From peterjames245 at gmail.com Mon Aug 3 16:29:54 2009 From: peterjames245 at gmail.com (Peter Baker) Date: Mon, 3 Aug 2009 19:29:54 -0400 Subject: [Chimera-users] Chimera pH Message-ID: I am trying to generate models of my protein at different pH. Any suggestions as to run how to accomplish this? I do have PBD2PQR files for the different pH but I am not sure how to apply them. Thanks -pjb -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Mon Aug 3 16:34:57 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 3 Aug 2009 16:34:57 -0700 Subject: [Chimera-users] transparent ring fill, color by attribute References: <40ED33F3-974A-4169-9639-C3F4BDD14A10@cgl.ucsf.edu> Message-ID: <3F018B0A-808E-43DA-A1D4-333757113A0D@cgl.ucsf.edu> On Aug 3, 2009, at 2:29 PM, Alexey V. Cherepanov wrote: > Dear Elaine, > > I have another question. On the structure, I color the atoms > according to > their attribute (in my case the chemical shift differences between the > solution and the solid state NMR). I show the residues as balls & > sticks and > fill the rings of riboses & bases. Can I show the filling (i) > semitransparent, and (ii) that it keeps the colors of the atoms > (e.g. if C1' > is blue, C2' is white and C3' is red in the ribose ring, then the > filling > should be blue close to C1, white close to C2' and red close to C3' > with the > gradient in between)? > > Many thanks in advance. > Warm regards, > > Alexey Dear Alexey, The answer to your question is mostly yes, except the color in the fill is not smoothly blended. Currently it shows a "pie slice" or wedge for each ring atom. Some tricky things: (1) the ring fill automatically matches the ring atoms, so that you cannot make the fill transparent unless the atoms are also transparent. However, you can get around that problem by opening another copy of the same structure in which the atoms/bonds are opaque. (2) the transparent ring fill must not be thick. Either it must be in the "thin" style, or if in the "thick" style, the atoms and bonds in that copy must be in the wire representation (which forces it to really be thin). Why? Because some mysterious extra bonds become visible through the transparent fill when it is thick. Example: - open your structure twice - assign your attribute (e.g. use bfactor column, or Add Charge, or Define Attribute to read your own arbitrary attribute values) --- for my example, I opened 6bna twice and will use bfactor -- - use one model to make the transparent rings and the other for whatever atom/bond display you want --- I used commands: delete solvent; rep stick -- - start Render by Attribute, move the color bars as you like; for each, click the square color well, and in the Color Editor turn on "Opacity" and adjust the "A" row (transparency). There is a "Keep opaque" option, and keep that turned on and only click Apply to test the coloring. When the coloring is how you like it, then in the "Models" list at the top of the dialog, only choose one of the models. Now do not move the coloring bars, only uncheck "Keep opaque" and click Apply again. You won't be able to see any change, but now the two models are colored the same except one has the transparency and the other does not. --- I made #0 my transparent model and #1 opaque. I colored blue->red- >yellow for increasing bfactor. - now, add thin ring fill to the transparent model, command: fill thin #0 Here is the documentation for the fillring command. Today it is only at my site (tomorrow it should show up on the "real" Chimera web site). The fillring command (or "fill" for short) is brand new and a couple things still need fixing: - to turn off filling, use ~fill ("fill off" and "fill unfilled" are not working today) - saving a session with ring fill should be available in the next daily build Here is a picture of the result: -------------- next part -------------- A non-text attachment was scrubbed... Name: thinfill.png Type: image/png Size: 153309 bytes Desc: not available URL: -------------- next part -------------- From meng at cgl.ucsf.edu Mon Aug 3 17:01:57 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 3 Aug 2009 17:01:57 -0700 Subject: [Chimera-users] Chimera pH In-Reply-To: References: Message-ID: <2F9BA856-E1CC-4077-B603-CEBF6575ABE4@cgl.ucsf.edu> Hi Peter, Chimera does not have any options to generate protonation states at different pHs. It just aims for a state that is reasonable for physiological pH (i.e. near 7). However, it sounds like you already have the desired protonation states in PQR format. Unfortunately Chimera doesn't read PQR format (although we would like to have that capability in the future) -- the last two columns, charge and radius, are wider than the occupancy and bfactor columns of standard PDB format. One possibility is to simply edit the PQR files to remove the last two columns, then read these now-acceptable PDB files into Chimera. That retains the hydrogens as output from PDB2PQR. I'm not sure what you mean by models... do you also need point charges? A disadvantage of column removal is that the PDB2PQR charges will be lost. However, you could use Add Charge in Chimera (or the addcharge command) to assign charges, and there are several AMBER options. Because the hydrogens are already present, less common protonation states such as neutral Lys, Asp, Glu will be recognized correctly and assigned the appropriate charges. Whether this approach is sufficient depends on whether you wanted to use the specific charge set from PDB2PQR as opposed to an AMBER charge set. If you did want the exact charges from PDB2PQR, you could reformat those charges (next-to-last column in the original PQR file) into an attribute assignment file and reassign them with Define Attribute (or command defattr), after reading in the edited PDB files (PQR files with last 2 columns removed). 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 http://www.cgl.ucsf.edu/home/meng/index.html On Aug 3, 2009, at 4:29 PM, Peter Baker wrote: > I am trying to generate models of my protein at different pH. Any > suggestions as to run how to accomplish this? I do have PBD2PQR > files for the different pH but I am not sure how to apply them. > > Thanks > -pjb From pett at cgl.ucsf.edu Mon Aug 3 17:25:12 2009 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 3 Aug 2009 17:25:12 -0700 Subject: [Chimera-users] Chimera pH In-Reply-To: <2F9BA856-E1CC-4077-B603-CEBF6575ABE4@cgl.ucsf.edu> References: <2F9BA856-E1CC-4077-B603-CEBF6575ABE4@cgl.ucsf.edu> Message-ID: <1D6B5425-2FAC-4E9F-BAED-147D9D39F121@cgl.ucsf.edu> On Aug 3, 2009, at 5:01 PM, Elaine Meng wrote: > If you did want the exact charges from PDB2PQR, you could reformat > those charges (next-to-last column in the original PQR file) into an > attribute assignment file and reassign them with Define Attribute (or > command defattr), after reading in the edited PDB files (PQR files > with last 2 columns removed). In this vein, I wrote a Python script (pqr2chimera.py) that will read a PQR file and output a PDB file that Chimera can read (chimera.pdb) and a defattr file (chimera.defattr) that could be used to assign the PQR charges to the model, if for some reason you prefer them to the charges that Chimera would assign. The script is attached. You run it from a Unix shell like this: python pqr2chimera.py my_pqr_file.pqr The two output files will appear in the directory you run it in. One caveat is that since the defattr output file uses "@/serialNumber=" as it's atom selector, defining the charge attribute in Chimera using that file is kind of slow -- it looks through the list of atoms every time to locate the one with the matching serial number. It probably would be faster if the selector were written in the ":res at atom" form, but since I'm not even sure you care about the defattr part I took the lazy road. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: pqr2chimera.py Type: text/x-python-script Size: 577 bytes Desc: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From alex.gawronski at gmail.com Mon Aug 3 13:32:43 2009 From: alex.gawronski at gmail.com (Alex Gawronski) Date: Mon, 3 Aug 2009 16:32:43 -0400 Subject: [Chimera-users] Minimize In-Reply-To: References: Message-ID: Hello, I'm preparing proteins for Delphi analysis using Chimera's minimize function (from a script). However this process is very time consuming. Is using minimize necessary to get accurate results from Delphi? If not, what is necessary? I've played around with the "spec" and "freeze" parameters and they either seem to have no affect or throw an error (which I submitted as a bug). What do you suggest I do? Thanks, Alex Gawronski Carleton University -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Tue Aug 4 08:19:34 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 4 Aug 2009 08:19:34 -0700 Subject: [Chimera-users] substitute single residue In-Reply-To: <391712D3-29D0-43A0-9DED-569B96685DFC@biochem.uthscsa.edu> References: <391712D3-29D0-43A0-9DED-569B96685DFC@biochem.uthscsa.edu> Message-ID: Dear Andy, Yes, there is a much easier way: use the Rotamers tool (under Tools... Structure Editing). You can specify residue type and rotamer library, and that will give you a "bouquet" of rotamers at that position. You can calculate H-bonds and clashes for the rotamers (or even how well they fit into a density map!) to help you choose the best one, and then have it replace the original sidechain. This tool could be used to generate different rotamers for the same amino acid type or to mutate to a different amino acid type. The "Structure Analysis and Comparison" tutorial includes use of Rotamers: There is also a command-line implementation, "swapaa": Enjoy! Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Jul 30, 2009, at 2:57 PM, Andrew P. Hinck wrote: > Dear all, > > I was hoping to make some single amino acid substitutions in the > context of a protein binding interface. I've only briefly poked > around, but so far the only way I see to do this is to delete > existing atoms/bonds one by one, and then rebuild (the alternate > amino acid) atom-by-atom/bond-by-bond. Is there an easier way > (like, telling the program to substitute an Asp for a Lys, or > something akin to this)? Thanks in advance for any suggestions. > > Andy Hinck From meng at cgl.ucsf.edu Tue Aug 4 08:38:35 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 4 Aug 2009 08:38:35 -0700 Subject: [Chimera-users] Minimize In-Reply-To: References: Message-ID: Hi Alex, I would never recommend minimization as part of a pipeline to prepare structures for DelPhi calculations. Is there some reason you expect these structures to be particularly bad? The minimization is intended for when you have done some manual building, or mutation, or docking, and want to clear up some local bad contacts or highly strained geometries. It is only a local minimization, and will not "refine" the structure if that requires crossing any energy barriers. I don't know what the issue with "spec" and "freeze" are, but they worked fine when I tried them today. There must be a selection for "freeze" to have any effect. "spec" only controls which models are minimized, so if you only have one model open at a time there is no reason to use it. For preparing structures for DelPhi, you might want to look at the Dock Prep tool (under Tools... Structure Editing). It has several structure "regularization" options such as changing selenomethionine to methionine, removing solvent, removing alternate locations of atoms, and rebuilding missing sidechains (although not backbone), as well as hydrogen addition. However, don't bother with the charge addition since that will be irrelevant to the DelPhi calculation --- DelPhi looks up charges from a separate parameter file. Actually "minimize" calls Dock Prep to fix up the structure beforehand. I say just use Dock Prep directly and don't bother with charge addition and don't minimize, unless there is some reason to think the structures are particularly warped. The main thing to worry about for an accurate DelPhi calculation is getting the charges and radii assigned correctly from the DelPhi parameter files. You should check the DelPhi log file. That is a DelPhi issue, fairly separate from Chimera. I hope this helps, ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Aug 3, 2009, at 1:32 PM, Alex Gawronski wrote: > Hello, > > I'm preparing proteins for Delphi analysis using Chimera's minimize > function (from a script). However this process is very time > consuming. Is using minimize necessary to get accurate results from > Delphi? If not, what is necessary? I've played around with the > "spec" and "freeze" parameters and they either seem to have no > affect or throw an error (which I submitted as a bug). What do you > suggest I do? > > Thanks, > Alex Gawronski > Carleton University From alex.gawronski at gmail.com Tue Aug 4 10:21:25 2009 From: alex.gawronski at gmail.com (Alex Gawronski) Date: Tue, 4 Aug 2009 13:21:25 -0400 Subject: [Chimera-users] Minimize In-Reply-To: References: Message-ID: Thanks for the info! I was just worried that the added hydrogen atoms would not be in the minimal position. They do move a little from the minimization. Do you think that is significant? Alex Gawronski On Tue, Aug 4, 2009 at 11:38 AM, Elaine Meng wrote: > Hi Alex, > I would never recommend minimization as part of a pipeline to prepare > structures for DelPhi calculations. Is there some reason you expect these > structures to be particularly bad? The minimization is intended for when > you have done some manual building, or mutation, or docking, and want to > clear up some local bad