users, >> >> I am trying to view molecules in sequential stereo in Chimera (v 1.5.3). When I >> choose Camera -> Sequential Stereo, I get an error that says: "Unable to >> turn on >> stereo viewing (Unable to find hardware support / couldn't choose pixel format / >> Couldn't configure tool widget)". >> >> Here is a little bit of the background: >> >> The machine is a new Dell desktop running 64-bit Windows 7. I installed a Quadro >> 600 graphic cards, and I am using the Nvidia 3D vision wireless glasses kit. The >> version of the Nvidia driver is 275.36, which I believe is the latest version. I >> should also note that I was able to successfully configure VMD and MOE to work >> in Stereo with set up described, so I know that 3D should work, I just can't get >> it to work in Chimera. >> >> Previous messages in the mailing archive seem to indicate that the specific type >> of graphics card or the version of the driver is usually the problem. From what >> I have read, the Quadro 600 should be compatible. I guess my only concern is the >> version of the driver. It seems there was some bugs in the 197.x, 258.x, and >> 259.x versions of the driver, and 266.45 was reported to work. I have version >> 275.36, should I be worried about a bug or is there something else I missed? >> >> Than you for your help, >> >> William Allen From gregc at cgl.ucsf.edu Mon Jun 27 13:42:59 2011 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Mon, 27 Jun 2011 13:42:59 -0700 Subject: [Chimera-users] Stereo vision with Quadro 600 In-Reply-To: <4E08DB29.6070502@vt.edu> References: <4E089BA0.2050206@vt.edu> <4E08C113.5040706@cgl.ucsf.edu> <4E08DB29.6070502@vt.edu> Message-ID: <4E08EB53.6080504@cgl.ucsf.edu> Those settings should work for Chimera too. Please download http://www.cgl.ucsf.edu/home/gregc/wglinfo.exe, run it in a terminal window (eg., All Programs / Accessories / Command Prompt), and send the results directly back to me. wglinfo lists all of the possible OpenGL framebuffer configurations and should confirm if OpenGL is reporting that stereo is available and with which graphics capabilities. I'll summarize what I find to chimera-users. -- Greg On 06/27/2011 12:34 PM, William Joseph Allen wrote: > Hi Greg, > > Thank you very much for your quick reply. > > I had actually already changed those settings in the Nvidia control > panel. They are as follows: > > Stereo - Enable: 'On' > Stereo - Display mode: 'Generic active stereo (with NVIDIA 3D vision)' > > The display mode you mentioned in your reply was not an option in my > Nvidia control panel. Although, this is the only setting that really > makes sense for what I am doing, and I tried most of the other > settings without success. I also tried toggling some of the other > features in a non-random way, but without success. > > These two settings, however, are the changes that made stereo in VMD > and MOE start working (both of which use OpenGL). But, for whatever > reason, Chimera still gives those previously mentioned errors when I > try to turn on stereo. If it helps, the monitor is an Asus 120 Hz LCD > display connected by a dual-link DVI cable directly to the graphics > card. No DIN connector is involved. > > Thanks again, > > William Allen > > > > On 6/27/11 1:42 PM, Greg Couch wrote: >> It's should be a driver configuration issue. There are two different >> 3D graphics APIs on Windows, Direct3D and OpenGL, and most Windows >> applications use the former and Chimera uses the latter (because it >> works on Linux and Mac OS X too). To configure OpenGL stereo in the >> Quadro driver on Windows, bring up the NVIDIA Control Panel, navigate >> to 3D Settings, then Manage 3D Settings. And in those options, set >> "Stereo - Enable" to on, and "Stereo - Display mode" to the >> appropriate type of stereo, in your case, my guess would be "On-board >> DIN connector (with NVIDIA 3D Vision)". >> >> HTH, >> >> Greg >> >> On 06/27/2011 08:02 AM, William Joseph Allen wrote: >>> Hello Chimera Users, >>> >>> I am trying to view molecules in sequential stereo in Chimera (v >>> 1.5.3). When I >>> choose Camera -> Sequential Stereo, I get an error that says: >>> "Unable to turn on >>> stereo viewing (Unable to find hardware support / couldn't choose >>> pixel format / >>> Couldn't configure tool widget)". >>> >>> Here is a little bit of the background: >>> >>> The machine is a new Dell desktop running 64-bit Windows 7. I >>> installed a Quadro >>> 600 graphic cards, and I am using the Nvidia 3D vision wireless >>> glasses kit. The >>> version of the Nvidia driver is 275.36, which I believe is the >>> latest version. I >>> should also note that I was able to successfully configure VMD and >>> MOE to work >>> in Stereo with set up described, so I know that 3D should work, I >>> just can't get >>> it to work in Chimera. >>> >>> Previous messages in the mailing archive seem to indicate that the >>> specific type >>> of graphics card or the version of the driver is usually the >>> problem. From what >>> I have read, the Quadro 600 should be compatible. I guess my only >>> concern is the >>> version of the driver. It seems there was some bugs in the 197.x, >>> 258.x, and >>> 259.x versions of the driver, and 266.45 was reported to work. I >>> have version >>> 275.36, should I be worried about a bug or is there something else I >>> missed? >>> >>> Than you for your help, >>> >>> William Allen > > From mmccully at uw.edu Mon Jun 27 14:44:20 2011 From: mmccully at uw.edu (Michelle E. McCully) Date: Mon, 27 Jun 2011 14:44:20 -0700 Subject: [Chimera-users] Capping a clipped sphere representation In-Reply-To: References: <8D72891D-FB87-449B-BFE7-960A8B296C30@cgl.ucsf.edu> Message-ID: The "conic" command was exactly what I was looking for! I ended up using the command: conic -s -f ps -o test.ps Thanks so much for your help, Elaine and Eric! Michelle On Sun, Jun 26, 2011 at 5:56 PM, Eric Pettersen wrote: > Hi Michelle, > If you're willing to use an image that is just atom spheres, i.e. no > surfaces, volumes, BILD objects, etc. then you can use the "conic" command: > > http://www.cgl.ucsf.edu/**chimera/current/docs/** > UsersGuide/midas/conic.html > > It will produce an image like the one I've attached. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > > > > > > On Jun 24, 2011, at 6:50 PM, Elaine Meng wrote: > > Hi Michelle, >> Sorry, Chimera doesn't have capping of atomic representations or ribbons. >> However, you can achieve something similar to the "sliced spheres" by: >> >> (a) showing a molecular surface >> (b) clipping and capping that surface (capping occurs by default) >> (c) coloring the molecular surface to match the atoms (this occurs by >> default) >> (d) the nonobvious step: coloring the cap to match the atoms too, using >> Color Zone >> >> See the picture here to get some idea if this will meet your needs: >> > tutorials/bfactor.html >> > >> >> It sounds like you figured out (a)-(c). Then open Color Zone (under >> Tools... Volume Data), select the protein atoms (for example, command "sel >> protein"), click "Color" on the Color Zone tool to color the MSMS surface >> (which includes the cap). Radius values >2.5 should all be fine, the >> closest atom is used. >> >> However, at this point the coloring may look jagged. You could use a finer >> triangulation of both the molecular surface and the surface cap to make the >> former smoother, and get rid of jagged coloring edges in both. >> >> There are several ways of increasing the vertex density of a molecular >> surface, but the easiest to describe in email is this command: >> setattr s density 5 >> ... where the default density is 2. You could try different numbers, >> being aware that finer triangulations (higher density values) use more >> memory and may make rotating the structure slower. >> >> To get a finer triangulation of the cap, start Surface Capping, for >> example by clicking the "Surface capping..." button in the side view, and >> increase the "Mesh subdivision factor," say to 3. >> >> Several of these steps are also covered in the "B-factor coloring" image >> tutorial. >> > tutorials/bfactor.html >> > >> >> I hope this helps, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. >> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >> On Jun 24, 2011, at 4:12 PM, Michelle E. McCully wrote: >> >> Hi, >>> I would like to create an image of a protein shown in van der Waals >>> spheres with a clipped surface. I'd like each individual sphere/atom to