contacts or highly strained geometries. It is only > a local minimization, and will not "refine" the structure if that requires > crossing any energy barriers. > > I don't know what the issue with "spec" and "freeze" are, but they worked > fine when I tried them today. There must be a selection for "freeze" to > have any effect. "spec" only controls which models are minimized, so if you > only have one model open at a time there is no reason to use it. > > > For preparing structures for DelPhi, you might want to look at the Dock > Prep tool (under Tools... Structure Editing). It has several structure > "regularization" options such as changing selenomethionine to methionine, > removing solvent, removing alternate locations of atoms, and rebuilding > missing sidechains (although not backbone), as well as hydrogen addition. > However, don't bother with the charge addition since that will be > irrelevant to the DelPhi calculation --- DelPhi looks up charges from a > separate parameter file. > < > http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/dockprep.html > > > > Actually "minimize" calls Dock Prep to fix up the structure beforehand. I > say just use Dock Prep directly and don't bother with charge addition and > don't minimize, unless there is some reason to think the structures are > particularly warped. > > The main thing to worry about for an accurate DelPhi calculation is getting > the charges and radii assigned correctly from the DelPhi parameter files. > You should check the DelPhi log file. That is a DelPhi issue, fairly > separate from Chimera. > > I hope this helps, > ----- > Elaine C. Meng, Ph.D. > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > http://www.cgl.ucsf.edu/home/meng/index.html > > > > > > On Aug 3, 2009, at 1:32 PM, Alex Gawronski wrote: > > Hello, >> >> I'm preparing proteins for Delphi analysis using Chimera's minimize >> function (from a script). However this process is very time consuming. Is >> using minimize necessary to get accurate results from Delphi? If not, what >> is necessary? I've played around with the "spec" and "freeze" parameters and >> they either seem to have no affect or throw an error (which I submitted as a >> bug). What do you suggest I do? >> >> Thanks, >> Alex Gawronski >> Carleton University >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Tue Aug 4 10:54:56 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 4 Aug 2009 10:54:56 -0700 Subject: [Chimera-users] Minimize In-Reply-To: References: Message-ID: <69B01CE5-5019-491D-B7F7-5A0B88F0DF9F@cgl.ucsf.edu> Hi Alex, I would not worry, just use the "also consider H-bonds" method when adding hydrogens in Chimera. That method is the default. In fact hydrogens might be totally irrelevant to DelPhi depending on what DelPhi parameter files you are using. If I recall correctly, their "default.crg" and "default.siz" files are for use on structures without hydrogens. By far the most difficult thing is making sure parameters are assigned correctly and that the net charge of your protein in the delphi log file is what you expect. Sometimes people use parameter files with hydrogen names that don't match those in the structure and the net charge of the protein is reported in the log file as a huge negative non-integer. 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 http://www.cgl.ucsf.edu/home/meng/index.html On Aug 4, 2009, at 10:21 AM, Alex Gawronski wrote: > Thanks for the info! > > I was just worried that the added hydrogen atoms would not be in the > minimal position. They do move a little from the minimization. Do > you think that is significant? > > Alex Gawronski From danielgurnon at depauw.edu Tue Aug 4 13:51:26 2009 From: danielgurnon at depauw.edu (Daniel Gurnon) Date: Tue, 04 Aug 2009 16:51:26 -0400 Subject: [Chimera-users] Stereo 3D on 120 Hz displays Message-ID: <4A78671002000003000C0B48@gwia-vs.depauw.edu> Just wanted to let everyone know that its finally possible to view sequential stereo in Chimera with 120 Hz LCD displays. I just confirmed that it works with my system- here's what you'll need: An appropriate Quadro card (I have a FX 4500), with the recent 190-series driver A 120Hz 3D ready LCD screen (I have the samsung 2233RZ. The other choice is a Viewsonic model) The Nvidia 3Dvision glasses kit, which includes a USB IR emitter The latest beta driver for 3Dvision, version 1.10, found here: http://www.nvidia.com/object/geforce_3D_vision_winvista_win7_CD_1.10.html Note that this only works for Vista. The 3Dvision software is supposed to only support Geforce cards, but it worked for my quadro fx 4500. After installing the drivers and the hardware I opened the Nvidia control panel 3D settings and set the following options: Stereo-Display mode: "Generic active stereo (with NVIDIA IR emitter)" Stereo-enable: "Yes" Then restart your computer, and enable sequential stereo from within Chimera. The only issue so far is that the accessory software (photo viewer and 3D preview pack) that installs with the drivers won't load; instead you get a message saying your hardware isn't compatible. ____________________________ Daniel Gurnon, Ph. D. Assistant Professor of Chemistry DePauw University Greencastle, IN 46135 p: 765-658-6279 e: danielgurnon at depauw.edu From vberk at berkeley.edu Wed Aug 5 02:52:20 2009 From: vberk at berkeley.edu (Veysel Berk) Date: Wed, 5 Aug 2009 02:52:20 -0700 Subject: [Chimera-users] loading atomic coordinates without drawing or calculating bonds In-Reply-To: References: Message-ID: > Hello, > > I am trying to load a large atomic coordinates file in xyz format. The > atomic coordinates are meaningless to crystallography in terms of distances > of atoms and as a result, while chimera try to load the coordinate and > calculate the bonding between atoms, it crashes or suspends for ever. The > data is from single molecule localization experiments where I want to use > chimera to visualize this 3D data by treating each localization as an atom. > I am trying to load about a million atoms. > > Is it possible to turn off automatic bonding calculations and only show > atoms without bonds to prevent crashing? or does anyone know any simple > method or software to convert atomic coordinates into voxel map which I can > use in volume visualizer module of chimera without worrying about bond > calculations? > > Thanks in advance, > > Bests, > > Veysel Berk > -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Wed Aug 5 09:58:56 2009 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 5 Aug 2009 09:58:56 -0700 Subject: [Chimera-users] loading atomic coordinates without drawing or calculating bonds In-Reply-To: References: Message-ID: <13996BCF-6A26-468C-ACDF-3FB65A1938CF@cgl.ucsf.edu> On Aug 5, 2009, at 2:52 AM, Veysel Berk wrote: > > Hello, > > I am trying to load a large atomic coordinates file in xyz format. > The atomic coordinates are meaningless to crystallography in terms > of distances of atoms and as a result, while chimera try to load the > coordinate and calculate the bonding between atoms, it crashes or > suspends for ever. The data is from single molecule localization > experiments where I want to use chimera to visualize this 3D data by > treating each localization as an atom. I am trying to load about a > million atoms. > > Is it possible to turn off automatic bonding calculations and only > show atoms without bonds to prevent crashing? or does anyone know > any simple method or software to convert atomic coordinates into > voxel map which I can use in volume visualizer module of chimera > without worrying about bond calculations? Hi Veysel, I don't know if there's a particular reason you want these points to be atoms, but one alternative is the use the ".sphere" directive of Chimera's BILD format (http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html ) to depict your points. If you do need them to be atoms, there is no way to suppress the connectivity search for XYZ files without editing the Python code for reading that file format. If you are willing to do that then the change is pretty trivial. In the __init__.py file of the ReadXYZ module there is a line that looks like this: connectMolecule(m) either delete that line or insert a '#' symbol just in front of the 'c' to comment it out. You will find ReadXYZ in the 'share' subdirectory of your Chimera installation. On a mac it will actually be in the 'Contents/Resources/share' subdirectory and you will have to right click on the Chimera icon and choose "Show Package Contents" to see the application subdirectories in the Finder. I hope this helps. --Eric Eric Pettersen UCSF Computer Graphics Lab From mpufall at cmpmail.ucsf.edu Tue Aug 4 23:44:21 2009 From: mpufall at cmpmail.ucsf.edu (Miles Pufall) Date: Tue, 04 Aug 2009 23:44:21 -0700 Subject: [Chimera-users] Zalman 3D Message-ID: Hi Guys - I got a Zalman 3D - it's pretty cool with Coot and Pymol. Your site says the row-interleaved stereo view under camera will work with this monitor, but I wasn't having much success. Do you have some more detailed instructions for this particular monitor? I can drop by and visit with it, or you can come see me if you's like. Thanks! Miles in Yamamoto Lab S574 Genentech Hall From vberk at berkeley.edu Wed Aug 5 02:49:52 2009 From: vberk at berkeley.edu (Veysel Berk) Date: Wed, 5 Aug 2009 02:49:52 -0700 Subject: [Chimera-users] loading atomic coordinates without drawing or calculating bonds Message-ID: Hello, I am trying to load a large atomic coordinates file in xyz format. The atomic coordinates are meaningless to crystallography in terms of distances of atoms and as a result, while chimera try to load the coordinate and calculate the bonding between atoms, it crashes or suspends for ever. The data is from single molecule localization experiments where I want to use chimera to visualize this 3D data by treating each localization as an atom. I am trying to load about a million atoms. Is it possible to turn off automatic bonding calculations and only show atoms without bonds to prevent crashing? or does anyone know any simple method or software to convert atomic coordinates into voxel map which I can use in volume visualizer module of chimera without worrying about bond calculations? Thanks in advance, Bests, Veysel Berk -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at cgl.ucsf.edu Wed Aug 5 10:34:51 2009 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Wed, 05 Aug 2009 10:34:51 -0700 Subject: [Chimera-users] loading atomic coordinates without drawing or calculating bonds In-Reply-To: References: Message-ID: <4A79C2BB.3010604@cgl.ucsf.edu> Hi Veysel, You will have a rough time trying to open 1 million atoms in Chimera because it is very memory inefficient, taking about 2 Kbytes per atom. So 1 million atoms will take about 2 Gbytes and this is unlikely to work with 32-bit versions of the program. Only the 64-bit linux version is likely to handle it. You are probably better off making a volume data set from your million points. There is a Python Chimera script called xyzmap.py you can use to do this. http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/Scripts Each point is treated as a Gaussian of specified width. After making the map you can save it with the volume dialog File / Save Map As... menu entry or the volume command. Tom -------- Original Message -------- Subject: [Chimera-users] loading atomic coordinates without drawing or calculating bonds From: Veysel Berk To: chimera-users at cgl.ucsf.edu Date: 8/5/09 2:52 AM > > Hello, > > I am trying to load a large atomic coordinates file in xyz format. > The atomic coordinates are meaningless to crystallography in terms > of distances of atoms and as a result, while chimera try to load > the coordinate and calculate the bonding between atoms, it crashes > or suspends for ever. The data is from single molecule > localization experiments where I want to use chimera to visualize > this 3D data by treating each localization as an atom. I am trying > to load about a million atoms. > > Is it possible to turn off automatic bonding calculations and only > show atoms without bonds to prevent crashing? or does anyone know > any simple method or software to convert atomic coordinates into > voxel map which I can use in volume visualizer module of chimera > without worrying about bond calculations? > > Thanks in advance, > > Bests, > > Veysel Berk > > From conrad at cgl.ucsf.edu Wed Aug 5 10:58:36 2009 From: conrad at cgl.ucsf.edu (Conrad Huang) Date: Wed, 05 Aug 2009 10:58:36 -0700 Subject: [Chimera-users] Zalman 3D In-Reply-To: References: Message-ID: <4A79C84C.9040201@cgl.ucsf.edu> Do you have multisampling turned on? Multisampling on different graphics cards work differently. Some cards use values from adjacent rows for computing pixel values, and this really doesn't work when using row-interleaved stereo mode. To check if multisampling is on, use the Tools->Viewing Control->Effects menu item to bring up the Viewing panel; the multisampling option should be the bottom-most one on the right. Conrad Miles Pufall wrote: > Hi Guys - > > I got a Zalman 3D - it's pretty cool with Coot and Pymol. > Your site says the row-interleaved stereo view under > camera will work with this monitor, but I wasn't having > much success. Do you have some more detailed instructions > for this particular monitor? > > I can drop by and visit with it, or you can come see me if > you's like. Thanks! > Miles in Yamamoto Lab > S574 Genentech Hall > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From pett at cgl.ucsf.edu Wed Aug 5 12:18:07 2009 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 5 Aug 2009 12:18:07 -0700 Subject: [Chimera-users] movie making In-Reply-To: References: <9E6930C3-7764-45A3-AC38-5A9A6E9CB45E@cgl.ucsf.edu> Message-ID: <2994CEF3-08ED-4A3F-9864-540F24732A51@cgl.ucsf.edu> On Aug 5, 2009, at 2:32 AM, Schulz-Gasch, Tanja wrote: > Dear Eric, > > your movie making recommendations were indeed very helpful. Thanks > again! Hi Tanja -- glad I could help! > I am currently preparing a show for visitors at Roche that are > interested in 3D modelling and I want to do this with > Chimera. I have alreday started scripting. However, I would like to > have breaks in the scripts in case that there are > questions. So my question is, is there a possibility to implement a > prompt in the Chimera script that waits only > the users presses 'return' or whatever and then Chimera is running > further through the script? The daily build has a few things that will help here. First, there is a "pause" command that will cause a script to pause until any key other than Escape or End is pressed. Those two keys will cause the script to abort instead of continuing. Secondly, even without an explicit "pause" command any script can be paused by hitting Shift-Escape. A second Shift-Escape will continue the script. Also, plain Escape (no Shift) will cause any script to abort. I hope the presentation goes well! --Eric Eric Pettersen UCSF Computer Graphics Lab -------------- next part -------------- An HTML attachment was scrubbed... URL: From tef at cgl.ucsf.edu Wed Aug 5 12:22:35 2009 From: tef at cgl.ucsf.edu (Tom Ferrin) Date: Wed, 05 Aug 2009 12:22:35 -0700 Subject: [Chimera-users] Zalman 3D In-Reply-To: <4A79C84C.9040201@cgl.ucsf.edu> References: <4A79C84C.9040201@cgl.ucsf.edu> Message-ID: <4A79DBFB.3060905@cgl.ucsf.edu> Miles, The other obvious thing is that you need a newer version of Chimera than the 1.3 production release. Just grab any of the daily builds from www.cgl.ucsf.edu/chimera/download.html. If you still have problems after trying Conrad's suggestion come on down to GH-N456 and check the graphics settings we are using with our Zalman 3D display. --tom Conrad Huang wrote: > Do you have multisampling turned on? Multisampling on different > graphics cards work differently. Some cards use values from adjacent > rows for computing pixel values, and this really doesn't work when using > row-interleaved stereo mode. > > To check if multisampling is on, use the Tools->Viewing Control->Effects > menu item to bring up the Viewing panel; the multisampling option should > be the bottom-most one on the right. > > Conrad > > Miles Pufall wrote: >> Hi Guys - >> >> I got a Zalman 3D - it's pretty cool with Coot and Pymol. >> Your site says the row-interleaved stereo view under >> camera will work with this monitor, but I wasn't having >> much success. Do you have some more detailed instructions >> for this particular monitor? >> >> I can drop by and visit with it, or you can come see me if >> you's like. Thanks! >> Miles in Yamamoto Lab >> S574 Genentech Hall >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From goddard at cgl.ucsf.edu Wed Aug 5 15:00:03 2009 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Wed, 05 Aug 2009 15:00:03 -0700 Subject: [Chimera-users] loading atomic coordinates without drawing or calculating bonds In-Reply-To: <4A79C2BB.3010604@cgl.ucsf.edu> References: <4A79C2BB.3010604@cgl.ucsf.edu> Message-ID: <4A7A00E3.6060808@cgl.ucsf.edu> Hi Veysel, Ok, I put a script xyzsdmap.py on the Chimera scripts web page that reads x,y,z and sigma x, sigma y, sigma z values (6 column text file) and makes the volume data set from Gaussians using those parameters. If you also have different amplitudes for the points that could be handled by reading another column and modifying the "weights" array in the script. http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/Scripts Tom -------- Original Message -------- Subject: Re: [Chimera-users] loading atomic coordinates without drawing or calculating bonds From: Veysel Berk To: Tom Goddard Date: 8/5/09 1:31 PM > Dear Tom, > > It looks like a great idea. I will try both options today and let's > see of it works for me. > > Thanks very much for your advise. > > would it be possible to implement to define three more column on the > xyz file for standard deviations of Gaussians in each dimensions to > calculate the volume data in future releases of the script? Is it > technically doable? My localization data have x, y, z and sigx, sigy, > sigz. > > Bests, > > Veysel Berk > Department of Molecular & Cell Biology > University of California, Berkeley > > > On Aug 5, 2009, at 10:34 AM, Tom Goddard wrote: > >> Hi Veysel, >> >> You will have a rough time trying to open 1 million atoms in Chimera >> because it is very memory inefficient, taking about 2 Kbytes per >> atom. So 1 million atoms will take about 2 Gbytes and this is >> unlikely to work with 32-bit versions of the program. Only the >> 64-bit linux version is likely to handle it. >> >> You are probably better off making a volume data set from your >> million points. There is a Python Chimera script called xyzmap.py >> you can use to do this. >> >> http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/Scripts >> >> Each point is treated as a Gaussian of specified width. After making >> the map you can save it with the volume dialog File / Save Map As... >> menu entry or the volume command. >> >> Tom >> >> -------- Original Message -------- >> Subject: [Chimera-users] loading atomic coordinates without drawing >> or calculating bonds >> From: Veysel Berk >> To: chimera-users at cgl.ucsf.edu >> Date: 8/5/09 2:52 AM >>> >>> Hello, >>> >>> I am trying to load a large atomic coordinates file in xyz format. >>> The atomic coordinates are meaningless to crystallography in terms >>> of distances of atoms and as a result, while chimera try to load >>> the coordinate and calculate the bonding between atoms, it crashes >>> or suspends for ever. The data is from single molecule >>> localization experiments where I want to use chimera to visualize >>> this 3D data by treating each localization as an atom. I am trying >>> to load about a million atoms. >>> >>> Is it possible to turn off automatic bonding calculations and only >>> show atoms without bonds to prevent crashing? or does anyone know >>> any simple method or software to convert atomic coordinates into >>> voxel map which I can use in volume visualizer module of chimera >>> without worrying about bond calculations? >>> >>> Thanks in advance, >>> >>> Bests, >>> >>> Veysel Berk >>> >>> >> -------- Original Message -------- Subject: Re: [Chimera-users] loading atomic coordinates without drawing or calculating bonds From: Tom Goddard To: Veysel Berk Date: 8/5/09 10:34 AM > Hi Veysel, > > You will have a rough time trying to open 1 million atoms in Chimera > because it is very memory inefficient, taking about 2 Kbytes per atom. > So 1 million atoms will take about 2 Gbytes and this is unlikely to work > with 32-bit versions of the program. Only the 64-bit linux version is > likely to handle it. > > You are probably better off making a volume data set from your million > points. There is a Python Chimera script called xyzmap.py you can use > to do this. > > http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/Scripts > > Each point is treated as a Gaussian of specified width. After making > the map you can save it with the volume dialog File / Save Map As... > menu entry or the volume command. > > Tom > > -------- Original Message -------- > Subject: [Chimera-users] loading atomic coordinates without drawing or > calculating bonds > From: Veysel Berk > To: chimera-users at cgl.ucsf.edu > Date: 8/5/09 2:52 AM > >> Hello, >> >> I am trying to load a large atomic coordinates file in xyz format. >> The atomic coordinates are meaningless to crystallography in terms >> of distances of atoms and as a result, while chimera try to load >> the coordinate and calculate the bonding between atoms, it crashes >> or suspends for ever. The data is from single molecule >> localization experiments where I want to use chimera to visualize >> this 3D data by treating each localization as an atom. I am trying >> to load about a million atoms. >> >> Is it possible to turn off automatic bonding calculations and only >> show atoms without bonds to prevent crashing? or does anyone know >> any simple method or software to convert atomic coordinates into >> voxel map which I can use in volume visualizer module of chimera >> without worrying about bond calculations? >> >> Thanks in advance, >> >> Bests, >> >> Veysel Berk >> >> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: From vberk at berkeley.edu Wed Aug 5 15:33:37 2009 From: vberk at berkeley.edu (Veysel Berk) Date: Wed, 5 Aug 2009 15:33:37 -0700 Subject: [Chimera-users] loading atomic coordinates without drawing or calculating bonds In-Reply-To: <4A7A00E3.6060808@cgl.ucsf.edu> References: <4A79C2BB.3010604@cgl.ucsf.edu> <4A7A00E3.6060808@cgl.ucsf.edu> Message-ID: Thanks Tom, It works very well for converting fluorescent localization data into volume data. Now, single molecule field may benefit on the great features of Chimera! Bests, Veysel Berk Department of Molecular & Cell Biology University of California, Berkeley Stanley Hall #431 Berkeley, CA 94720 510-666 2740 On Wed, Aug 5, 2009 at 3:00 PM, Tom Goddard wrote: > Hi Veysel, > > Ok, I put a script xyzsdmap.py on the Chimera scripts web page that > reads x,y,z and sigma x, sigma y, sigma z values (6 column text file) and > makes the volume data set from Gaussians using those parameters. If you > also have different amplitudes for the points that could be handled by > reading another column and modifying the "weights" array in the script. > > http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/Scripts > > Tom > > > -------- Original Message -------- > Subject: Re: [Chimera-users] loading atomic coordinates without drawing or > calculating bonds > From: Veysel Berk > To: Tom Goddard > Date: 8/5/09 1:31 PM > > Dear Tom, > > It looks like a great idea. I will try both options today and let's see of > it works for me. > > Thanks very much for your advise. > > would it be possible to implement to define three more column on the xyz > file for standard deviations of Gaussians in each dimensions to calculate > the volume data in future releases of the script? Is it technically doable? > My localization data have x, y, z and sigx, sigy, sigz. > > Bests, > > Veysel Berk > Department of Molecular & Cell Biology > University of California, Berkeley > > > On Aug 5, 2009, at 10:34 AM, Tom Goddard wrote: > > Hi Veysel, > > You will have a rough time trying to open 1 million atoms in Chimera > because it is very memory inefficient, taking about 2 Kbytes per atom. So 1 > million atoms will take about 2 Gbytes and this is unlikely to work with > 32-bit versions of the program. Only the 64-bit linux version is likely to > handle it. > > You are probably better off making a volume data set from your million > points. There is a Python Chimera script called xyzmap.py you can use to do > this. > > http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/Scripts > > Each point is treated as a Gaussian of specified width. After making the > map you can save it with the volume dialog File / Save Map As... menu entry > or the volume command. > > Tom > > -------- Original Message -------- > Subject: [Chimera-users] loading atomic coordinates without drawing or > calculating bonds > From: Veysel Berk > To: chimera-users at cgl.ucsf.edu > Date: 8/5/09 2:52 AM > > > Hello, > > I am trying to load a large atomic coordinates file in xyz format. > The atomic coordinates are meaningless to crystallography in terms > of distances of atoms and as a result, while chimera try to load > the coordinate and calculate the bonding between atoms, it crashes > or suspends for ever. The data is from single molecule > localization experiments where I want to use chimera to visualize > this 3D data by treating each localization as an atom. I am trying > to load about a million atoms. > > Is it possible to turn off automatic bonding calculations and only > show atoms without bonds to prevent crashing? or does anyone know > any simple method or software to convert atomic coordinates into > voxel map which I can use in volume visualizer module of chimera > without worrying about bond calculations? > > Thanks in advance, > > Bests, > > Veysel Berk > > > > > > > -------- Original Message -------- > Subject: Re: [Chimera-users] loading atomic coordinates without drawing or > calculating bonds > From: Tom Goddard > To: Veysel Berk > Date: 8/5/09 10:34 AM > > Hi Veysel, > > You will have a rough time trying to open 1 million atoms in Chimera > because it is very memory inefficient, taking about 2 Kbytes per atom. > So 1 million atoms will take about 2 Gbytes and this is unlikely to work > with 32-bit versions of the program. Only the 64-bit linux version is > likely to handle it. > > You are probably better off making a volume data set from your million > points. There is a Python Chimera script called xyzmap.py you can use > to do this. > > http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/Scripts > > Each point is treated as a Gaussian of specified width. After making > the map you can save it with the volume dialog File / Save Map As... > menu entry or the volume command. > > Tom > > -------- Original Message -------- > Subject: [Chimera-users] loading atomic coordinates without drawing or > calculating bonds > From: Veysel Berk > To: chimera-users at cgl.ucsf.edu > Date: 8/5/09 2:52 AM > > > Hello, > > I am trying to load a large atomic coordinates file in xyz format. > The atomic coordinates are meaningless to crystallography in terms > of distances of atoms and as a result, while chimera try to load > the coordinate and calculate the bonding between atoms, it crashes > or suspends for ever. The data is from single molecule > localization experiments where I want to use chimera to visualize > this 3D data by treating each localization as an atom. I am trying > to load about a million atoms. > > Is it possible to turn off automatic bonding calculations and only > show atoms without bonds to prevent crashing? or does anyone know > any simple method or software to convert atomic coordinates into > voxel map which I can use in volume visualizer module of chimera > without worrying about bond calculations? > > Thanks in advance, > > Bests, > > Veysel Berk > > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ffsyed at syr.edu Thu Aug 6 11:08:50 2009 From: ffsyed at syr.edu (Farhana F Syed) Date: Thu, 6 Aug 2009 18:08:50 +0000 Subject: [Chimera-users] Q about opening two structures in the same window Message-ID: Hello, I recently downloaded chimera and have been using to view my protein homology model - mainly to show the 2 residues that could be involved in binding to a molecule inside the cell. For that purpose, I need to be able to open the small molecule (citrate or phosphate) in the same window with protein; so I can show the small molecule binds to the specific amino acid residues. But even if I open the two together, how do I pick the small molecule and move it around where I need it? Please help. Thanks, Farhana -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Thu Aug 6 11:49:36 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 6 Aug 2009 11:49:36 -0700 Subject: [Chimera-users] Q about opening two structures in the same window In-Reply-To: References: Message-ID: Hi Farhana, You can open several different structures from different files and display them all in the same window. It sounds like you figured that part out already. Then you can freeze/freeze structures (we call that "activation" and "deactivation" for motion) so that only the active ones can be moved with the mouse. Activation/deactivation can be controlled in several ways: - checkboxes under the Command Line (show with Favorites... Command Line) - Model Panel (Favorites... Model Panel), checkboxes in the Active column and/or various "activate" function buttons on the right - with the "select" command See Or if you are moving structures with commands, in newer versions of Chimera (1.4, so daily builds), you can specify which models you want to move. Movement commands include "move" (translation) and "turn" (rotation). 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 http://www.cgl.ucsf.edu/home/meng/index.html On Aug 6, 2009, at 11:08 AM, Farhana F Syed wrote: > Hello, > > I recently downloaded chimera and have been using to view my protein > homology model - mainly to show the 2 residues that could be > involved in binding to a molecule inside the cell. For that purpose, > I need to be able to open the small molecule (citrate or phosphate) > in the same window with protein; so I can show the small molecule > binds to the specific amino acid residues. But even if I open the > two together, how do I pick the small molecule and move it around > where I need it? > > Please help. > Thanks, > Farhana From damien.lariviere at fourmentinguilbert.org Thu Aug 6 11:11:29 2009 From: damien.lariviere at fourmentinguilbert.org (=?ISO-8859-1?Q?Damien_Larivi=E8re?=) Date: Thu, 06 Aug 2009 20:11:29 +0200 Subject: [Chimera-users] Orientation and quaternion Message-ID: <4A7B1CD1.3080202@fourmentinguilbert.org> Dear all, In the attached image, two copies of the FtsZ protein (pdb 1FSZ) are displayed in Chimera. I would like to know the orientation of one copy with respect to the other one. Is there a way to get this information ? Is it possible to get a quaternion instead of a set of Euler angles ? My best regards Damien -------------- next part -------------- A non-text attachment was scrubbed... Name: FtsZ_1FSZ.JPG Type: image/jpeg Size: 94391 bytes Desc: not available URL: From mikeday at caltech.edu Thu Aug 6 18:02:59 2009 From: mikeday at caltech.edu (Michael Day) Date: Thu, 6 Aug 2009 18:02:59 -0700 Subject: [Chimera-users] Moving atom labels Message-ID: How does one change the position of atom labels? For small coordination complexes the default atom labels land on the atom and it would be nice to move them as a whole or individually so they are alongside the atom ball or anisotropic ellipsoid. While I'm on the ellipsoid topic; has there been progress on overlaying axis on the ellipsoids? I know I originally asked about axis and shaded octants but after using the anisotropic option for the last month or so I notice tat there is a tremendous amount of information conveyed with just the color and shape and shaded octants may not add much information (in fact it may just confuse the issue). Your implementation of thermal ellipsoids is very, very useful! Cheers, Mike <<< ------------------------------------------------------------------------> >> Dr. Michael W. Day Director - X-ray Crystallography Lab & Molecular Observatory California Institute of Technology Mail Code 139-74 Pasadena, CA 91125 <>< <>< <>< <>< <>< <>< <>< <>< <>< <>< Beckman Institute, Room 116 Phone: (626) 395-2734 Fax: (626) 449-4159 e-mail: mikeday at caltech.edu <<< ------------------------------------------------------------------------> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at cgl.ucsf.edu Thu Aug 6 18:27:51 2009 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Thu, 06 Aug 2009 18:27:51 -0700 Subject: [Chimera-users] Orientation and quaternion In-Reply-To: <4A7B1CD1.3080202@fourmentinguilbert.org> References: <4A7B1CD1.3080202@fourmentinguilbert.org> Message-ID: <4A7B8317.4010807@cgl.ucsf.edu> Hi Damien, You can measure the relative orientation of the two models with the "measure rotation" command: measure rot #0 #1 which produces output in the reply log (Favorites / Reply Log) like Position of 2gbp.pdb (#1) relative to 1a0m.pdb (#0) coordinates: Matrix rotation and translation 0.90028335 0.21178251 -0.38031310 38.41870000 0.30675800 0.31121759 0.89946825 -28.00030000 0.30885177 -0.92644038 0.21521804 53.80560000 Axis -0.93447169 -0.35270388 0.04860698 Axis point 0.00000000 15.26078714 51.99569332 Rotation angle (degrees) 77.68070000 Shift along axis -23.41004496 Also it draws the rotation axis on the screen (append "show false" to suppress that). The rotation is shown as a matrix and as axis/angle in the output. You can compute the quaternion equivalent of the rotation if you need that: (sin(a/2)*axis, cos(a/2)) where a is the angle. The "measure" command is only in Chimera 1.4 so get a daily build to use it. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation Tom -------- Original Message -------- Subject: [Chimera-users] Orientation and quaternion From: Damien Larivi?re To: chimera-users at cgl.ucsf.edu Date: 8/6/09 11:11 AM > Dear all, > > In the attached image, two copies of the FtsZ protein (pdb 1FSZ) are > displayed in Chimera. > > I would like to know the orientation of one copy with respect to the > other one. Is there a way to get this information ? Is it possible to > get a quaternion instead of a set of Euler angles ? > > My best regards > > Damien > > > > ------------------------------------------------------------------------ > > > ------------------------------------------------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From gregc at cgl.ucsf.edu Fri Aug 7 14:44:53 2009 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Fri, 7 Aug 2009 14:44:53 -0700 (PDT) Subject: [Chimera-users] Moving atom labels In-Reply-To: References: Message-ID: On Thu, 6 Aug 2009, Michael Day wrote: > How does one change the position of atom labels? For small coordination > complexes the default atom labels land on the atom and it would be nice to > move them as a whole or individually so they are alongside the atom ball or > anisotropic ellipsoid. > > Cheers, > Mike In the next daily build, we will have interactive label moving, where you can pick a label and drag it around, and if you hold down the shift key, it will move in Z. It will default to the Control-button-3 mouse mode, but can be reassigned using the mouse mode preferences. You will also be able to change the label offsets using the command line, the "labeloffset x y z atom-spec" and "rlabeloffset x y z atom-spec" commands to set the offsets and "~labeloffset" and "~rlabeloffset" to reset them to the default behavior of adjusting the offset with the representation. For users with existing saved preferences, you might need to turn label dragging on by resetting the mouse mode preferences or by explicitly assigning it to Control-button-3. There's no icon for it yet in the mouse modes interface, but it will be the rightmost column for now. Since the label moving code is new, please send me feedback about how well it works for you. - Greg From pett at cgl.ucsf.edu Fri Aug 7 14:51:52 2009 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Fri, 7 Aug 2009 14:51:52 -0700 Subject: [Chimera-users] Moving atom labels In-Reply-To: References: Message-ID: Hi Mike, On Aug 6, 2009, at 6:02 PM, Michael Day wrote: > How does one change the position of atom labels? For small > coordination complexes the default atom labels land on the atom and > it would be nice to move them as a whole or individually so they are > alongside the atom ball or anisotropic ellipsoid. For the 1.4 release we hope to have label repositioning with the mouse available (as listed on this Wiki page: http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/Release1.4) . We don't have it yet. However, the underlying mechanism is in place and I have modified Thermal Ellipsoids to offset atom labels by an amount equal to the longest half-axis of the atom's displayed ellipsoid. That will be in tomorrow's build. Furthermore, I made it so that you can set the label-offset attribute with the "setattr" command. This required some mods to that command since the label-offset attribute is a vector and the setattr command didn't support non-scalar values. So in tomorrow's build this command will move selected atom's labels half an angstrom to the right: setattr a labelOffset 0.5,0,0 sel It's not 100% certain that this is how setting vector attributes will work in the 1.4 release, but if it changes I'll let people know. > While I'm on the ellipsoid topic; has there been progress on > overlaying axis on the ellipsoids? I know I originally asked about > axis and shaded octants but after using the anisotropic option for > the last month or so I notice tat there is a tremendous amount of > information conveyed with just the color and shape and shaded > octants may not add much information (in fact it may just confuse > the issue). Well....no, not really. I've had a lot of my time tied up with system administration issues related to a new Linux cluster we're converting over to (principally getting an efficient reliable backup system implemented), but the good news is that that time commitment is winding down and I will have more time for issues such as these that I would prefer to work on. So hopefully soon. The only thing I've managed to do is get some of the underlying infrastructure for the probability calculator done (basically conscripting a Simpson's Rule numerical integrator once I understood what I needed). > Your implementation of thermal ellipsoids is very, very useful! Thanks! --Eric Eric Pettersen UCSF Computer Graphics Lab From pett at cgl.ucsf.edu Sun Aug 9 16:43:39 2009 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Sun, 9 Aug 2009 16:43:39 -0700 Subject: [Chimera-users] Moving atom labels In-Reply-To: References: Message-ID: On Aug 7, 2009, at 2:51 PM, Eric Pettersen wrote: > Furthermore, I made it so that you can set the label-offset attribute > with the "setattr" command. Ignore this. Use the commands Greg implemented for now (assuming for some reason that you wanted to use the command version). Those commands will likely change before the production release. Specifically, they will likely be incorporated as options to the label/ rlabel commands. --Eric Eric Pettersen USCF Computer Graphics Lab From mikeday at caltech.edu Mon Aug 10 18:05:42 2009 From: mikeday at caltech.edu (Michael Day) Date: Mon, 10 Aug 2009 18:05:42 -0700 Subject: [Chimera-users] Moving atom labels In-Reply-To: References: Message-ID: <37A69CAD-83BF-4BD7-B82D-8385A35E5DDF@caltech.edu> Greg and Eric, Thank you. I installed the build and it works great. The default offset when using thermal ellipsoids is very nice. I haven't figured out how to drag individual labels but that may be me or that I'm using a trackball, but the labeloffset command works well. I'm getting very positive feedback from my users! Thanks. New question, Is it possible to calculate electron density maps from a standard PDB format fcf file with the structure factors in it? SHELX is the small molecule standard and it will output reflection files. I know COOT will calculate the maps on the fly from this format but figures from COOT are NO MATCH for Chimera. It would be nice to be able to read the .fcf file and get maps back. If I try to use COOT calculated maps I have no control over the position of the map and it can be the same for trying to use CCP4 maps. Maps calculated in Chimera centered on the molecule would be useful beyond description. From the SHELX manual m = 6:Write a free-format CIF file containing h,k,l, Fo, ?