be >>> capped and colored the same color as the atom. Is this possible? >>> >>> I can show the protein in spheres and clip it using the side view dialog, >>> but the clipped spheres show up as shells instead of solid balls. I also >>> have found directions for capping and coloring surfaces, but I don't see a >>> way to make the clipped surface colored by atom. It seems that building my >>> protein out of sphere shapes and clipping that would give me the desired >>> effect, but I was hoping there was something easier and built-in that I'm >>> missing. >>> >>> Thanks for your help, >>> Michelle >>> >> >> >> ______________________________**_________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://plato.cgl.ucsf.edu/**mailman/listinfo/chimera-users >> > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From sp.or.bb at gmail.com Mon Jun 27 15:05:56 2011 From: sp.or.bb at gmail.com (S. Pea) Date: Mon, 27 Jun 2011 15:05:56 -0700 Subject: [Chimera-users] ViewDock compound state Message-ID: <4E08FEC4.6060607@gmail.com> Hello, I was wondering if there is an option in ViewDock to create more bins (flags) in the "change compound state"? Currently there is an option to change the compound state from Viable, to either Deleted or Purged but is there an option to put extra user defined states. Thanks, Magdalena From meng at cgl.ucsf.edu Mon Jun 27 15:30:49 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 27 Jun 2011 15:30:49 -0700 Subject: [Chimera-users] ViewDock compound state In-Reply-To: <4E08FEC4.6060607@gmail.com> References: <4E08FEC4.6060607@gmail.com> Message-ID: <7A9F1656-FFCA-4F69-9FA3-322C7B35BF4B@cgl.ucsf.edu> Hi Magdalena, Sorry, there is no "user interface" way to do that ... it would require programming. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jun 27, 2011, at 3:05 PM, S. Pea wrote: > Hello, > > I was wondering if there is an option in ViewDock to create more bins > (flags) in the "change compound state"? > > Currently there is an option to change the compound state from Viable, > to either Deleted or Purged but is there an option to put extra user > defined states. > > Thanks, > Magdalena From meng at cgl.ucsf.edu Mon Jun 27 16:15:25 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 27 Jun 2011 16:15:25 -0700 Subject: [Chimera-users] ViewDock compound state In-Reply-To: <7A9F1656-FFCA-4F69-9FA3-322C7B35BF4B@cgl.ucsf.edu> References: <4E08FEC4.6060607@gmail.com> <7A9F1656-FFCA-4F69-9FA3-322C7B35BF4B@cgl.ucsf.edu> Message-ID: Hi Magdalena, One idea for categorizing your dock hits or poses is to define a model attribute. This would not be shown or settable in the ViewDock dialog, so it would not be as friendly/easy as what you suggest, but it would let you specify or select subsets of the hits based on your own defined categories. If your dock hits were opened as model #0, then the individual ones are "submodels" #0.1, 0.2, 0.3 .... You can create an attribute named whatever you want, say "rating" and assign values to the individual hits. This could be done in a text file called an "attribute assignment file" or with the command "setattr." The command approach can be used to assign one value at a time and would look something like: setattr m rating 0 #0.133 ... which would assign a value of rating=0 to the 133rd result in the file. Not as convenient as checking a button, obviously, but the model specifier of the one you are viewing is shown in the ViewDock dialog, and later you could do things like select #/rating=3 (select all hits with a rating of 3) select #/rating>2 (select hits with a rating greater than 2) ... then save to a file or delete only the ones that are selected. The alternative way to assign an attribute, with an assignment file, can be used to make several assignments at once; file contents would look something like: # Use this file to assign the attribute in Chimera with the # Define Attribute tool or the command defattr. # attribute: rating recipient: molecules #0.1 1 #0.2 3 #0.3 0 #0.4 1 (etc., tab-separated columns of specifier and value) File format description and more examples: Perhaps this approach is not worth it for what you had in mind, but I thought I would put the idea out there! Elaine On Jun 27, 2011, at 3:30 PM, Elaine Meng wrote: > Hi Magdalena, > Sorry, there is no "user interface" way to do that ... it would require programming. > Best, > Elaine > ---------- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > > On Jun 27, 2011, at 3:05 PM, S. Pea wrote: > >> Hello, >> >> I was wondering if there is an option in ViewDock to create more bins >> (flags) in the "change compound state"? >> >> Currently there is an option to change the compound state from Viable, >> to either Deleted or Purged but is there an option to put extra user >> defined states. >> >> Thanks, >> Magdalena > From george at compbio.washington.edu Mon Jun 27 17:14:31 2011 From: george at compbio.washington.edu (George White) Date: Mon, 27 Jun 2011 17:14:31 -0700 Subject: [Chimera-users] preserving the serial numbering Message-ID: Hi, I am wondering is there any way to write a pdb from Chimera that preserves the original atom serial numbering of the input pdb. Chimera seems to apply its own renumbering (i.e. making the number of the 1st atom #1 etc.) . Thanks in advance, George -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Mon Jun 27 18:18:53 2011 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 27 Jun 2011 18:18:53 -0700 Subject: [Chimera-users] preserving the serial numbering In-Reply-To: References: Message-ID: Hi George, The short answer is no. Generally speaking, unless your structure is unmodified (in which case, why not use the original file?) there is no way to write a standard-conformant PDB file while preserving original serial numbers. Let's say you opened a structure, added hydrogens, and wanted to write it out with unchanged serial numbers. Well, the hydrogens are going to have serial numbers larger than any heavy atom, so since they will be written along with their residue-mates in the file (else TER card conventions would be violated), the serial numbers will not be... serial. Nonetheless, I can imagine scenarios where you would be willing to ignore the not-strictly-legal nature of such a file, so I'll add a feature-request ticket to the Chimera Trac database with you on the recipient list. If anyone else would also like to be on the notification list, send me an email... --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Jun 27, 2011, at 5:14 PM, George White wrote: > Hi, > > I am wondering is there any way to write a pdb from Chimera that > preserves the original atom serial numbering of the input pdb. > Chimera seems to apply its own renumbering (i.e. making the number > of the 1st atom #1 etc.) . > > Thanks in advance, > George > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From sunyeping at yahoo.com.cn Tue Jun 28 05:32:03 2011 From: sunyeping at yahoo.com.cn (yp sun) Date: Tue, 28 Jun 2011 20:32:03 +0800 (CST) Subject: [Chimera-users] chimera setup Message-ID: <1309264323.74432.YahooMailClassic@web15605.mail.cnb.yahoo.com> Dear sir, ? ???? I want to setup the chimera 1.5.3 program on windows XP system, but the setup cannot be finished, it retures a error information that says: "Unable to excute file: C:/program file/chimera 1.5.3/bin/pythonn.exe." ??? How can I solve the problem? Thanks. Best regards Yeping Sun PhD CAS Key Laboratory of Pathogenic Microbiology & Immunology INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china -------------- next part -------------- An HTML attachment was scrubbed... URL: From gwcombio at gmail.com Tue Jun 28 08:16:08 2011 From: gwcombio at gmail.com (George White) Date: Tue, 28 Jun 2011 08:16:08 -0700 Subject: [Chimera-users] preserving the serial numbering In-Reply-To: References: Message-ID: Dear Eric, Thank you so much for your quick response. We were using the minimization routines in Chimera, and needed consistency in the atom numbering to integrate with other components of our application. George On Mon, Jun 27, 2011 at 6:18 PM, Eric Pettersen wrote: > Hi George, > The short answer is no. Generally speaking, unless your structure is > unmodified (in which case, why not use the original file?) there is no way > to write a standard-conformant PDB file while preserving original serial > numbers. Let's say you opened a structure, added hydrogens, and wanted to > write it out with unchanged serial numbers. Well, the hydrogens are going > to have serial numbers larger than any heavy atom, so since they will be > written along with their residue-mates in the file (else TER card > conventions would be violated), the serial numbers will not be... serial. > Nonetheless, I can imagine scenarios where you would be willing to ignore > the not-strictly-legal nature of such a file, so I'll add a feature-request > ticket to the Chimera Trac database with you on the recipient list. If > anyone else would also like to be on the notification list, send me an > email... > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > On Jun 27, 2011, at 5:14 PM, George White wrote: > > Hi, > > I am wondering is there any way to write a pdb from Chimera that preserves > the original atom serial numbering of the input pdb. Chimera seems to apply > its own renumbering (i.e. making the number of the 1st atom #1 etc.) . > > Thanks in advance, > George > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guy.hughes at postgrad.manchester.ac.uk Tue Jun 28 07:58:13 2011 From: guy.hughes at postgrad.manchester.ac.uk (Guy Hughes) Date: Tue, 28 Jun 2011 14:58:13 +0000 Subject: [Chimera-users] Stable 64bit version Message-ID: <16835027EAB72D40A23F0C249277F51802C7B1@MBXP11.ds.man.ac.uk> Hello, I am an MPhil researcher at the University of Manchester based in laboratory of Professor Bob Ford. I have been using cryo-electron tomography to build a 3D volume containing mucins (High Mr heavily glycosylated polypeptides) which are what my research focusses on. We use a Tecnai 300kV Polara and Gatan's Digital Micrograph software to create tomograms of our samples and then IMOD to view them. Recently I was told that Chimera would be a very useful tool when married with the data from IMOD so I downloaded a copy from your website. I regret to admit that I had several problems with the programme and eventually had to delete. The main problem was that my computer continued to blue-screen and perform very slowly if at all. The labtop I was using has the following spec.; CPU: Intel Core i5 VGA: NVIDIA Geforce 310M/1GB DDR3 RAM: DDRIII 4GB (2GB*2) OS: Windows 7 64-bit Is my PC inadequate or is it possible I downloades a corrupted/unstable version of Chimera? I would very much like to try and start using Chimera again but would first like some advice on what the original problem may have been. Any suggestions or help would be greatly appreciated. Thanks, Guy Hughes. -------------- next part -------------- An HTML attachment was scrubbed... URL: From gregc at cgl.ucsf.edu Tue Jun 28 11:12:53 2011 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Tue, 28 Jun 2011 11:12:53 -0700 Subject: [Chimera-users] chimera setup In-Reply-To: <1309264323.74432.YahooMailClassic@web15605.mail.cnb.yahoo.com> References: <1309264323.74432.YahooMailClassic@web15605.mail.cnb.yahoo.com> Message-ID: <4E0A19A5.9050108@cgl.ucsf.edu> On 6/28/2011 5:32 AM, yp sun wrote: > I want to setup the chimera 1.5.3 program on windows XP system, > but the setup cannot be finished, it retures a error information that > says: "Unable to excute file: C:/program file/chimera > 1.5.3/bin/pythonn.exe." > > The only thing I can think of here is that maybe you don't already have the Microsoft Visual C++ 2008 SP1 runtime components installed. The 32-bit runtime is available from Microsoft at http://www.microsoft.com/download/en/details.aspx?id=5582, and the 64-bit runtime is available at http://www.microsoft.com/download/en/details.aspx?id=2092. If installing the runtime does fix (or doesn't fix) the problem you're having, please let me know. HTH, Greg -------------- next part -------------- An HTML attachment was scrubbed... URL: From gregc at cgl.ucsf.edu Tue Jun 28 11:28:09 2011 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Tue, 28 Jun 2011 11:28:09 -0700 Subject: [Chimera-users] Stable 64bit version In-Reply-To: <16835027EAB72D40A23F0C249277F51802C7B1@MBXP11.ds.man.ac.uk> References: <16835027EAB72D40A23F0C249277F51802C7B1@MBXP11.ds.man.ac.uk> Message-ID: <4E0A1D39.6050409@cgl.ucsf.edu> On 6/28/2011 7:58 AM, Guy Hughes wrote: > Recently I was told that Chimera would be a very useful tool when > married with the data from IMOD so I downloaded a copy from your > website. I regret to admit that I had several problems with the > programme and eventually had to delete. The main problem was that my > computer continued to blue-screen and perform very slowly if at all. > The labtop I was using has the following spec.; > CPU: Intel Core i5 > VGA: NVIDIA Geforce 310M/1GB DDR3 > RAM: DDRIII 4GB (2GB*2) > OS: Windows 7 64-bit > > Is my PC inadequate or is it possible I downloades a > corrupted/unstable version of Chimera? > > I would very much like to try and start using Chimera again but would > first like some advice on what the original problem may have been. > > Any suggestions or help would be greatly appreciated. Your PC is adequate. Chimera should not be able to blue-screen your computer even if it had bug or two in it. The most likely culprit is your graphics driver. Graphics/video drivers provided by the laptop vendor are frequently buggy and are updated rarely. Still, you should first go to the laptop vendor's support website to get the latest driver for your computer, and if that doesn't fix things, then get a newer driver directly from NVIDIA. There may be other updates from your laptop vendor that are important too -- in one case, the BIOS needed to be updated. Good luck, Greg -------------- next part -------------- An HTML attachment was scrubbed... URL: From lecan at ibt.unam.mx Tue Jun 28 13:25:24 2011 From: lecan at ibt.unam.mx (lecan) Date: Tue, 28 Jun 2011 15:25:24 -0500 Subject: [Chimera-users] Polar hydrogens In-Reply-To: <8D72891D-FB87-449B-BFE7-960A8B296C30@cgl.ucsf.edu> References: <8D72891D-FB87-449B-BFE7-960A8B296C30@cgl.ucsf.edu> Message-ID: <0a4fc2720b7ff90ec10ee42857758d78@ibt.unam.mx> Hi everybody, Is there a way to put only polar hydrogens on a protein structure with chimera? Regards, Luis L. From meng at cgl.ucsf.edu Tue Jun 28 13:59:51 2011 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 28 Jun 2011 13:59:51 -0700 Subject: [Chimera-users] Polar hydrogens In-Reply-To: <0a4fc2720b7ff90ec10ee42857758d78@ibt.unam.mx> References: <8D72891D-FB87-449B-BFE7-960A8B296C30@cgl.ucsf.edu> <0a4fc2720b7ff90ec10ee42857758d78@ibt.unam.mx> Message-ID: <0D0DD16B-E6D2-4E90-AD16-A7FF7472BCFC@cgl.ucsf.edu> Hi Luis, No, but after adding all hydrogens, you can delete the "nonpolar" ones if you really don't want them. This could be done with the command: delete HC ...or equivalently with menu operations: Select... Chemistry... IDATM type... HC Actions... Atoms/Bonds... delete I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jun 28, 2011, at 1:25 PM, lecan wrote: > Hi everybody, > Is there a way to put only polar hydrogens on a protein structure with > chimera? > Regards, > Luis L. From pett at cgl.ucsf.edu Tue Jun 28 14:15:11 2011 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Tue, 28 Jun 2011 14:15:11 -0700 Subject: [Chimera-users] creating a peptide bond between two fragments In-Reply-To: <173D696B-41BE-4EB6-B685-E5619717DA7A@cgl.ucsf.edu> References: <8C3F698A-3844-4349-8A36-00795AC3794D@cgl.ucsf.edu> <173D696B-41BE-4EB6-B685-E5619717DA7A@cgl.ucsf.edu> Message-ID: <02FCB8B8-8370-46DD-854B-0CD6ECEF88E4@cgl.ucsf.edu> On Jun 8, 2011, at 9:12 AM, Elaine Meng wrote: > If you were building out from the C-term, the "addaa" command would > probably be the easiest approach in Chimera. > > > However, for putting residues on the N-term or for joining two > experimentally determined structures, Join Models (part of Build > Structure) is generally the way to go. Start Structure (another > part of Build Structure) allows creating peptides with specified > phi,psi angles. > > As of tomorrow's daily build, addaa will allow adding the the N terminus as well. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From wjallen at vt.edu Wed Jun 29 12:36:16 2011 From: wjallen at vt.edu (William Joseph Allen) Date: Wed, 29 Jun 2011 15:36:16 -0400 Subject: [Chimera-users] Stereo vision with Quadro 600 In-Reply-To: <4E09E76A.7050207@cgl.ucsf.edu> References: <4E089BA0.2050206@vt.edu> <4E08C113.5040706@cgl.ucsf.edu> <4E08DB29.6070502@vt.edu> <4E08EB53.6080504@cgl.ucsf.edu> <4E08FDBB.8030200@vt.edu> <4E09E76A.7050207@cgl.ucsf.edu> Message-ID: <4E0B7EB0.1050908@vt.edu> Hi Greg, I was finally able to figure out what I was doing wrong. On the Nvidia control panel, I was changing the following settings: Stereo - Enable: 'On' Stereo - Display mode: 'Generic active stereo (with NVIDIA 3D vision)' For only specific programs (VMD, MOE, Chimera). That worked for VMD and MOE, but not for Chimera. As soon as I made those settings global, I was able to use stereo in Chimera. There must be other programs, like python.exe or something, that must also be stereo-enabled for this setup to work. Thanks again for your help, William Allen On 6/28/11 10:38 AM, Greg Couch wrote: > So according to the wglinfo output, your driver is not configured for stereo. > Check out the st/ro column, it is always a '.' and there should be some 'y's. > So no OpenGL stereo program should work. I did try the 275.36 driver with our > Quadro FX 3700, and stereo did work, so it is unclear why stereo isn't working > for you. To confirm that the driver configuration is working, try one of the > passive stereo options for the "Stereo - Display mode" and rerun wglinfo (or > Chimera) to see if stereo is supported. You also might want to go over the > driver settings with a colleague to see if either of you can spot anything, > and if that doesn't work, try an earlier version of the driver. > > Good luck, > > Greg > > On 6/27/2011 3:01 PM, William Joseph Allen wrote: >> Hi Greg, Here are the results: Thanks for your help! >> >> ########## >> C:\Users\William\Desktop>wglinfo.exe >> OpenGL vendor string: NVIDIA Corporation >> OpenGL renderer string: Quadro 600/PCI/SSE2 >> OpenGL version string: 4.1.0 >> OpenGL extensions (GL_): >> GL_ARB_blend_func_extended, GL_ARB_color_buffer_float, GL_ARB_compatibility, >> >> GL_ARB_copy_buffer, GL_ARB_depth_buffer_float, GL_ARB_depth_clamp, >> GL_ARB_depth_texture, GL_ARB_draw_buffers, GL_ARB_draw_buffers_blend, >> GL_ARB_draw_indirect, GL_ARB_draw_elements_base_vertex, >> GL_ARB_draw_instanced, GL_ARB_ES2_compatibility, >> GL_ARB_explicit_attrib_location, GL_ARB_fragment_coord_conventions, >> GL_ARB_fragment_program, GL_ARB_fragment_program_shadow, >> GL_ARB_fragment_shader, GL_ARB_framebuffer_object, GL_ARB_framebuffer_sRGB, >> GL_ARB_geometry_shader4, GL_ARB_get_program_binary, GL_ARB_gpu_shader5, >> GL_ARB_gpu_shader_fp64, GL_ARB_half_float_pixel, GL_ARB_half_float_vertex, >> GL_ARB_imaging, GL_ARB_instanced_arrays, GL_ARB_map_buffer_range, >> GL_ARB_multisample, GL_ARB_multitexture, GL_ARB_occlusion_query, >> GL_ARB_occlusion_query2, GL_ARB_pixel_buffer_object, >> GL_ARB_point_parameters, GL_ARB_point_sprite, GL_ARB_provoking_vertex, >> GL_ARB_robustness, GL_ARB_sample_shading, GL_ARB_sampler_objects, >> GL_ARB_seamless_cube_map, GL_ARB_separate_shader_objects, >> GL_ARB_shader_bit_encoding, GL_ARB_shader_objects, GL_ARB_shader_precision, >> GL_ARB_shader_subroutine, GL_ARB_shading_language_100, >> GL_ARB_shading_language_include, GL_ARB_shadow, GL_ARB_sync, >> GL_ARB_tessellation_shader, GL_ARB_texture_border_clamp, >> GL_ARB_texture_buffer_object, GL_ARB_texture_buffer_object_rgb32, >> GL_ARB_texture_compression, GL_ARB_texture_compression_bptc, >> GL_ARB_texture_compression_rgtc, GL_ARB_texture_cube_map, >> GL_ARB_texture_cube_map_array, GL_ARB_texture_env_add, >> GL_ARB_texture_env_combine, GL_ARB_texture_env_crossbar, >> GL_ARB_texture_env_dot3, GL_ARB_texture_float, GL_ARB_texture_gather, >> GL_ARB_texture_mirrored_repeat, GL_ARB_texture_multisample, >> GL_ARB_texture_non_power_of_two, GL_ARB_texture_query_lod, >> GL_ARB_texture_rectangle, GL_ARB_texture_rg, GL_ARB_texture_rgb10_a2ui, >> GL_ARB_texture_swizzle, GL_ARB_timer_query, GL_ARB_transform_feedback2, >> GL_ARB_transform_feedback3, GL_ARB_transpose_matrix, >> GL_ARB_uniform_buffer_object, GL_ARB_vertex_array_bgra, >> GL_ARB_vertex_array_object, GL_ARB_vertex_attrib_64bit, >> GL_ARB_vertex_buffer_object, GL_ARB_vertex_program, GL_ARB_vertex_shader, >> GL_ARB_vertex_type_2_10_10_10_rev, GL_ARB_viewport_array, GL_ARB_window_pos, >> >> GL_ATI_draw_buffers, GL_ATI_texture_float, GL_ATI_texture_mirror_once, >> GL_S3_s3tc, GL_EXT_texture_env_add, GL_EXT_abgr, GL_EXT_bgra, >> GL_EXT_bindable_uniform, GL_EXT_blend_color, GL_EXT_blend_equation_separate, >> >> GL_EXT_blend_func_separate, GL_EXT_blend_minmax, GL_EXT_blend_subtract, >> GL_EXT_compiled_vertex_array, GL_EXT_Cg_shader, GL_EXT_depth_bounds_test, >> GL_EXT_direct_state_access, GL_EXT_draw_buffers2, GL_EXT_draw_instanced, >> GL_EXT_draw_range_elements, GL_EXT_fog_coord, GL_EXT_framebuffer_blit, >> GL_EXT_framebuffer_multisample, GL_EXTX_framebuffer_mixed_formats, >> GL_EXT_framebuffer_object, GL_EXT_framebuffer_sRGB, GL_EXT_geometry_shader4, >> >> GL_EXT_gpu_program_parameters, GL_EXT_gpu_shader4, GL_EXT_multi_draw_arrays, >> >> GL_EXT_packed_depth_stencil, GL_EXT_packed_float, GL_EXT_packed_pixels, >> GL_EXT_pixel_buffer_object, GL_EXT_point_parameters, >> GL_EXT_provoking_vertex, GL_EXT_rescale_normal, GL_EXT_secondary_color, >> GL_EXT_separate_shader_objects, GL_EXT_separate_specular_color, >> GL_EXT_shader_image_load_store, GL_EXT_shadow_funcs, >> GL_EXT_stencil_two_side, GL_EXT_stencil_wrap, GL_EXT_texture3D, >> GL_EXT_texture_array, GL_EXT_texture_buffer_object, >> GL_EXT_texture_compression_dxt1, GL_EXT_texture_compression_latc, >> GL_EXT_texture_compression_rgtc, GL_EXT_texture_compression_s3tc, >> GL_EXT_texture_cube_map, GL_EXT_texture_edge_clamp, >> GL_EXT_texture_env_combine, GL_EXT_texture_env_dot3, >> GL_EXT_texture_filter_anisotropic, GL_EXT_texture_format_BGRA8888, >> GL_EXT_texture_integer, GL_EXT_texture_lod, GL_EXT_texture_lod_bias, >> GL_EXT_texture_mirror_clamp, GL_EXT_texture_object, >> GL_EXT_texture_shared_exponent, GL_EXT_texture_sRGB, GL_EXT_texture_swizzle, >> >> GL_EXT_texture_type_2_10_10_10_REV, GL_EXT_timer_query, >> GL_EXT_transform_feedback2, GL_EXT_vertex_array, GL_EXT_vertex_array_bgra, >> GL_EXT_vertex_attrib_64bit, GL_IBM_rasterpos_clip, >> GL_IBM_texture_mirrored_repeat, GL_KTX_buffer_region, GL_NV_alpha_test, >> GL_NV_blend_minmax, GL_NV_blend_square, GL_NV_complex_primitives, >> GL_NV_conditional_render, GL_NV_copy_depth_to_color, GL_NV_copy_image, >> GL_NV_depth_buffer_float, GL_NV_depth_clamp, GL_NV_explicit_multisample, >> GL_NV_fbo_color_attachments, GL_NV_fence, GL_NV_float_buffer, >> GL_NV_fog_distance, GL_NV_fragdepth, GL_NV_fragment_program, >> GL_NV_fragment_program_option, GL_NV_fragment_program2, >> GL_NV_framebuffer_multisample_coverage, GL_NV_geometry_shader4, >> GL_NV_gpu_program4, GL_NV_gpu_program4_1, GL_NV_gpu_program5, >> GL_NV_gpu_program_fp64, GL_NV_gpu_shader5, GL_NV_half_float, >> GL_NV_light_max_exponent, GL_NV_multisample_coverage, >> GL_NV_multisample_filter_hint, GL_NV_occlusion_query, >> GL_NV_packed_depth_stencil, GL_NV_parameter_buffer_object, >> GL_NV_parameter_buffer_object2, GL_NV_path_rendering, >> GL_NV_pixel_data_range, GL_NV_point_sprite, GL_NV_primitive_restart, >> GL_NV_register_combiners, GL_NV_register_combiners2, >> GL_NV_shader_buffer_load, GL_NV_texgen_reflection, GL_NV_texture_barrier, >> GL_NV_texture_compression_vtc, GL_NV_texture_env_combine4, >> GL_NV_texture_expand_normal, GL_NV_texture_lod_clamp, >> GL_NV_texture_multisample, GL_NV_texture_rectangle, GL_NV_texture_shader, >> GL_NV_texture_shader2, GL_NV_texture_shader3, GL_NV_transform_feedback, >> GL_NV_transform_feedback2, GL_NV_vertex_array_range, >> GL_NV_vertex_array_range2, GL_NV_vertex_attrib_integer_64bit, >> GL_NV_vertex_buffer_unified_memory, GL_NV_vertex_program, >> GL_NV_vertex_program1_1, GL_NV_vertex_program2, >> GL_NV_vertex_program2_option, GL_NV_vertex_program3, >> GL_NVX_conditional_render, GL_NVX_gpu_memory_info, GL_OES_depth24, >> GL_OES_depth32, GL_OES_depth_texture, GL_OES_element_index_uint, >> GL_OES_fbo_render_mipmap, GL_OES_get_program_binary, GL_OES_mapbuffer, >> GL_OES_packed_depth_stencil, GL_OES_rgb8_rgba8, GL_OES_standard_derivatives, >> >> GL_OES_texture_3D, GL_OES_texture_float, GL_OES_texture_float_linear, >> GL_OES_texture_half_float, GL_OES_texture_half_float_linear, >> GL_OES_texture_npot, GL_OES_vertex_array_object, GL_OES_vertex_half_float, >> GL_SGIS_generate_mipmap, GL_SGIS_texture_lod, GL_SGIX_depth_texture, >> GL_SGIX_shadow, GL_SUN_slice_accum, GL_WIN_swap_hint, WGL_EXT_swap_control. >> >> WGL extensions: >> WGL_ARB_buffer_region, WGL_ARB_create_context, >> WGL_ARB_create_context_profile, WGL_ARB_create_context_robustness, >> WGL_ARB_extensions_string, WGL_ARB_make_current_read, WGL_ARB_multisample, >> WGL_ARB_pbuffer, WGL_ARB_pixel_format, WGL_ARB_pixel_format_float, >> WGL_ARB_render_texture, WGL_ATI_pixel_format_float, >> WGL_EXT_create_context_es2_profile, WGL_EXT_extensions_string, >> WGL_EXT_framebuffer_sRGB, WGL_EXT_pixel_format_packed_float, >> WGL_EXT_swap_control, WGL_NVX_DX_interop, WGL_NV_DX_interop, >> WGL_NV_DX_interop2, WGL_NV_copy_image, WGL_NV_float_buffer, >> WGL_NV_gpu_affinity, WGL_NV_multisample_coverage, >> WGL_NV_render_depth_texture, WGL_NV_render_texture_rectangle, >> WGL_NV_swap_group, WGL_NV_video_capture. >> >> visual x bf lv rg d st ge ge r g b a ax dp st accum buffs ms >> id dep cl sp sz l ci b ro ne ac sz sz sz sz bf th cl r g b a ns b >> ----------------------------------------------------------------------- >> 0x01 32 wn . 