(Fo), Fc and ? (phase angle in degrees) for the reflection list as defined for m = 1. This is the recommended format for the deposition of reflection data with the PDB, and is also the format required for the generation of refinement statistics and electron density maps using SHELXPRO An actal file # # h,k,l, Fo-squared, sigma(Fo-squared), Fc and phi(calc) # data_ta36 _shelx_title ' ta36 in P-1' _shelx_refln_list_code 6 _shelx_F_calc_maximum 147.61 _exptl_crystal_F_000 628.00 _reflns_d_resolution_high 0.7205 loop_ _symmetry_equiv_pos_as_xyz 'x, y, z' '-x, -y, -z' _cell_length_a 10.9827 _cell_length_b 11.4038 _cell_length_c 12.1961 _cell_angle_alpha 65.918 _cell_angle_beta 73.507 _cell_angle_gamma 76.655 loop_ _refln_index_h _refln_index_k _refln_index_l _refln_F_squared_meas _refln_F_squared_sigma _refln_F_calc _refln_phase_calc 1 0 0 548.13 8.13 23.91 0.0 2 0 0 713.05 6.90 27.04 0.0 3 0 0 4487.70 36.52 61.90 0.0 4 0 0 5185.71 41.46 70.98 0.0 And the relevant part of the corresponding SHELX ins file TITL ta36 in P-1 CELL 0.71073 10.9827 11.4038 12.1961 65.918 73.507 76.655 ZERR 1.00 0.0005 0.0006 0.0006 0.003 0.003 0.003 LATT 1 SFAC C H N O F S Cu UNIT 52 45 9 8 6 2 2 WGHT 0.000000 FVAR 0.66533 0.53147 CU1 7 -0.011240 0.599643 0.665074 11.00000 0.02325 0.03784 = 0.02594 -0.00922 -0.00439 -0.00980 O1 4 0.323760 0.794114 0.628981 11.00000 0.02076 0.03749 = 0.07654 -0.03652 -0.01288 -0.00180 Cheers, Mike <<< ------------------------------------------------------------------------> >> Dr. Michael W. Day Director - X-ray Crystallography Lab & Molecular Observatory California Institute of Technology Mail Code 139-74 Pasadena, CA 91125 <>< <>< <>< <>< <>< <>< <>< <>< <>< <>< Beckman Institute, Room 116 Phone: (626) 395-2734 Fax: (626) 449-4159 e-mail: mikeday at caltech.edu <<< ------------------------------------------------------------------------> >> On Aug 7, 2009, at 2:44 PM, Greg Couch wrote: On Thu, 6 Aug 2009, Michael Day wrote: > How does one change the position of atom labels? For small > coordination complexes the default atom labels land on the atom and > it would be nice to move them as a whole or individually so they are > alongside the atom ball or anisotropic ellipsoid. > > Cheers, > Mike In the next daily build, we will have interactive label moving, where you can pick a label and drag it around, and if you hold down the shift key, it will move in Z. It will default to the Control-button-3 mouse mode, but can be reassigned using the mouse mode preferences. You will also be able to change the label offsets using the command line, the "labeloffset x y z atom-spec" and "rlabeloffset x y z atom- spec" commands to set the offsets and "~labeloffset" and "~rlabeloffset" to reset them to the default behavior of adjusting the offset with the representation. For users with existing saved preferences, you might need to turn label dragging on by resetting the mouse mode preferences or by explicitly assigning it to Control-button-3. There's no icon for it yet in the mouse modes interface, but it will be the rightmost column for now. Since the label moving code is new, please send me feedback about how well it works for you. - Greg -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at cgl.ucsf.edu Tue Aug 11 11:22:05 2009 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Tue, 11 Aug 2009 11:22:05 -0700 Subject: [Chimera-users] Moving atom labels In-Reply-To: <37A69CAD-83BF-4BD7-B82D-8385A35E5DDF@caltech.edu> References: <37A69CAD-83BF-4BD7-B82D-8385A35E5DDF@caltech.edu> Message-ID: <4A81B6CD.5060202@cgl.ucsf.edu> Hi Michael, How difficult would it be for Chimera to compute x-ray maps from structure factors? For deposited Protein Databank models with structure factors, the Uppsala Electron Density Server (EDS) provides maps. http://eds.bmc.uu.se/eds/ These maps can be fetched by Chimera (File / Fetch by ID). The procedure the describe for computing 2fo-fc maps is quite intricate http://eds.bmc.uu.se/eds/eds_help.html#NITTY_GRITTY They are trying to verify the reported R-factor and do other sanity checks. Still it may be too complex a procedure even without the quality controls for us to put into Chimera. But we don't know much about crystallographic refinement software. Maybe you could provide more details to show us that it is in fact easy to compute the maps? It may be there are easy solutions to get externally generated maps to align with the models in Chimera. Both COOT and CCP4 know how to correctly align the PDB models and maps they calculate so that should be possible in Chimera too. I am not very knowledgable about COOT or CCP4 and any information about the alignment they use that you could provide might help us improve use of those maps in Chimera. Tom -------- Original Message -------- Subject: Re: [Chimera-users] Moving atom labels From: Michael Day To: Greg Couch , Eric Pettersen Date: 8/10/09 6:05 PM > Greg and Eric, > > Thank you. I installed the build and it works great. The default > offset when using thermal ellipsoids is very nice. I haven't figured > out how to drag individual labels but that may be me or that I'm using > a trackball, but the labeloffset command works well. > > I'm getting very positive feedback from my users! > > Thanks. > > New question, > > Is it possible to calculate electron density maps from a standard PDB > format fcf file with the structure factors in it? SHELX is the small > molecule standard and it will output reflection files. I know COOT > will calculate the maps on the fly from this format but figures from > COOT are NO MATCH for Chimera. It would be nice to be able to read the > .fcf file and get maps back. If I try to use COOT calculated maps I > have no control over the position of the map and it can be the same > for trying to use CCP4 maps. Maps calculated in Chimera centered on > the molecule would be useful beyond description. > * > * > *From the SHELX manual* > *m = 6*:Write a free-format CIF file containing h,k,l, Fo, ?(Fo), Fc > and ? (phase angle in > degrees) for the reflection list as defined for m = 1. This is the > recommended format for > the deposition of reflection data with the PDB, and is also the format > required for the > generation of refinement statistics and electron density maps using > SHELXPRO > > *An actal file* > # > # h,k,l, Fo-squared, sigma(Fo-squared), Fc and phi(calc) > # > data_ta36 > _shelx_title ' ta36 in P-1' > _shelx_refln_list_code 6 > _shelx_F_calc_maximum 147.61 > _exptl_crystal_F_000 628.00 > _reflns_d_resolution_high 0.7205 > > loop_ > _symmetry_equiv_pos_as_xyz > 'x, y, z' > '-x, -y, -z' > > _cell_length_a 10.9827 > _cell_length_b 11.4038 > _cell_length_c 12.1961 > _cell_angle_alpha 65.918 > _cell_angle_beta 73.507 > _cell_angle_gamma 76.655 > > loop_ > _refln_index_h > _refln_index_k > _refln_index_l > _refln_F_squared_meas > _refln_F_squared_sigma > _refln_F_calc > _refln_phase_calc > 1 0 0 548.13 8.13 23.91 0.0 > 2 0 0 713.05 6.90 27.04 0.0 > 3 0 0 4487.70 36.52 61.90 0.0 > 4 0 0 5185.71 41.46 70.98 0.0? > > *And the relevant part of the corresponding SHELX ins file* > TITL ta36 in P-1 > CELL 0.71073 10.9827 11.4038 12.1961 65.918 73.507 76.655 > ZERR 1.00 0.0005 0.0006 0.0006 0.003 0.003 0.003 > LATT 1 > SFAC C H N O F S Cu > UNIT 52 45 9 8 6 2 2 > > WGHT 0.000000 > FVAR 0.66533 0.53147 > CU1 7 -0.011240 0.599643 0.665074 11.00000 0.02325 > 0.03784 = > 0.02594 -0.00922 -0.00439 -0.00980 > O1 4 0.323760 0.794114 0.628981 11.00000 0.02076 > 0.03749 = > 0.07654 -0.03652 -0.01288 -0.00180? > > > Cheers, > Mike > > <<< > ------------------------------------------------------------------------>>> > Dr. Michael W. Day > Director - X-ray Crystallography Lab & Molecular Observatory > California Institute of Technology > Mail Code 139-74 > Pasadena, CA 91125 > > <>< <>< <>< <>< <>< <>< <>< <>< <>< <>< > > Beckman Institute, Room 116 > Phone: (626) 395-2734 > Fax: (626) 449-4159 > e-mail: mikeday at caltech.edu > <<< > ------------------------------------------------------------------------>>> > > On Aug 7, 2009, at 2:44 PM, Greg Couch wrote: > > On Thu, 6 Aug 2009, Michael Day wrote: > >> How does one change the position of atom labels? For small >> coordination complexes the default atom labels land on the atom and >> it would be nice to move them as a whole or individually so they are >> alongside the atom ball or anisotropic ellipsoid. >> >> Cheers, >> Mike > > In the next daily build, we will have interactive label moving, where > you can pick a label and drag it around, and if you hold down the > shift key, it will move in Z. It will default to the Control-button-3 > mouse mode, but can be reassigned using the mouse mode preferences. > You will also be able to change the label offsets using the command > line, the "labeloffset x y z atom-spec" and "rlabeloffset x y z > atom-spec" commands to set the offsets and "~labeloffset" and > "~rlabeloffset" to reset them to the default behavior of adjusting the > offset with the representation. > > For users with existing saved preferences, you might need to turn > label dragging on by resetting the mouse mode preferences or by > explicitly assigning it to Control-button-3. There's no icon for it > yet in the mouse modes interface, but it will be the rightmost column > for now. > > Since the label moving code is new, please send me feedback about how > well it works for you. > > - Greg > > ------------------------------------------------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From hbahudha at fau.edu Tue Aug 11 19:59:08 2009 From: hbahudha at fau.edu (Harinathachari Bahudhanapati) Date: Tue, 11 Aug 2009 22:59:08 -0400 (EDT) Subject: [Chimera-users] command 'buriedArea' Message-ID: <1234147.1250045948800.JavaMail.hbahudha@fau.edu> Hi all, Could you explain the command 'measure buriedArea' ? I am trying yesterday's daily build. Could you give me an example how to use this command? I think I am mangling the command, somehow. Could you help me? Thank you very much. Sincerely, Hari From goddard at cgl.ucsf.edu Tue Aug 11 20:11:41 2009 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Tue, 11 Aug 2009 20:11:41 -0700 Subject: [Chimera-users] command 'buriedArea' In-Reply-To: <1234147.1250045948800.JavaMail.hbahudha@fau.edu> References: <1234147.1250045948800.JavaMail.hbahudha@fau.edu> Message-ID: <4A8232ED.8010909@cgl.ucsf.edu> Hi Hari, open 1a0m measure buried :.A :.B This measures the buried area between chains A and B. Here's the measure command documentation http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html and some info on how to specify different sets of atoms http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html Tom -------- Original Message -------- Subject: [Chimera-users] command 'buriedArea' From: Harinathachari Bahudhanapati To: chimera-users at cgl.ucsf.edu Date: 8/11/09 7:59 PM > Hi all, > Could you explain the command 'measure buriedArea' ? I am > trying yesterday's daily build. Could you give me an example how to use > this command? I think I am mangling the command, somehow. Could you > help me? > > Thank you very much. > > Sincerely, > Hari > From hbahudha at fau.edu Wed Aug 12 09:57:54 2009 From: hbahudha at fau.edu (Harinath) Date: Wed, 12 Aug 2009 12:57:54 -0400 Subject: [Chimera-users] command 'buriedArea' - question In-Reply-To: <4A8232ED.8010909@cgl.ucsf.edu> References: <1234147.1250045948800.JavaMail.hbahudha@fau.edu> <4A8232ED.8010909@cgl.ucsf.edu> Message-ID: <999890C2-A0D1-481B-B2AD-E52F7784962C@fau.edu> Dear Tom, Here is the reply log when I used the 'measure buried' command in a modeled complex. What am I missing in the pdb file and how erroneous are the calculations? Please find the pdb file at the bottom to repeat the error. ______________________________________ Calculation of some surface components failed. Using only single surface component. This may give inaccurate areas if surfaces of either set of atoms or the combined set are disconnected. Buried solvent accessible surface area = 1333.97 (A1 = 10302.4, A2 = 7673.48, A12 = 15307.9) Buried solvent excluded surface area = 818.456 (A1 = 8044.45, A2 = 6390.68, A12 = 12798.2) ______________________________________ Sincerely, Hari -------------- next part -------------- A non-text attachment was scrubbed... Name: mp9-1br9-best.pdb Type: application/octet-stream Size: 191867 bytes Desc: not available URL: -------------- next part -------------- On Aug 11, 2009, at 11:11 PM, Tom Goddard wrote: > Hi Hari, > > open 1a0m > measure buried :.A :.B > > This measures the buried area between chains A and B. Here's the > measure command documentation > > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html > > and some info on how to specify different sets of atoms > > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html > > Tom > > > > -------- Original Message -------- > Subject: [Chimera-users] command 'buriedArea' > From: Harinathachari Bahudhanapati > To: chimera-users at cgl.ucsf.edu > Date: 8/11/09 7:59 PM >> Hi all, >> Could you explain the command 'measure buriedArea' ? I am >> trying yesterday's daily build. Could you give me an example how to >> use this command? I think I am mangling the command, somehow. Could >> you help me? >> >> Thank you very much. >> >> Sincerely, >> Hari >> > From goddard at cgl.ucsf.edu Wed Aug 12 10:24:34 2009 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Wed, 12 Aug 2009 10:24:34 -0700 Subject: [Chimera-users] command 'buriedArea' - question In-Reply-To: <999890C2-A0D1-481B-B2AD-E52F7784962C@fau.edu> References: <1234147.1250045948800.JavaMail.hbahudha@fau.edu> <4A8232ED.8010909@cgl.ucsf.edu> <999890C2-A0D1-481B-B2AD-E52F7784962C@fau.edu> Message-ID: <4A82FAD2.4030605@cgl.ucsf.edu> Hi Hari, This warning message happens because the Chimera code that computes solvent excluded surfaces does not always work. The code is complex (~20000 lines of fortran) and we are working on replacing it with some more reliable code in the Chimera 1.4 release in a few months. Here's what the warning means and how to determine if there is a problem. The surface calculation computes each connected part of the solvent excluded surface. There might be disconnected patches of surface for two reasons. The common one is that there are cavities on the interior of the protein, so a surface bubble appears on the inside of the protein and it is not connected to the exterior surface. The second case is if the set of atoms is in 2 or more clumps that don't touch each other. The message that calculating some surface components failed means that either that surfaces for some interior cavities or some extra exterior clumps of atoms could not be computed. If you have disconnected clumps of atoms in either of your two atom sets that are involved in buried surface contacts and you get this warning then the reported areas will be wrong. That is a somewhat unusual case. If you have interior cavities, those generally are not part of the contacts and the reported areas will be correct. The case to watch out for here is if the surface for the combined set of atoms has a cavity at the interface between the two atom sets, then that cavity won't be computed and the answer will be wrong. There are two things you can do. You can try to get the surface computation to work using some tricks suggested in this mailing list message http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-March/002417.html or you can try to figure out whether your case is in fact giving correct areas in spite of the surface calculation problem. For the latter you could make PDB files for each atom set, and for the combined atom sets, and use menu entry Actions / Surface / Show to create the three solvent excluded surfaces and see which ones fail to compute all components, and for those look at where the cavities are (at interface or not) and whether external atom clumps are present. Tom -------- Original Message -------- Subject: command 'buriedArea' - question From: Harinath To: Tom Goddard Date: 8/12/09 9:57 AM > Dear Tom, > Here is the reply log when I used the 'measure > buried' command in a modeled complex. What am I missing in the pdb > file and how erroneous are the calculations? > > Please find the pdb file at the bottom to repeat the error. > ______________________________________ > Calculation of some surface components failed. Using only single > surface component. This may give inaccurate areas if surfaces of > either set of atoms or the combined set are disconnected. > Buried solvent accessible surface area = 1333.97 (A1 = 10302.4, A2 = > 7673.48, A12 = 15307.9) > Buried solvent excluded surface area = 818.456 (A1 = 8044.45, A2 = > 6390.68, A12 = 12798.2) > ______________________________________ > > Sincerely, > Hari > > > > > > > On Aug 11, 2009, at 11:11 PM, Tom Goddard wrote: > >> Hi Hari, >> >> open 1a0m >> measure buried :.A :.B >> >> This measures the buried area between chains A and B. Here's the >> measure command documentation >> >> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html >> >> and some info on how to specify different sets of atoms >> >> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html >> >> Tom >> >> >> >> -------- Original Message -------- >> Subject: [Chimera-users] command 'buriedArea' >> From: Harinathachari Bahudhanapati >> To: chimera-users at cgl.ucsf.edu >> Date: 8/11/09 7:59 PM >>> Hi all, >>> Could you explain the command 'measure buriedArea' ? I am >>> trying yesterday's daily build. Could you give me an example how to >>> use this command? I think I am mangling the command, somehow. Could >>> you help me? >>> >>> Thank you very much. >>> >>> Sincerely, >>> Hari >>> >> > From huy.bui at mol.biol.ethz.ch Thu Aug 13 00:58:24 2009 From: huy.bui at mol.biol.ethz.ch (Bui Khanh Huy) Date: Thu, 13 Aug 2009 09:58:24 +0200 Subject: [Chimera-users] Saving session with IMOD model Message-ID: <7B0340B3488BF24DAEB8C70665C6B058981F4C@EX4.d.ethz.ch> Hi all, I opened an IMOD model in Chimera. After I opened a saved session with Chimera, the IMOD model disappeared. Is this because of my version (alpha 1.4 (build 26844))? Best, Huy -------------------------------- Huy K. Bui Institute of Molecular Biology and Biophysics Swiss Federal Institute of Technology (ETH Z?rich) ETH H?nggerberg, HPK F7 CH-8093 Z?rich, Switzerland phone: +41 1-633-2462 fax: : +41 1-633-1073 e-mail: huy.bui at mol.biol.ethz.ch -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Thu Aug 13 08:18:42 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 13 Aug 2009 08:18:42 -0700 Subject: [Chimera-users] Saving session with IMOD model In-Reply-To: <7B0340B3488BF24DAEB8C70665C6B058981F4C@EX4.d.ethz.ch> References: <7B0340B3488BF24DAEB8C70665C6B058981F4C@EX4.d.ethz.ch> Message-ID: <8FA09FC8-733F-41CF-A9A6-648299FAF3E4@cgl.ucsf.edu> Hi Huy, Sorry, but in all versions of Chimera (so far), IMOD surfaces are not saved in sessions. 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 http://www.cgl.ucsf.edu/home/meng/index.html On Aug 13, 2009, at 12:58 AM, Bui Khanh Huy wrote: > Hi all, > I opened an IMOD model in Chimera. After I opened a saved session > with Chimera, the IMOD model disappeared. Is this because of my > version (alpha 1.4 (build 26844))? > Best, > Huy From meng at cgl.ucsf.edu Thu Aug 13 09:33:05 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 13 Aug 2009 09:33:05 -0700 Subject: [Chimera-users] extending DNA for a figure References: Message-ID: On Aug 13, 2009, at 12:00 AM, Janet G Yang wrote: > Hi Elaine, > > I'm a grad student in Geeta Narlikar's lab, and I've been to a few > of your Chimera tutorials at UCSF and found them very helpful. I > have a less analytical and more aesthetic structural task, and I'm > wondering if you might have any insight. I would like to make a > figure showing the structure of the nucleosome with some extra DNA > docked in at the edges. The crystal structure of the nucleosome > contains 147 bp wrapped around the histone octamer, and I would like > to extend out the DNA on one side. I think I could just take the > structure of the nucleosome, and that of some B form DNA, and > somehow align them together. Is there a good way to do this? > > Thanks a bunch > janet Hi Janet, My guess is that lots of people run across similar aesthetic issues -- making a figure is partly art, after all! Everything you say sounds reasonable. First you would need to get the extra B-form DNA, then position it relative to the nucleosome structure. (1) Getting the extra DNA. This could be from another PDB structure, or built using standard B-form parameters. The NDB atlas lists nucleic acid structures in categories such as B-DNA; you can use "File...Fetch by ID" in Chimera to fetch using NDB identifiers. Those structures might be shorter or less regular than what you need. Here is a server that will build canonical structures to order: (I admit I haven't actually tried using it, but it looks promising) (2) Positioning the extra DNA relative to the nucleosome structure. You could position it by hand and/or by matching overlapping sets of atoms. Positioning by hand requires activating/deactivating models for motion so that they can be moved relative to one another -- you would do that with the checkboxes below the Command Line, or with the "A(ctive)" checkboxes in the Model Panel. Matching would be done with the "match" command. It may be tedious to figure out the atom naming in the two structures and then figure out which sets of atoms to match to get the best result, but I don't really see any way around that trial and error process, unless you are really skilled at just positioning the structures by hand. I would probably do some matching and then maybe make slight manual adjustments depending on how it looked. My answer was based on the understanding that you just want the DNA to trail away in a somewhat straight path, rather than continuing on curling as in the nucleosome. If you wanted that continued curling, there might be some fancy ways to do it with several copies of a curved segment and symmetry operators, but that is beyond my skill set! 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 http://www.cgl.ucsf.edu/home/meng/index.html From goddard at cgl.ucsf.edu Thu Aug 13 11:13:45 2009 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Thu, 13 Aug 2009 11:13:45 -0700 Subject: [Chimera-users] Saving session with IMOD model In-Reply-To: <7B0340B3488BF24DAEB8C70665C6B058981F4C@EX4.d.ethz.ch> References: <7B0340B3488BF24DAEB8C70665C6B058981F4C@EX4.d.ethz.ch> Message-ID: <4A8457D9.4060005@cgl.ucsf.edu> Hi Huy, As Elaine mentioned, IMOD models aren't recorded in Chimera session files. The IMOD files can be very large so I'm not sure we want the data embedded in Chimera session files. An alternative is to remember the path to the IMOD file in the session file. If you recolor or delete parts of the IMOD model that method won't work. Another request to save IMOD models in sessions is already on the Chimera request list, item 101. http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/requests I've added your name to that request. Tom -------- Original Message -------- Subject: [Chimera-users] Saving session with IMOD model From: Bui Khanh Huy Date: 8/13/09 12:58 AM > Hi all, > > > > I opened an IMOD model in Chimera. After I opened a saved session with > Chimera, the IMOD model disappeared. Is this because of my version > (alpha 1.4 (build 26844))? > > > > Best, > > Huy > > > > -------------------------------- > > Huy K. Bui > Institute of Molecular Biology and Biophysics > Swiss Federal Institute of Technology (ETH Z?rich) > ETH H?nggerberg, HPK F7 > CH-8093 Z?rich, Switzerland > From simon_sauve at hc-sc.gc.ca Thu Aug 13 13:13:10 2009 From: simon_sauve at hc-sc.gc.ca (Simon Sauve) Date: Thu, 13 Aug 2009 16:13:10 -0400 Subject: [Chimera-users] Dr. Simon Sauve is out of the office. Message-ID: I will be out of the office starting 2009-08-07 and will not return until 2009-08-24. You can reach me at simsauve at yahoo.ca & 819-776-2134 (cell: 819-923-2143). In case of an emergency, please contact Dr. Yves Aubin by e-mail or @ 613-941-6155 From svetlana.lockwood at email.wsu.edu Thu Aug 13 13:40:05 2009 From: svetlana.lockwood at email.wsu.edu (Lockwood, Svetlana) Date: Thu, 13 Aug 2009 20:40:05 +0000 Subject: [Chimera-users] Scripting with Chimera Message-ID: <18BE8643117BC843900B286926446554055D3EF4@BL2PRD0102MB007.prod.exchangelabs.com> Hi All, Here's my problem: I need to calculate hydrogen bonds for several thousand PDB files. Chimera has nice hbonds command line command - sweet! Since Chimera was vanishing from Ubuntu, I had to switch to other available tools, i.e. Windows. After I got my python up and running and communicating with Chimera modules. Here's my very simple pseudo-idea: foreach file in the list: open PDB file construct output filename from input filename calculate & and write out hydrogen bonds using hbonds command close file end foreach Short and sweet. Except that one cannot use a command line command within python code. Command files don't work either because they do not understand python commands. Someone must have run into the same problem before me :-) Is there a way around this problem? Thank you, Svetlana -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Thu Aug 13 14:05:37 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 13 Aug 2009 14:05:37 -0700 Subject: [Chimera-users] Scripting with Chimera In-Reply-To: <18BE8643117BC843900B286926446554055D3EF4@BL2PRD0102MB007.prod.exchangelabs.com> References: <18BE8643117BC843900B286926446554055D3EF4@BL2PRD0102MB007.prod.exchangelabs.com> Message-ID: <932A6B93-082B-4E54-BF04-04007A38C393@cgl.ucsf.edu> Hi Svetlana, Every Chimera command can be pythonized with runCommand, as detailed in this previous post by Eric: We have reproduced the Ubuntu problem and are looking into it. 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 http://www.cgl.ucsf.edu/home/meng/index.html On Aug 13, 2009, at 1:40 PM, Lockwood, Svetlana wrote: > Hi All, > > Here's my problem: I need to calculate hydrogen bonds for several > thousand PDB files. Chimera has nice hbonds command line command - > sweet! Since Chimera was vanishing from Ubuntu, I had to switch to > other available tools, i.e. Windows. After I got my python up and > running and communicating with Chimera modules. Here's my very > simple pseudo-idea: > > foreach file in the list: > open PDB file > construct output filename from input filename > calculate & and write out hydrogen bonds using hbonds command > close file > end foreach > > Short and sweet. Except that one cannot use a command line command > within python code. Command files don't work either because they do > not understand python commands. Someone must have run into the same > problem before me :-) Is there a way around this problem? > > Thank you, > Svetlana From svetlana.lockwood at email.wsu.edu Thu Aug 13 14:19:48 2009 From: svetlana.lockwood at email.wsu.edu (Lockwood, Svetlana) Date: Thu, 13 Aug 2009 21:19:48 +0000 Subject: [Chimera-users] Scripting with Chimera In-Reply-To: <932A6B93-082B-4E54-BF04-04007A38C393@cgl.ucsf.edu> References: <18BE8643117BC843900B286926446554055D3EF4@BL2PRD0102MB007.prod.exchangelabs.com>, <932A6B93-082B-4E54-BF04-04007A38C393@cgl.ucsf.edu> Message-ID: <18BE8643117BC843900B286926446554055D3F16@BL2PRD0102MB007.prod.exchangelabs.com> Thank you! --sv ________________________________________ From: Elaine Meng [meng at cgl.ucsf.edu] Sent: Thursday, August 13, 2009 2:05 PM To: Lockwood, Svetlana Cc: chimera-users at cgl.ucsf.edu Subject: Re: [Chimera-users] Scripting with Chimera Hi Svetlana, Every Chimera command can be pythonized with runCommand, as detailed in this previous post by Eric: We have reproduced the Ubuntu problem and are looking into it. 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 http://www.cgl.ucsf.edu/home/meng/index.html On Aug 13, 2009, at 1:40 PM, Lockwood, Svetlana wrote: > Hi All, > > Here's my problem: I need to calculate hydrogen bonds for several > thousand PDB files. Chimera has nice hbonds command line command - > sweet! Since Chimera was vanishing from Ubuntu, I had to switch to > other available tools, i.e. Windows. After I got my python up and > running and communicating with Chimera modules. Here's my very > simple pseudo-idea: > > foreach file in the list: > open PDB file > construct output filename from input filename > calculate & and write out hydrogen bonds using hbonds command > close file > end foreach > > Short and sweet. Except that one cannot use a command line command > within python code. Command files don't work either because they do > not understand python commands. Someone must have run into the same > problem before me :-) Is there a way around this problem? > > Thank you, > Svetlana From carr at berkeley.edu Thu Aug 13 17:50:04 2009 From: carr at berkeley.edu (Marcus Carr) Date: Thu, 13 Aug 2009 17:50:04 -0700 Subject: [Chimera-users] displaying two surfaces Message-ID: <3fe750ba0908131750n67d9dbd1q991f2e0db430506a@mail.gmail.com> I am trying to create a figure that encloses three residues in a protein in one surface and the rest of the protein in another. I put the three residues into one group using surfcat and the rest of the protein in another. When I try adjust the surface transparency, the three-residue surface all but disappears. If I set transparency to 0%, I appears normal. If I increase it even to just 1%, it almost completely disappears. It looks like wherever this three-residue surface is inside the protein surface, it only shows if the transparency of three-residue is set to 0%. All this is with the protein surface set to 50%. I'm not sure whether this list accepts attachments, but I put in screen shots of what it looks like. marcus -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 0pct-surface.png Type: image/png Size: 150236 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 10pct-surface.png Type: image/png Size: 153150 bytes Desc: not available URL: From goddard at cgl.ucsf.edu Thu Aug 13 18:05:59 2009 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Thu, 13 Aug 2009 18:05:59 -0700 Subject: [Chimera-users] displaying two surfaces In-Reply-To: <3fe750ba0908131750n67d9dbd1q991f2e0db430506a@mail.gmail.com> References: <3fe750ba0908131750n67d9dbd1q991f2e0db430506a@mail.gmail.com> Message-ID: <4A84B877.40408@cgl.ucsf.edu> Hi Marcus, Unfortunately Chimera does not handle transparency correctly when 2 or more models are transparent. Maybe there is a way to get your two surfaces as pieces of a single surface model which could have there transparency set and would display correctly, but I can't think how. Another trick that would help you is to make the yellow surface have a higher model number so it is drawn after the white surface. With the yellow surface in front that will give more correct appearance as the white transparent surface won't overdraw the yellow one. I guess the surface command is going to produce the same model number as the molecule for both surfaces. Maybe creating the yellow one after the white one will control the drawing order. If that fails you may need to save the 3 residues in a separate PDB and surface it so it can have a distinct model number. Tom -------- Original Message -------- Subject: [Chimera-users] displaying two surfaces From: Marcus Carr To: chimera-users at cgl.ucsf.edu Date: 8/13/09 5:50 PM > I am trying to create a figure that encloses three residues in a protein > in one surface and the rest of the protein in another. I put the three > residues into one group using surfcat and the rest of the protein in > another. > > When I try adjust the surface transparency, the three-residue surface > all but disappears. If I set transparency to 0%, I appears normal. If > I increase it even to just 1%, it almost completely disappears. It > looks like wherever this three-residue surface is inside the protein > surface, it only shows if the transparency of three-residue is set to > 0%. All this is with the protein surface set to 50%. I'm not sure > whether this list accepts attachments, but I put in screen shots of what > it looks like. > > marcus > > From meng at cgl.ucsf.edu Fri Aug 14 09:23:53 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 14 Aug 2009 09:23:53 -0700 Subject: [Chimera-users] displaying two surfaces In-Reply-To: <4A84B877.40408@cgl.ucsf.edu> References: <3fe750ba0908131750n67d9dbd1q991f2e0db430506a@mail.gmail.com> <4A84B877.40408@cgl.ucsf.edu> Message-ID: Hi Marcus et al., You can see which surface model is "first" by looking in the Model Panel. If you want the opposite order than what is listed in the Model Panel, just use the Model Panel to close the one that is listed first. Then when you recreate that surface it will be listed below the other. Example 1d86, with DNA (category main) and netropsin (category ligand). Commands: open 1d86 color yellow main color red ligand set bg_color white surface main surface ligand surftransparency 50 start Model Panel -- the red transparent surface is disappearing behind the yellow transparent surface, and the Model Panel shows the main surface listed above the ligand surface. In the Model Panel, click the line for the main surface on the left and click the "close" button on the right (not the main "Close" button on the bottom!). surface main -- now the main surface is listed lower in the Model Panel and the red ligand surface shows through the yellow main surface I hope this helps, Elaine On Aug 13, 2009, at 6:05 PM, Thomas Goddard wrote: > Hi Marcus, > > Unfortunately Chimera does not handle transparency correctly when > 2 or > more models are transparent. Maybe there is a way to get your two > surfaces as pieces of a single surface model which could have there > transparency set and would display correctly, but I can't think how. > Another trick that would help you is to make the yellow surface have a > higher model number so it is drawn after the white surface. With the > yellow surface in front that will give more correct appearance as the > white transparent surface won't overdraw the yellow one. I guess the > surface command is going to produce the same model number as the > molecule for both surfaces. Maybe creating the yellow one after the > white one will control the drawing order. If that fails you may > need to > save the 3 residues in a separate PDB and surface it so it can have a > distinct model number. > > Tom > > > -------- Original Message -------- > Subject: [Chimera-users] displaying two surfaces > From: Marcus Carr > To: chimera-users at cgl.ucsf.edu > Date: 8/13/09 5:50 PM > >> I am trying to create a figure that encloses three residues in a >> protein >> in one surface and the rest of the protein in another. I put the >> three >> residues into one group using surfcat and the rest of the protein in >> another. >> >> When I try adjust the surface transparency, the three-residue surface >> all but disappears. If I set transparency to 0%, I appears >> normal. If >> I increase it even to just 1%, it almost completely disappears. It >> looks like wherever this three-residue surface is inside the protein >> surface, it only shows if the transparency of three-residue is set to >> 0%. All this is with the protein surface set to 50%. I'm not sure >> whether this list accepts attachments, but I put in screen shots >> of what >> it looks like. >> >> marcus >> >> > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From meng at cgl.ucsf.edu Fri Aug 14 13:13:59 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 14 Aug 2009 13:13:59 -0700 Subject: [Chimera-users] Chimera frame storage director In-Reply-To: References: Message-ID: <73130CD0-EAF6-4D44-8DF6-D6672190DF2C@cgl.ucsf.edu> On Aug 14, 2009, at 12:34 PM, Tom Guu wrote: > Dear Dr. Meng, > > This is Tom Guu from Rice University. I am using chimera to make > some animation for my virus structure, that I would like to present > at my defense ten days from today. I encountered a problem with > Chimera with the image storage issues. > > I am able to make movies, but they are generally very short, last > for a few seconds, and the frames are generally stored at a /tmp > folder. Since the /tmp folder in our computer server has quite > limited spaces, once I perform a more complex animation, errors > messages would pop up (each ppm is about 4MB and sometime that's > over 300 frames will fill up the tmp dictory). I am thinking about > storing frame files onto an external hard drive (200-300GB), which > can handle many more frames. So I go into 'movie recorder" under > which there is a "frame options". I specified the dictory for > frames to my external dirve (also clicked on "Set Input > Location"). Then re-execute my command (Open, click on cmd file > which cotains the script), well... the frames seemed to be stored > at the same /tmp location (nothing was written onto my external > drive). Is there a way that I can do to make the frames stored at > the external drive? If the frames are stored on the external > drive, is it going to affect the encoding process? > > In addition, I am also trying Chimera on my windows system > (Vista). I was able to excute the command (cmd files) without any > problem. The molecule is spinning as it should in the chimera. > However, when I opened up the encoded movie, it is just a blank > screen (with no molecule in sight). I check the directory (also > another /tmp directory), and I can see the ppm files were being > written. Then a screen popped up on my computer, C:\Program Files > \Chimera\bin\ffmpeg.exe The screen was on for at lesat 20-30 secs, > then the movie is made. However, as I said, I didn't see any movie > on my computer screen though I did find the "help command" and I > am currently don't seem to be able to find the answers to my > problems. Any suggestion? > > Thanks for such a long email. I much appreciate your help. > > Regards, > Tom Hi Tom, If you are using the movie command to record the movie, you should use the movie command options to specify the directory (for example, a command something like "movie record directory my-directory-path"). The "frame options" in the Movie Recorder graphical interface only affect recording with that graphical interface, not with the command. However, if you *are* using the Movie Recorder to record and it seems to be ignoring your setting, please use "Help... Report a Bug" in the Chimera menu to send us a problem report. Include a description, and if you want feedback, your email address. I am not sure I understand your second issue. All I can say is that even though a movie file may appear, it takes a while for the ffmpeg program to fully create it, so you have to be patient and wait until ffmpeg is done before you can open the movie and play it back. Was the movie OK after ffmpeg was done? If not, again you may want to use "Help... Report a Bug" and include any relevant information. This mechanism also allows files to be attached to the report. Besides "help command" for commands (for example, "help movie" to see your local copy of the URL given above), the Chimera Help menu provides several routes into the documentation (including "Help... Search documentation") and you can click the Help button on most dialogs to see the corresponding manual pages. For future reference, it is better to send Chimera questions to chimera-users at cgl.ucsf.edu than to me personally, unless you are including private data. This allows others to benefit from the information, and other staff to answer your question if I am unavailable or don't know the answer. Best wishes for success and triumph at your defense! Elaine ===== Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco From tomguu at rice.edu Fri Aug 14 14:17:25 2009 From: tomguu at rice.edu (Tom Guu) Date: Fri, 14 Aug 2009 16:17:25 -0500 Subject: [Chimera-users] surftransparency Message-ID: <1CDF46F8044B482AA3F43289520C9DBC@TomPC> Hi, I am trying to use the surftransparecy function on a EM-map (surface), and don't seem to be able to get it to work. I read on the documentation page, is this command specific for atoms and not for an entire EM map? I know I can use show or hide for displaying EM map, just wonder what other command can make the EM map gradually disappear or appear. Thanks a bunch. Regards, Tom -------------- next part -------------- An HTML attachment was scrubbed... URL: From kparent at ucsd.edu Mon Aug 17 11:23:06 2009 From: kparent at ucsd.edu (Kristin Parent) Date: Mon, 17 Aug 2009 11:23:06 -0700 (PDT) Subject: [Chimera-users] erase octant question Message-ID: <45512.132.239.185.230.1250533386.squirrel@acs-webmail.ucsd.edu> Hello, I was wondering if you could help me. I am trying to visualize a 3D density map from a cryo-TEM reconstruction of a virus (ccp4 format). I would like to use the "erase octant" function (link below), but actually erase a full quarter of the map to see inside the interior. I would like to do it accurately, and not by dragging the subregions box by hand. Can you help me understand how to set the command line function in order to do this? Thanks in advance. Kristin http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#octant Kristin Parent, Ph.D. University of California, San Diego Department of Chemistry and Biochemistry 9500 Gilman Drive, NSB 4104A, MC-0378 La Jolla, CA, 92093-0378 (858) 534-8038 From meng at cgl.ucsf.edu Tue Aug 18 13:08:04 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 18 Aug 2009 13:08:04 -0700 Subject: [Chimera-users] surftransparency In-Reply-To: <1CDF46F8044B482AA3F43289520C9DBC@TomPC> References: <1CDF46F8044B482AA3F43289520C9DBC@TomPC> Message-ID: Hi Tom, It depends what version of Chimera you are using. In older versions it only works for molecular surfaces. In newer versions (daily builds from late June 2009 onwards) it works for the kind of surface you have and has a "frames" argument for scripting gradual changes. You might be looking at documentation that is not synchronized with your download. If you use the Help menu or "help" command, that will show documentation that goes with your downloaded version. If you go to the Web, it may be for a totally different version. It should work if you have a daily build from sometime in the last several weeks. Here is the latest documentation: You would just specify your surface by model number, for example "surftrans 100 #0 120" (change transparency of surface model #0 to completely transparent over 120 frames). 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 http://www.cgl.ucsf.edu/home/meng/index.html On Aug 14, 2009, at 2:17 PM, Tom Guu wrote: > Hi, > > I am trying to use the surftransparecy function on a EM-map > (surface), and don't seem to be able to get it to work. I read on > the documentation page, is this command specific for atoms and not > for an entire EM map? I know I can use show or hide for displaying > EM map, just wonder what other command can make the EM map gradually > disappear or appear. Thanks a bunch. > > Regards, > Tom From goddard at cgl.ucsf.edu Tue Aug 18 14:04:28 2009 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Tue, 18 Aug 2009 14:04:28 -0700 Subject: [Chimera-users] erase octant question In-Reply-To: <45512.132.239.185.230.1250533386.squirrel@acs-webmail.ucsd.edu> References: <45512.132.239.185.230.1250533386.squirrel@acs-webmail.ucsd.edu> Message-ID: <4A8B175C.3060008@cgl.ucsf.edu> Hi Kristin, Here are some commands to take a wedge out of a virus. I'll use example EMDB 1408 which is a small 63^3 map. volume #0 region 0,0,0,31,31,62 This shows a 90 degree wedge of the map, grid points with x and y indices from 0 to 31 (region argument is imin,jmin,kmin,imax,jmax,kmax). If I wanted to see the complement of this wedge (the remaining 3/4 of the virus) one trick would be to open the map 4 times, or one time and use the volume dialog File / Duplicate 3 times. Then create the 4 wedges: volume #0 region 0,0,0,31,31,62 volume #1 region 31,0,0,62,31,62 volume #2 region 0,31,0,31,62,62 volume #3 region 31,31,0,62,62,62 then just show 3 of the maps. You can also use the vop octant command to get a similar effect. Normally that command removes just one octant (1/8 of the virus) and you asked for 1/4. But it can be tricked into removing 1/4 by specifying a center vop #0 octant center 31,31,0 shows the quadrant (indices 31 <= i <= 62, 31 <= j <= 62) while vop #0 ~octant center 31,31,0 shows the complement. This is different from the volume region command in that it makes a new map and sets some of the grid values to zero. The volume region command simply restricts display of the original map to a sub-box. This creates a different appearance where the volume region result gives flat surface faces where the map was clipped (due to volume cap high values at box faces option), while the vop octant version gives curved surfaces at the cut because it is just making a contour surface between the high map density values and the zero values at the next grid point. To produce flatter surface appearance at the cut value with the vop octant command you can fill the masked out grid points with a large negative number instead of 0. vop #0 octant center 31,31,0 fill -1000 Use commands "help vop" and "help volume" to show the Chimera documentation for more details. None of these commands are working in the Chimera 1.4 daily builds from the past 2 weeks because of a bug introduced in command parsing. So use the Chimera 1.3 production release. The bug should be fixed in the daily builds by Thursday. Tom -------- Original Message -------- Subject: [Chimera-users] erase octant question From: Kristin Parent To: chimera-users at cgl.ucsf.edu Date: 8/17/09 11:23 AM > Hello, > > I was wondering if you could help me. I am trying to visualize a 3D > density map from a cryo-TEM reconstruction of a virus (ccp4 format). I > would like to use the "erase octant" function (link below), but actually > erase a full quarter of the map to see inside the interior. I would like > to do it accurately, and not by dragging the subregions box by hand. Can > you help me understand how to set the command line function in order to do > this? Thanks in advance. Kristin > > http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#octant > > Kristin Parent, Ph.D. > University of California, San Diego > Department of Chemistry and Biochemistry > 9500 Gilman Drive, NSB 4104A, MC-0378 > La Jolla, CA, 92093-0378 > (858) 534-8038 > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > -------------- next part -------------- A non-text attachment was scrubbed... Name: emd1408.jpg Type: image/jpeg Size: 38121 bytes Desc: not available URL: From goddard at cgl.ucsf.edu Tue Aug 18 15:14:39 2009 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Tue, 18 Aug 2009 15:14:39 -0700 Subject: [Chimera-users] erase octant question In-Reply-To: <4A8B175C.3060008@cgl.ucsf.edu> References: <45512.132.239.185.230.1250533386.squirrel@acs-webmail.ucsd.edu> <4A8B175C.3060008@cgl.ucsf.edu> Message-ID: <4A8B27CF.3080402@cgl.ucsf.edu> Hi Kristin, The "vop octant" command examples in my previous email should have used the "icenter" option instead of "center". The "icenter" option specifies the center in grid index units, while the "center" option specifies it in physical units (usually Angstroms). For the map I tested on the grid plane spacing was reported as 1 Angstrom so it didn't make any difference. Tom -------- Original Message -------- Subject: Re: [Chimera-users] erase octant question From: Tom Goddard To: Kristin Parent Date: 8/18/09 2:04 PM > Hi Kristin, > > Here are some commands to take a wedge out of a virus. I'll use > example EMDB 1408 which is a small 63^3 map. > > volume #0 region 0,0,0,31,31,62 > > This shows a 90 degree wedge of the map, grid points with x and y > indices from 0 to 31 (region argument is > imin,jmin,kmin,imax,jmax,kmax). If I wanted to see the complement of > this wedge (the remaining 3/4 of the virus) one trick would be to open > the map 4 times, or one time and use the volume dialog File / > Duplicate 3 times. Then create the 4 wedges: > > volume #0 region 0,0,0,31,31,62 > volume #1 region 31,0,0,62,31,62 > volume #2 region 0,31,0,31,62,62 > volume #3 region 31,31,0,62,62,62 > > then just show 3 of the maps. > > You can also use the vop octant command to get a similar effect. > Normally that command removes just one octant (1/8 of the virus) and > you asked for 1/4. But it can be tricked into removing 1/4 by > specifying a center > > vop #0 octant center 31,31,0 > > shows the quadrant (indices 31 <= i <= 62, 31 <= j <= 62) while > > vop #0 ~octant center 31,31,0 > > shows the complement. This is different from the volume region > command in that it makes a new map and sets some of the grid values to > zero. The volume region command simply restricts display of the > original map to a sub-box. This creates a different appearance where > the volume region result gives flat surface faces where the map was > clipped (due to volume cap high values at box faces option), while the > vop octant version gives curved surfaces at the cut because it is just > making a contour surface between the high map density values and the > zero values at the next grid point. To produce flatter surface > appearance at the cut value with the vop octant command you can fill > the masked out grid points with a large negative number instead of 0. > > vop #0 octant center 31,31,0 fill -1000 > > Use commands "help vop" and "help volume" to show the Chimera > documentation for more details. > > None of these commands are working in the Chimera 1.4 daily builds > from the past 2 weeks because of a bug introduced in command parsing. > So use the Chimera 1.3 production release. The bug should be fixed in > the daily builds by Thursday. > > Tom > > > > -------- Original Message -------- > Subject: [Chimera-users] erase octant question > From: Kristin Parent > To: chimera-users at cgl.ucsf.edu > Date: 8/17/09 11:23 AM >> Hello, >> >> I was wondering if you could help me. I am trying to visualize a 3D >> density map from a cryo-TEM reconstruction of a virus (ccp4 format). I >> would like to use the "erase octant" function (link below), but actually >> erase a full quarter of the map to see inside the interior. I would like >> to do it accurately, and not by dragging the subregions box by hand. Can >> you help me understand how to set the command line function in order >> to do >> this? Thanks in advance. Kristin >> >> http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#octant >> >> >> Kristin Parent, Ph.D. >> University of California, San Diego >> Department of Chemistry and Biochemistry >> 9500 Gilman Drive, NSB 4104A, MC-0378 >> La Jolla, CA, 92093-0378 >> From oliver.koch at sp.intervet.com Wed Aug 19 04:15:42 2009 From: oliver.koch at sp.intervet.com (Koch, O (Oliver)) Date: Wed, 19 Aug 2009 13:15:42 +0200 Subject: [Chimera-users] Problems open Amber trajectory Message-ID: Dear Chimera Team, I have a problem opening an AMBER trajectory using chimera v1.3 (2000/12/09). When I look at the frames, they show this "spider web" phenomenon: Connections between atoms that should not be there. Furthermore, I got errors throughout the whole file: "Error: line too long in:" I have a topology file and a coordinate file created using leap/ptraj from the Amber Tools 1.2. I could look at the files using vmd with the options "Amber 7 parm" for the topology file and "Amber coordinates with periodic box" for the coordinate file. Therefore, the files should not be corrupt, but, of course, I would prefer to use Chimera for visualizing... Can you give me any advice how to open the files correctly? Thanks in advance. Kind regards, Oliver Dr. Oliver Koch BioChemInformatics Postdoctoral-Fellow Intervet Innovation GmbH Zur Propstei 55270 Schwabenheim, Germany E-Mail: oliver.koch at sp.intervet.com Phone: +49 (6130) 948 396 Fax: +49 (6130) 948 517 Home http://www.intervet.com Sitz der Gesellschaft: Schwabenheim Amtsgericht Mainz, HRB 23 166 Gesch?ftsf?hrer: Dr. Peter Schmid -------------------------------------- This message and any attachments are solely for the intended recipient. If you are not the intended recipient, disclosure, copying, use or distribution of the information included in this message is prohibited -- please immediately and permanently delete. -------------------------------------- From damien.lariviere at fourmentinguilbert.org Wed Aug 19 06:44:00 2009 From: damien.lariviere at fourmentinguilbert.org (=?ISO-8859-1?Q?Damien_Larivi=E8re?=) Date: Wed, 19 Aug 2009 15:44:00 +0200 Subject: [Chimera-users] Script Message-ID: <4A8C01A0.4050906@fourmentinguilbert.org> Dear all, Sorry for this simple question : Is there an example of how to use a command in a script ? For example, the command "open" is described in the documentation but I confess (i'm not a programmer) that I do not understand how to use it for opening a pdb file in a specific directory : C:\Users\damien\Fondation\LifeExplorer\3D models\FtsZ_ring\Bond_Set\Docking_Hex\Results_190809\dock0001.pdb I would like to create a script that does : 1/ Open a PDB file (dock0001.pdb) 2/ open Tools - Structure analysis - Sequence 3/ select residues 203 to 227 chain A 4/ Actions Color Red 5/ open Tools - Structure analysis - Sequence 6/ select residues 54 to 87 chain A 7/ Actions Color Magenta Many thanks for your help Damien From pett at cgl.ucsf.edu Wed Aug 19 11:22:04 2009 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 19 Aug 2009 11:22:04 -0700 Subject: [Chimera-users] Script In-Reply-To: <4A8C01A0.4050906@fourmentinguilbert.org> References: <4A8C01A0.4050906@fourmentinguilbert.org> Message-ID: <40138F97-710A-42E9-9DF6-43951D4CE6E2@cgl.ucsf.edu> Hi Damien, You can use "open" with the full path to the file, or you can "cd" to the folder and then just use the file's name. See below... On Aug 19, 2009, at 6:44 AM, Damien Larivi?re wrote: > Dear all, > > Sorry for this simple question : Is there an example of how to use a > command in a script ? For example, the command "open" is described in > the documentation but I confess (i'm not a programmer) that I do not > understand how to use it for opening a pdb file in a specific > directory > : C:\Users\damien\Fondation\LifeExplorer\3D > models\FtsZ_ring\Bond_Set\Docking_Hex\Results_190809\dock0001.pdb > > I would like to create a script that does : > > 1/ Open a PDB file (dock0001.pdb) Either: open C:\Users\damien