32 . r . . . . 8 8 8 . 4 24 . 16 16 16 16 0 0 >> 0x02 32 wn . 32 . r . . . . 8 8 8 8 4 24 . 16 16 16 16 0 0 >> 0x03 32 wn . 32 . r . . . . 8 8 8 . 4 24 8 16 16 16 16 0 0 >> 0x04 32 wn . 32 . r . . . . 8 8 8 8 4 24 8 16 16 16 16 0 0 >> 0x05 32 wn . 32 . r . . . . 8 8 8 . 4 . . 16 16 16 16 0 0 >> 0x06 32 wn . 32 . r . . . . 8 8 8 8 4 . . 16 16 16 16 0 0 >> 0x07 32 wn . 32 . r y . . . 8 8 8 . 4 24 . 16 16 16 16 0 0 >> 0x08 32 wn . 32 . r y . . . 8 8 8 8 4 24 . 16 16 16 16 0 0 >> 0x09 32 wn . 32 . r y . . . 8 8 8 . 4 24 8 16 16 16 16 0 0 >> 0x0a 32 wn . 32 . r y . . . 8 8 8 8 4 24 8 16 16 16 16 0 0 >> 0x0b 32 wn . 32 . r y . . . 8 8 8 . 4 . . 16 16 16 16 0 0 >> 0x0c 32 wn . 32 . r y . . . 8 8 8 8 4 . . 16 16 16 16 0 0 >> 0x0d 32 wn . 32 . r y . . . 8 8 8 . 4 24 . 16 16 16 16 0 0 >> 0x0e 32 wn . 32 . r y . . . 8 8 8 8 4 24 . 16 16 16 16 0 0 >> 0x0f 32 wn . 32 . r y . . . 8 8 8 . 4 24 8 16 16 16 16 0 0 >> 0x10 32 wn . 32 . r y . . . 8 8 8 8 4 24 8 16 16 16 16 0 0 >> 0x11 32 wn . 32 . r y . . . 8 8 8 . 4 . . 16 16 16 16 0 0 >> 0x12 32 wn . 32 . r y . . . 8 8 8 8 4 . . 16 16 16 16 0 0 >> 0xf5 32 wn . 32 . r . . . . 8 8 8 . 4 24 . 16 16 16 16 0 0 >> 0xf6 32 wn . 32 . r . . . . 8 8 8 8 4 24 . 16 16 16 16 0 0 >> 0xf7 32 wn . 32 . r . . . . 8 8 8 . 4 24 8 16 16 16 16 0 0 >> 0xf8 32 wn . 32 . r . . . . 8 8 8 8 4 24 8 16 16 16 16 0 0 >> 0xf9 32 wn . 32 . r . . . . 8 8 8 . 4 . . 16 16 16 16 0 0 >> 0xfa 32 wn . 32 . r . . . . 8 8 8 8 4 . . 16 16 16 16 0 0 >> 0xfb 32 wn . 32 . r y . . . 8 8 8 . 4 24 . 16 16 16 16 0 0 >> 0xfc 32 wn . 32 . r y . . . 8 8 8 8 4 24 . 16 16 16 16 0 0 >> 0xfd 32 wn . 32 . r y . . . 8 8 8 . 4 24 8 16 16 16 16 0 0 >> 0xfe 32 wn . 32 . r y . . . 8 8 8 8 4 24 8 16 16 16 16 0 0 >> 0xff 32 wn . 32 . r y . . . 8 8 8 . 4 . . 16 16 16 16 0 0 >> 0x100 32 wn . 32 . r y . . . 8 8 8 8 4 . . 16 16 16 16 0 0 >> 0x101 32 wn . 32 . r y . . . 8 8 8 . 4 24 . 16 16 16 16 0 0 >> 0x102 32 wn . 32 . r y . . . 8 8 8 8 4 24 . 16 16 16 16 0 0 >> 0x103 32 wn . 32 . r y . . . 8 8 8 . 4 24 8 16 16 16 16 0 0 >> 0x104 32 wn . 32 . r y . . . 8 8 8 8 4 24 8 16 16 16 16 0 0 >> 0x105 32 wn . 32 . r y . . . 8 8 8 . 4 . . 16 16 16 16 0 0 >> 0x106 32 wn . 32 . r y . . . 8 8 8 8 4 . . 16 16 16 16 0 0 >> 0x16f 32 wn . 32 . r . . y . 8 8 8 . . 32 8 16 16 16 . 0 0 >> 0x170 32 wn . 32 . r . . y . 8 8 8 . . 16 8 16 16 16 . 0 0 >> 0x171 32 wn . 32 . r y . y . 8 8 8 . . 32 8 16 16 16 . 0 0 >> 0x172 32 wn . 32 . r y . y . 8 8 8 . . 16 8 16 16 16 . 0 0 >> 0x173 32 wn . 32 . r . . y . 8 8 8 8 . 32 8 16 16 16 16 0 0 >> 0x174 32 wn . 32 . r . . y . 8 8 8 8 . 16 8 16 16 16 16 0 0 >> 0x175 32 wn . 32 . r y . y . 8 8 8 8 . 32 8 16 16 16 16 0 0 >> 0x176 32 wn . 32 . r y . y . 8 8 8 8 . 16 8 16 16 16 16 0 0 >> 0x177 32 wn . 32 . c . . y . . . . . . 32 8 . . . . 0 0 >> 0x178 32 wn . 32 . c . . y . . . . . . 16 8 . . . . 0 0 >> 0x179 32 wn . 32 . c y . y . . . . . . 32 8 . . . . 0 0 >> 0x17a 32 wn . 32 . c y . y . . . . . . 16 8 . . . . 0 0 >> 0x17b 24 bm . 24 . r . . y . 8 8 8 . . 32 8 16 16 16 . 0 0 >> 0x17c 24 bm . 24 . r . . y . 8 8 8 . . 16 8 16 16 16 . 0 0 >> 0x17d 24 bm . 24 . r . . y . 8 8 8 8 . 32 8 16 16 16 16 0 0 >> 0x17e 24 bm . 24 . r . . y . 8 8 8 8 . 16 8 16 16 16 16 0 0 >> 0x17f 24 bm . 24 . c . . y . . . . . . 32 8 . . . . 0 0 >> 0x180 24 bm . 24 . c . . y . . . . . . 16 8 . . . . 0 0 >> 0x181 16 bm . 16 . r . . y . 5 5 5 . . 32 8 11 11 10 . 0 0 >> 0x182 16 bm . 16 . r . . y . 5 5 5 . . 16 8 11 11 10 . 0 0 >> 0x183 16 bm . 16 . r . . y . 5 5 5 8 . 32 8 8 8 8 8 0 0 >> 0x184 16 bm . 16 . r . . y . 5 5 5 8 . 16 8 8 8 8 8 0 0 >> 0x185 16 bm . 16 . c . . y . . . . . . 32 8 . . . . 0 0 >> 0x186 16 bm . 16 . c . . y . . . . . . 16 8 . . . . 0 0 >> 0x187 8 bm . 8 . r . . y . 3 3 2 . . 32 8 11 11 10 . 0 0 >> 0x188 8 bm . 8 . r . . y . 3 3 2 . . 16 8 11 11 10 . 0 0 >> 0x189 8 bm . 8 . r . . y . 3 3 2 8 . 32 8 8 8 8 8 0 0 >> 0x18a 8 bm . 8 . r . . y . 3 3 2 8 . 16 8 8 8 8 8 0 0 >> 0x18b 8 bm . 8 . c . . y . . . . . . 32 8 . . . . 0 0 >> 0x18c 8 bm . 8 . c . . y . . . . . . 16 8 . . . . 0 0 >> 0x18d 4 bm . 4 . r . . y . 1 1 1 . . 32 8 5 6 5 . 0 0 >> 0x18e 4 bm . 4 . r . . y . 1 1 1 . . 16 8 5 6 5 . 0 0 >> 0x18f 4 bm . 4 . r . . y . 1 1 1 8 . 32 8 4 4 4 4 0 0 >> 0x190 4 bm . 4 . r . . y . 1 1 1 8 . 16 8 4 4 4 4 0 0 >> 0x191 4 bm . 4 . c . . y . . . . . . 32 8 . . . . 0 0 >> 0x192 4 bm . 4 . c . . y . . . . . . 16 8 . . . . 0 0 >> ----------------------------------------------------------------------- >> visual x bf lv rg d st ge ge r g b a ax dp st accum buffs ms >> id dep cl sp sz l ci b ro ne ac sz sz sz sz bf th cl r g b a ns b >> ----------------------------------------------------------------------- >> ########## >> >> >> >> >> >> On 6/27/11 4:42 PM, Greg Couch wrote: >>> Those settings should work for Chimera too. Please download >>> http://www.cgl.ucsf.edu/home/gregc/wglinfo.exe, run it in a terminal window >>> (eg., All Programs / Accessories / Command Prompt), and send the results >>> directly back to me. wglinfo lists all of the possible OpenGL framebuffer >>> configurations and should confirm if OpenGL is reporting that stereo is >>> available and with which graphics capabilities. I'll summarize what I find >>> to chimera-users. >>> >>> -- Greg >>> >>> On 06/27/2011 12:34 PM, William Joseph Allen wrote: >>>> Hi Greg, >>>> >>>> Thank you very much for your quick reply. >>>> >>>> I had actually already changed those settings in the Nvidia control panel. >>>> They are as follows: >>>> >>>> Stereo - Enable: 'On' >>>> Stereo - Display mode: 'Generic active stereo (with NVIDIA 3D vision)' >>>> >>>> The display mode you mentioned in your reply was not an option in my Nvidia >>>> control panel. Although, this is the only setting that really makes sense >>>> for what I am doing, and I tried most of the other settings without >>>> success. I also tried toggling some of the other features in a non-random >>>> way, but without success. >>>> >>>> These two settings, however, are the changes that made stereo in VMD and >>>> MOE start working (both of which use OpenGL). But, for whatever reason, >>>> Chimera still gives those previously mentioned errors when I try to turn on >>>> stereo. If it helps, the monitor is an Asus 120 Hz LCD display connected by >>>> a dual-link DVI cable directly to the graphics card. No DIN connector is >>>> involved. >>>> >>>> Thanks again, >>>> >>>> William Allen >>>> >>>> >>>> >>>> On 6/27/11 1:42 PM, Greg Couch wrote: >>>>> It's should be a driver configuration issue. There are two different 3D >>>>> graphics APIs on Windows, Direct3D and OpenGL, and most Windows >>>>> applications use the former and Chimera uses the latter (because it works >>>>> on Linux and Mac OS X too). To configure OpenGL stereo in the Quadro >>>>> driver on Windows, bring up the NVIDIA Control Panel, navigate to 3D >>>>> Settings, then Manage 3D Settings. And in those options, set "Stereo - >>>>> Enable" to on, and "Stereo - Display mode" to the appropriate type of >>>>> stereo, in your case, my guess would be "On-board DIN connector (with >>>>> NVIDIA 3D Vision)". >>>>> >>>>> HTH, >>>>> >>>>> Greg >>>>> >>>>> On 06/27/2011 08:02 AM, William Joseph Allen wrote: >>>>>> Hello Chimera Users, >>>>>> >>>>>> I am trying to view molecules in sequential stereo in Chimera (v 1.5.3). >>>>>> When I >>>>>> choose Camera -> Sequential Stereo, I get an error that says: "Unable to >>>>>> turn on >>>>>> stereo viewing (Unable to find hardware support / couldn't choose pixel >>>>>> format / >>>>>> Couldn't configure tool widget)". >>>>>> >>>>>> Here is a little bit of the background: >>>>>> >>>>>> The machine is a new Dell desktop running 64-bit Windows 7. I installed a >>>>>> Quadro >>>>>> 600 graphic cards, and I am using the Nvidia 3D vision wireless glasses >>>>>> kit. The >>>>>> version of the Nvidia driver is 275.36, which I believe is the latest >>>>>> version. I >>>>>> should also note that I was able to successfully configure VMD and MOE to >>>>>> work >>>>>> in Stereo with set up described, so I know that 3D should work, I just >>>>>> can't get >>>>>> it to work in Chimera. >>>>>> >>>>>> Previous messages in the mailing archive seem to indicate that the >>>>>> specific type >>>>>> of graphics card or the version of the driver is usually the problem. >>>>>> From what >>>>>> I have read, the Quadro 600 should be compatible. I guess my only concern >>>>>> is the >>>>>> version of the driver. It seems there was some bugs in the 197.x, 258.x, and >>>>>> 259.x versions of the driver, and 266.45 was reported to work. I have >>>>>> version >>>>>> 275.36, should I be worried about a bug or is there something else I missed? >>>>>> >>>>>> Than you for your help, >>>>>> >>>>>> William Allen >>>> >>>> >>> >>> >> > > -- William Joseph Allen, Ph.D. Robert C. Rizzo Research Group Department of Applied Mathematics and Statistics Stony Brook University http://rizzo.ams.sunysb.edu/~wjallen/ From gregc at cgl.ucsf.edu Wed Jun 29 13:08:11 2011 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Wed, 29 Jun 2011 13:08:11 -0700 Subject: [Chimera-users] Stereo vision with Quadro 600 In-Reply-To: <4E0B7EB0.1050908@vt.edu> References: <4E089BA0.2050206@vt.edu> <4E08C113.5040706@cgl.ucsf.edu> <4E08DB29.6070502@vt.edu> <4E08EB53.6080504@cgl.ucsf.edu> <4E08FDBB.8030200@vt.edu> <4E09E76A.7050207@cgl.ucsf.edu> <4E0B7EB0.1050908@vt.edu> Message-ID: <4E0B862B.5060307@cgl.ucsf.edu> That makes sense. On Windows, Chimera is a wrapper around CHIMERA/bin/pythonw.exe (or CHIMERA/bin/python.exe if debugging). Thank you for following up on this, Greg On 06/29/2011 12:36 PM, William Joseph Allen wrote: > Hi Greg, > > I was finally able to figure out what I was doing wrong. On the Nvidia > control panel, I was changing the following settings: > > Stereo - Enable: 'On' > Stereo - Display mode: 'Generic active stereo (with NVIDIA 3D vision)' > > For only specific programs (VMD, MOE, Chimera). That worked for VMD > and MOE, but not for Chimera. As soon as I made those settings global, > I was able to use stereo in Chimera. There must be other programs, > like python.exe or something, that must also be stereo-enabled for > this setup to work. > > Thanks again for your help, > > William Allen > > > > On 6/28/11 10:38 AM, Greg Couch wrote: >> So according to the wglinfo output, your driver is not configured for >> stereo. Check out the st/ro column, it is always a '.' and there >> should be some 'y's. So no OpenGL stereo program should work. I did >> try the 275.36 driver with our Quadro FX 3700, and stereo did work, >> so it is unclear why stereo isn't working for you. To confirm that >> the driver configuration is working, try one of the passive stereo >> options for the "Stereo - Display mode" and rerun wglinfo (or >> Chimera) to see if stereo is supported. You also might want to go >> over the driver settings with a colleague to see if either of you can >> spot anything, and if that doesn't work, try an earlier version of >> the driver. >> >> Good luck, >> >> Greg >> >> On 6/27/2011 3:01 PM, William Joseph Allen wrote: >>> Hi Greg, Here are the results: Thanks for your help! >>> >>> ########## >>> C:\Users\William\Desktop>wglinfo.exe >>> OpenGL vendor string: NVIDIA Corporation >>> OpenGL renderer string: Quadro 600/PCI/SSE2 >>> OpenGL version string: 4.1.0 >>> OpenGL extensions (GL_): >>> GL_ARB_blend_func_extended, GL_ARB_color_buffer_float, >>> GL_ARB_compatibility, >>> >>> GL_ARB_copy_buffer, GL_ARB_depth_buffer_float, GL_ARB_depth_clamp, >>> GL_ARB_depth_texture, GL_ARB_draw_buffers, >>> GL_ARB_draw_buffers_blend, >>> GL_ARB_draw_indirect, GL_ARB_draw_elements_base_vertex, >>> GL_ARB_draw_instanced, GL_ARB_ES2_compatibility, >>> GL_ARB_explicit_attrib_location, GL_ARB_fragment_coord_conventions, >>> GL_ARB_fragment_program, GL_ARB_fragment_program_shadow, >>> GL_ARB_fragment_shader, GL_ARB_framebuffer_object, >>> GL_ARB_framebuffer_sRGB, >>> GL_ARB_geometry_shader4, GL_ARB_get_program_binary, >>> GL_ARB_gpu_shader5, >>> GL_ARB_gpu_shader_fp64, GL_ARB_half_float_pixel, >>> GL_ARB_half_float_vertex, >>> GL_ARB_imaging, GL_ARB_instanced_arrays, GL_ARB_map_buffer_range, >>> GL_ARB_multisample, GL_ARB_multitexture, GL_ARB_occlusion_query, >>> GL_ARB_occlusion_query2, GL_ARB_pixel_buffer_object, >>> GL_ARB_point_parameters, GL_ARB_point_sprite, >>> GL_ARB_provoking_vertex, >>> GL_ARB_robustness, GL_ARB_sample_shading, GL_ARB_sampler_objects, >>> GL_ARB_seamless_cube_map, GL_ARB_separate_shader_objects, >>> GL_ARB_shader_bit_encoding, GL_ARB_shader_objects, >>> GL_ARB_shader_precision, >>> GL_ARB_shader_subroutine, GL_ARB_shading_language_100, >>> GL_ARB_shading_language_include, GL_ARB_shadow, GL_ARB_sync, >>> GL_ARB_tessellation_shader, GL_ARB_texture_border_clamp, >>> GL_ARB_texture_buffer_object, GL_ARB_texture_buffer_object_rgb32, >>> GL_ARB_texture_compression, GL_ARB_texture_compression_bptc, >>> GL_ARB_texture_compression_rgtc, GL_ARB_texture_cube_map, >>> GL_ARB_texture_cube_map_array, GL_ARB_texture_env_add, >>> GL_ARB_texture_env_combine, GL_ARB_texture_env_crossbar, >>> GL_ARB_texture_env_dot3, GL_ARB_texture_float, >>> GL_ARB_texture_gather, >>> GL_ARB_texture_mirrored_repeat, GL_ARB_texture_multisample, >>> GL_ARB_texture_non_power_of_two, GL_ARB_texture_query_lod, >>> GL_ARB_texture_rectangle, GL_ARB_texture_rg, >>> GL_ARB_texture_rgb10_a2ui, >>> GL_ARB_texture_swizzle, GL_ARB_timer_query, >>> GL_ARB_transform_feedback2, >>> GL_ARB_transform_feedback3, GL_ARB_transpose_matrix, >>> GL_ARB_uniform_buffer_object, GL_ARB_vertex_array_bgra, >>> GL_ARB_vertex_array_object, GL_ARB_vertex_attrib_64bit, >>> GL_ARB_vertex_buffer_object, GL_ARB_vertex_program, >>> GL_ARB_vertex_shader, >>> GL_ARB_vertex_type_2_10_10_10_rev, GL_ARB_viewport_array, >>> GL_ARB_window_pos, >>> >>> GL_ATI_draw_buffers, GL_ATI_texture_float, >>> GL_ATI_texture_mirror_once, >>> GL_S3_s3tc, GL_EXT_texture_env_add, GL_EXT_abgr, GL_EXT_bgra, >>> GL_EXT_bindable_uniform, GL_EXT_blend_color, >>> GL_EXT_blend_equation_separate, >>> >>> GL_EXT_blend_func_separate, GL_EXT_blend_minmax, >>> GL_EXT_blend_subtract, >>> GL_EXT_compiled_vertex_array, GL_EXT_Cg_shader, >>> GL_EXT_depth_bounds_test, >>> GL_EXT_direct_state_access, GL_EXT_draw_buffers2, >>> GL_EXT_draw_instanced, >>> GL_EXT_draw_range_elements, GL_EXT_fog_coord, >>> GL_EXT_framebuffer_blit, >>> GL_EXT_framebuffer_multisample, GL_EXTX_framebuffer_mixed_formats, >>> GL_EXT_framebuffer_object, GL_EXT_framebuffer_sRGB, >>> GL_EXT_geometry_shader4, >>> >>> GL_EXT_gpu_program_parameters, GL_EXT_gpu_shader4, >>> GL_EXT_multi_draw_arrays, >>> >>> GL_EXT_packed_depth_stencil, GL_EXT_packed_float, >>> GL_EXT_packed_pixels, >>> GL_EXT_pixel_buffer_object, GL_EXT_point_parameters, >>> GL_EXT_provoking_vertex, GL_EXT_rescale_normal, >>> GL_EXT_secondary_color, >>> GL_EXT_separate_shader_objects, GL_EXT_separate_specular_color, >>> GL_EXT_shader_image_load_store, GL_EXT_shadow_funcs, >>> GL_EXT_stencil_two_side, GL_EXT_stencil_wrap, GL_EXT_texture3D, >>> GL_EXT_texture_array, GL_EXT_texture_buffer_object, >>> GL_EXT_texture_compression_dxt1, GL_EXT_texture_compression_latc, >>> GL_EXT_texture_compression_rgtc, GL_EXT_texture_compression_s3tc, >>> GL_EXT_texture_cube_map, GL_EXT_texture_edge_clamp, >>> GL_EXT_texture_env_combine, GL_EXT_texture_env_dot3, >>> GL_EXT_texture_filter_anisotropic, GL_EXT_texture_format_BGRA8888, >>> GL_EXT_texture_integer, GL_EXT_texture_lod, >>> GL_EXT_texture_lod_bias, >>> GL_EXT_texture_mirror_clamp, GL_EXT_texture_object, >>> GL_EXT_texture_shared_exponent, GL_EXT_texture_sRGB, >>> GL_EXT_texture_swizzle, >>> >>> GL_EXT_texture_type_2_10_10_10_REV, GL_EXT_timer_query, >>> GL_EXT_transform_feedback2, GL_EXT_vertex_array, >>> GL_EXT_vertex_array_bgra, >>> GL_EXT_vertex_attrib_64bit, GL_IBM_rasterpos_clip, >>> GL_IBM_texture_mirrored_repeat, GL_KTX_buffer_region, >>> GL_NV_alpha_test, >>> GL_NV_blend_minmax, GL_NV_blend_square, GL_NV_complex_primitives, >>> GL_NV_conditional_render, GL_NV_copy_depth_to_color, >>> GL_NV_copy_image, >>> GL_NV_depth_buffer_float, GL_NV_depth_clamp, >>> GL_NV_explicit_multisample, >>> GL_NV_fbo_color_attachments, GL_NV_fence, GL_NV_float_buffer, >>> GL_NV_fog_distance, GL_NV_fragdepth, GL_NV_fragment_program, >>> GL_NV_fragment_program_option, GL_NV_fragment_program2, >>> GL_NV_framebuffer_multisample_coverage, GL_NV_geometry_shader4, >>> GL_NV_gpu_program4, GL_NV_gpu_program4_1, GL_NV_gpu_program5, >>> GL_NV_gpu_program_fp64, GL_NV_gpu_shader5, GL_NV_half_float, >>> GL_NV_light_max_exponent, GL_NV_multisample_coverage, >>> GL_NV_multisample_filter_hint, GL_NV_occlusion_query, >>> GL_NV_packed_depth_stencil, GL_NV_parameter_buffer_object, >>> GL_NV_parameter_buffer_object2, GL_NV_path_rendering, >>> GL_NV_pixel_data_range, GL_NV_point_sprite, >>> GL_NV_primitive_restart, >>> GL_NV_register_combiners, GL_NV_register_combiners2, >>> GL_NV_shader_buffer_load, GL_NV_texgen_reflection, >>> GL_NV_texture_barrier, >>> GL_NV_texture_compression_vtc, GL_NV_texture_env_combine4, >>> GL_NV_texture_expand_normal, GL_NV_texture_lod_clamp, >>> GL_NV_texture_multisample, GL_NV_texture_rectangle, >>> GL_NV_texture_shader, >>> GL_NV_texture_shader2, GL_NV_texture_shader3, >>> GL_NV_transform_feedback, >>> GL_NV_transform_feedback2, GL_NV_vertex_array_range, >>> GL_NV_vertex_array_range2, GL_NV_vertex_attrib_integer_64bit, >>> GL_NV_vertex_buffer_unified_memory, GL_NV_vertex_program, >>> GL_NV_vertex_program1_1, GL_NV_vertex_program2, >>> GL_NV_vertex_program2_option, GL_NV_vertex_program3, >>> GL_NVX_conditional_render, GL_NVX_gpu_memory_info, GL_OES_depth24, >>> GL_OES_depth32, GL_OES_depth_texture, GL_OES_element_index_uint, >>> GL_OES_fbo_render_mipmap, GL_OES_get_program_binary, >>> GL_OES_mapbuffer, >>> GL_OES_packed_depth_stencil, GL_OES_rgb8_rgba8, >>> GL_OES_standard_derivatives, >>> >>> GL_OES_texture_3D, GL_OES_texture_float, >>> GL_OES_texture_float_linear, >>> GL_OES_texture_half_float, GL_OES_texture_half_float_linear, >>> GL_OES_texture_npot, GL_OES_vertex_array_object, >>> GL_OES_vertex_half_float, >>> GL_SGIS_generate_mipmap, GL_SGIS_texture_lod, >>> GL_SGIX_depth_texture, >>> GL_SGIX_shadow, GL_SUN_slice_accum, GL_WIN_swap_hint, >>> WGL_EXT_swap_control. >>> >>> WGL extensions: >>> WGL_ARB_buffer_region, WGL_ARB_create_context, >>> WGL_ARB_create_context_profile, WGL_ARB_create_context_robustness, >>> WGL_ARB_extensions_string, WGL_ARB_make_current_read, >>> WGL_ARB_multisample, >>> WGL_ARB_pbuffer, WGL_ARB_pixel_format, WGL_ARB_pixel_format_float, >>> WGL_ARB_render_texture, WGL_ATI_pixel_format_float, >>> WGL_EXT_create_context_es2_profile, WGL_EXT_extensions_string, >>> WGL_EXT_framebuffer_sRGB, WGL_EXT_pixel_format_packed_float, >>> WGL_EXT_swap_control, WGL_NVX_DX_interop, WGL_NV_DX_interop, >>> WGL_NV_DX_interop2, WGL_NV_copy_image, WGL_NV_float_buffer, >>> WGL_NV_gpu_affinity, WGL_NV_multisample_coverage, >>> WGL_NV_render_depth_texture, WGL_NV_render_texture_rectangle, >>> WGL_NV_swap_group, WGL_NV_video_capture. >>> >>> visual x bf lv rg d st ge ge r g b a ax dp st accum buffs ms >>> id dep cl sp sz l ci b ro ne ac sz sz sz sz bf th cl r g b a ns b >>> ----------------------------------------------------------------------- >>> 0x01 32 wn . 32 . r . . . . 8 8 8 . 4 24 . 16 16 16 16 0 0 >>> 0x02 32 wn . 32 . r . . . . 8 8 8 8 4 24 . 16 16 16 16 0 0 >>> 0x03 32 wn . 32 . r . . . . 8 8 8 . 4 24 8 16 16 16 16 0 0 >>> 0x04 32 wn . 32 . r . . . . 8 8 8 8 4 24 8 16 16 16 16 0 0 >>> 0x05 32 wn . 32 . r . . . . 8 8 8 . 4 . . 16 16 16 16 0 0 >>> 0x06 32 wn . 32 . r . . . . 8 8 8 8 4 . . 16 16 16 16 0 0 >>> 0x07 32 wn . 32 . r y . . . 8 8 8 . 4 24 . 16 16 16 16 0 0 >>> 0x08 32 wn . 32 . r y . . . 8 8 8 8 4 24 . 16 16 16 16 0 0 >>> 0x09 32 wn . 32 . r y . . . 8 8 8 . 4 24 8 16 16 16 16 0 0 >>> 0x0a 32 wn . 32 . r y . . . 8 8 8 8 4 24 8 16 16 16 16 0 0 >>> 0x0b 32 wn . 32 . r y . . . 8 8 8 . 4 . . 16 16 16 16 0 0 >>> 0x0c 32 wn . 32 . r y . . . 8 8 8 8 4 . . 16 16 16 16 0 0 >>> 0x0d 32 wn . 32 . r y . . . 8 8 8 . 4 24 . 16 16 16 16 0 0 >>> 0x0e 32 wn . 32 . r y . . . 8 8 8 8 4 24 . 16 16 16 16 0 0 >>> 0x0f 32 wn . 32 . r y . . . 8 8 8 . 4 24 8 16 16 16 16 0 0 >>> 0x10 32 wn . 32 . r y . . . 8 8 8 8 4 24 8 16 16 16 16 0 0 >>> 0x11 32 wn . 32 . r y . . . 8 8 8 . 4 . . 16 16 16 16 0 0 >>> 0x12 32 wn . 32 . r y . . . 8 8 8 8 4 . . 16 16 16 16 0 0 >>> 0xf5 32 wn . 32 . r . . . . 8 8 8 . 4 24 . 16 16 16 16 0 0 >>> 0xf6 32 wn . 32 . r . . . . 8 8 8 8 4 24 . 16 16 16 16 0 0 >>> 0xf7 32 wn . 32 . r . . . . 8 8 8 . 4 24 8 16 16 16 16 0 0 >>> 0xf8 32 wn . 32 . r . . . . 8 8 8 8 4 24 8 16 16 16 16 0 0 >>> 0xf9 32 wn . 32 . r . . . . 8 8 8 . 4 . . 16 16 16 16 0 0 >>> 0xfa 32 wn . 32 . r . . . . 8 8 8 8 4 . . 16 16 16 16 0 0 >>> 0xfb 32 wn . 32 . r y . . . 8 8 8 . 4 24 . 16 16 16 16 0 0 >>> 0xfc 32 wn . 32 . r y . . . 8 8 8 8 4 24 . 16 16 16 16 0 0 >>> 0xfd 32 wn . 32 . r y . . . 8 8 8 . 4 24 8 16 16 16 16 0 0 >>> 0xfe 32 wn . 32 . r y . . . 8 8 8 8 4 24 8 16 16 16 16 0 0 >>> 0xff 32 wn . 32 . r y . . . 8 8 8 . 4 . . 16 16 16 16 0 0 >>> 0x100 32 wn . 32 . r y . . . 8 8 8 8 4 . . 16 16 16 16 >>> 0 0 >>> 0x101 32 wn . 32 . r y . . . 8 8 8 . 4 24 . 16 16 16 16 >>> 0 0 >>> 0x102 32 wn . 32 . r y . . . 8 8 8 8 4 24 . 16 16 16 16 >>> 0 0 >>> 0x103 32 wn . 32 . r y . . . 8 8 8 . 4 24 8 16 16 16 16 >>> 0 0 >>> 0x104 32 wn . 32 . r y . . . 8 8 8 8 4 24 8 16 16 16 16 >>> 0 0 >>> 0x105 32 wn . 32 . r y . . . 8 8 8 . 4 . . 16 16 16 16 >>> 0 0 >>> 0x106 32 wn . 32 . r y . . . 8 8 8 8 4 . . 16 16 16 16 >>> 0 0 >>> 0x16f 32 wn . 32 . r . . y . 8 8 8 . . 32 8 16 16 16 . >>> 0 0 >>> 0x170 32 wn . 32 . r . . y . 8 8 8 . . 16 8 16 16 16 . >>> 0 0 >>> 0x171 32 wn . 32 . r y . y . 8 8 8 . . 32 8 16 16 16 . >>> 0 0 >>> 0x172 32 wn . 32 . r y . y . 8 8 8 . . 16 8 16 16 16 . >>> 0 0 >>> 0x173 32 wn . 32 . r . . y . 8 8 8 8 . 32 8 16 16 16 16 >>> 0 0 >>> 0x174 32 wn . 32 . r . . y . 8 8 8 8 . 16 8 16 16 16 16 >>> 0 0 >>> 0x175 32 wn . 32 . r y . y . 8 8 8 8 . 32 8 16 16 16 16 >>> 0 0 >>> 0x176 32 wn . 32 . r y . y . 8 8 8 8 . 16 8 16 16 16 16 >>> 0 0 >>> 0x177 32 wn . 32 . c . . y . . . . . . 32 8 . . . . >>> 0 0 >>> 0x178 32 wn . 32 . c . . y . . . . . . 16 8 . . . . >>> 0 0 >>> 0x179 32 wn . 32 . c y . y . . . . . . 32 8 . . . . >>> 0 0 >>> 0x17a 32 wn . 32 . c y . y . . . . . . 16 8 . . . . >>> 0 0 >>> 0x17b 24 bm . 24 . r . . y . 8 8 8 . . 32 8 16 16 16 . >>> 0 0 >>> 0x17c 24 bm . 24 . r . . y . 8 8 8 . . 16 8 16 16 16 . >>> 0 0 >>> 0x17d 24 bm . 24 . r . . y . 8 8 8 8 . 32 8 16 16 16 16 >>> 0 0 >>> 0x17e 24 bm . 24 . r . . y . 8 8 8 8 . 16 8 16 16 16 16 >>> 0 0 >>> 0x17f 24 bm . 24 . c . . y . . . . . . 32 8 . . . . >>> 0 0 >>> 0x180 24 bm . 24 . c . . y . . . . . . 16 8 . . . . >>> 0 0 >>> 0x181 16 bm . 16 . r . . y . 5 5 5 . . 32 8 11 11 10 . >>> 0 0 >>> 0x182 16 bm . 16 . r . . y . 5 5 5 . . 16 8 11 11 10 . >>> 0 0 >>> 0x183 16 bm . 16 . r . . y . 5 5 5 8 . 32 8 8 8 8 8 >>> 0 0 >>> 0x184 16 bm . 16 . r . . y . 5 5 5 8 . 16 8 8 8 8 8 >>> 0 0 >>> 0x185 16 bm . 16 . c . . y . . . . . . 32 8 . . . . >>> 0 0 >>> 0x186 16 bm . 16 . c . . y . . . . . . 16 8 . . . . >>> 0 0 >>> 0x187 8 bm . 8 . r . . y . 3 3 2 . . 32 8 11 11 10 . >>> 0 0 >>> 0x188 8 bm . 8 . r . . y . 3 3 2 . . 16 8 11 11 10 . >>> 0 0 >>> 0x189 8 bm . 8 . r . . y . 3 3 2 8 . 32 8 8 8 8 8 >>> 0 0 >>> 0x18a 8 bm . 8 . r . . y . 3 3 2 8 . 16 8 8 8 8 8 >>> 0 0 >>> 0x18b 8 bm . 8 . c . . y . . . . . . 32 8 . . . . >>> 0 0 >>> 0x18c 8 bm . 8 . c . . y . . . . . . 16 8 . . . . >>> 0 0 >>> 0x18d 4 bm . 4 . r . . y . 1 1 1 . . 32 8 5 6 5 . >>> 0 0 >>> 0x18e 4 bm . 4 . r . . y . 1 1 1 . . 16 8 5 6 5 . >>> 0 0 >>> 0x18f 4 bm . 4 . r . . y . 1 1 1 8 . 32 8 4 4 4 4 >>> 0 0 >>> 0x190 4 bm . 4 . r . . y . 1 1 1 8 . 16 8 4 4 4 4 >>> 0 0 >>> 0x191 4 bm . 4 . c . . y . . . . . . 32 8 . . . . >>> 0 0 >>> 0x192 4 bm . 4 . c . . y . . . . . . 16 8 . . . . >>> 0 0 >>> ----------------------------------------------------------------------- >>> visual x bf lv rg d st ge ge r g b a ax dp st accum buffs ms >>> id dep cl sp sz l ci b ro ne ac sz sz sz sz bf th cl r g b a ns b >>> ----------------------------------------------------------------------- >>> ########## >>> >>> >>> >>> >>> >>> On 6/27/11 4:42 PM, Greg Couch wrote: >>>> Those settings should work for Chimera too. Please download >>>> http://www.cgl.ucsf.edu/home/gregc/wglinfo.exe, run it in a >>>> terminal window (eg., All Programs / Accessories / Command Prompt), >>>> and send the results directly back to me. wglinfo lists all of the >>>> possible OpenGL framebuffer configurations and should confirm if >>>> OpenGL is reporting that stereo is available and with which >>>> graphics capabilities. I'll summarize what I find to chimera-users. >>>> >>>> -- Greg >>>> >>>> On 06/27/2011 12:34 PM, William Joseph Allen wrote: >>>>> Hi Greg, >>>>> >>>>> Thank you very much for your quick reply. >>>>> >>>>> I had actually already changed those settings in the Nvidia >>>>> control panel. They are as follows: >>>>> >>>>> Stereo - Enable: 'On' >>>>> Stereo - Display mode: 'Generic active stereo (with NVIDIA 3D >>>>> vision)' >>>>> >>>>> The display mode you mentioned in your reply was not an option in >>>>> my Nvidia control panel. Although, this is the only setting that >>>>> really makes sense for what I am doing, and I tried most of the >>>>> other settings without success. I also tried toggling some of the >>>>> other features in a non-random way, but without success. >>>>> >>>>> These two settings, however, are the changes that made stereo in >>>>> VMD and MOE start working (both of which use OpenGL). But, for >>>>> whatever reason, Chimera still gives those previously mentioned >>>>> errors when I try to turn on stereo. If it helps, the monitor is >>>>> an Asus 120 Hz LCD display connected by a dual-link DVI cable >>>>> directly to the graphics card. No DIN connector is involved. >>>>> >>>>> Thanks again, >>>>> >>>>> William Allen >>>>> >>>>> >>>>> >>>>> On 6/27/11 1:42 PM, Greg Couch wrote: >>>>>> It's should be a driver configuration issue. There are two >>>>>> different 3D graphics APIs on Windows, Direct3D and OpenGL, and >>>>>> most Windows applications use the former and Chimera uses the >>>>>> latter (because it works on Linux and Mac OS X too). To >>>>>> configure OpenGL stereo in the Quadro driver on Windows, bring up >>>>>> the NVIDIA Control Panel, navigate to 3D Settings, then Manage 3D >>>>>> Settings. And in those options, set "Stereo - Enable" to on, and >>>>>> "Stereo - Display mode" to the appropriate type of stereo, in >>>>>> your case, my guess would be "On-board DIN connector (with NVIDIA >>>>>> 3D Vision)". >>>>>> >>>>>> HTH, >>>>>> >>>>>> Greg >>>>>> >>>>>> On 06/27/2011 08:02 AM, William Joseph Allen wrote: >>>>>>> Hello Chimera Users, >>>>>>> >>>>>>> I am trying to view molecules in sequential stereo in Chimera (v >>>>>>> 1.5.3). When I >>>>>>> choose Camera -> Sequential Stereo, I get an error that says: >>>>>>> "Unable to turn on >>>>>>> stereo viewing (Unable to find hardware support / couldn't >>>>>>> choose pixel format / >>>>>>> Couldn't configure tool widget)". >>>>>>> >>>>>>> Here is a little bit of the background: >>>>>>> >>>>>>> The machine is a new Dell desktop running 64-bit Windows 7. I >>>>>>> installed a Quadro >>>>>>> 600 graphic cards, and I am using the Nvidia 3D vision wireless >>>>>>> glasses kit. The >>>>>>> version of the Nvidia driver is 275.36, which I believe is the >>>>>>> latest version. I >>>>>>> should also note that I was able to successfully configure VMD >>>>>>> and MOE to work >>>>>>> in Stereo with set up described, so I know that 3D should work, >>>>>>> I just can't get >>>>>>> it to work in Chimera. >>>>>>> >>>>>>> Previous messages in the mailing archive seem to indicate that >>>>>>> the specific type >>>>>>> of graphics card or the version of the driver is usually the >>>>>>> problem. From what >>>>>>> I have read, the Quadro 600 should be compatible. I guess my >>>>>>> only concern is the >>>>>>> version of the driver. It seems there was some bugs in the >>>>>>> 197.x, 258.x, and >>>>>>> 259.x versions of the driver, and 266.45 was reported to work. I >>>>>>> have version >>>>>>> 275.36, should I be worried about a bug or is there something >>>>>>> else I missed? >>>>>>> >>>>>>> Than you for your help, >>>>>>> >>>>>>> William Allen >>>>> >>>>> >>>> >>>> >>> >> >> > From junkermeier at yahoo.com Thu Jun 30 11:36:27 2011 From: junkermeier at yahoo.com (Chad Junkermeier) Date: Thu, 30 Jun 2011 11:36:27 -0700 (PDT) Subject: [Chimera-users] Not Responding Message-ID: <1309458987.40276.YahooMailRC@web111015.mail.gq1.yahoo.com> Hello, I have been having strange behavior lately with opening coordinate files. I am using xyz format files with up to 500 atoms. When I tell Chimera to open one of these files the computer sits for a moment and then starts reporting that Chimera is "Not Responding." I have tried this on three different Mac computers, one using OS X 10.6.7 (iMac Core i7, 8 GB Ram, ATI Radeon HD 4850) with all of the latest updates, one using OS X 10.6.7 (iMac Core 2 Duo, 4 GB Ram, NVIDIA GeForce 9400), and one 3 or 4 year old Macbook that has (4GB RAM, and I don't know anything else). On each of these machines I have tried using a variety of different versions of your code, and I continually find that I have the same problem. I also just installed Chimera on a Windows XP machine and it has similar issues. The xyz files are the product of relaxing a graphene sheet in Quantum Espresso, and then copying and pasting the final configuration out of the QE output file into a xyz file. Here are a few of the things that puzzle me. First, if I place the input configuration of atoms into a xyz file, Chimera will read in the structures without any problems. The output xyz files work in VMD and in iMol. I thought that it might be an issue with the xyz data structure and transformed it to PBD and it still wouldn't load. I also wondered if it was an issue of too many decimal points (higher precision than the input file), but after reducing the number of decimal points of each coordinate on all of the atoms, it still wouldn't work. I have looked through some of the output files and there doesn't appear to be any weirdness in any of the files. Further complicating this issue is that sometimes, after if I let it sit for a while, the program magically starts working. Again, I have no problem opening other files. Does anyone have any ideas on what to do to fix this problem? Chad -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Thu Jun 30 16:05:52 2011 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Thu, 30 Jun 2011 16:05:52 -0700 Subject: [Chimera-users] Not Responding In-Reply-To: <1309458987.40276.YahooMailRC@web111015.mail.gq1.yahoo.com> References: <1309458987.40276.YahooMailRC@web111015.mail.gq1.yahoo.com> Message-ID: <5EFA30BE-D4B3-43B7-9D68-BCA5868D6B4B@cgl.ucsf.edu> Hi Chad, My first inclination would be to think that the culprit is Chimera's ring-finding code, but the fact your input files work while your output files don't is perplexing. I don't think I can really help unless you send me some files to work with (one input and one output would be good). --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Jun 30, 2011, at 11:36 AM, Chad Junkermeier wrote: > Hello, > I have been having strange behavior lately with opening coordinate > files. I am using xyz format files with up to 500 atoms. When I > tell Chimera to open one of these files the computer sits for a > moment and then starts reporting that Chimera is "Not Responding." > I have tried this on three different Mac computers, one using OS X > 10.6.7 (iMac Core i7, 8 GB Ram, ATI Radeon HD 4850) with all of the > latest updates, one using OS X 10.6.7 (iMac Core 2 Duo, 4 GB Ram, > NVIDIA GeForce 9400), and one 3 or 4 year old Macbook that has (4GB > RAM, and I don't know anything else). On each of these machines I > have tried using a variety of different versions of your code, and I > continually find that I have the same problem. I also just > installed Chimera on a Windows XP machine and it has similar issues. > > The xyz files are the product of relaxing a graphene sheet in > Quantum Espresso, and then copying and pasting the final > configuration out of the QE output file into a xyz file. > > Here are a few of the things that puzzle me. First, if I place the > input configuration of atoms into a xyz file, Chimera will read in > the structures without any problems. The output xyz files work in > VMD and in iMol. I thought that it might be an issue with the xyz > data structure and transformed it to PBD and it still wouldn't > load. I also wondered if it was an issue of too many decimal points > (higher precision than the input file), but after reducing the > number of decimal points of each coordinate on all of the atoms, it > still wouldn't work. I have looked through some of the output files > and there doesn't appear to be any weirdness in any of the files. > > Further complicating this issue is that sometimes, after if I let it > sit for a while, the program magically starts working. > > Again, I have no problem opening other files. > > Does anyone have any ideas on what to do to fix this problem? > > > Chad > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: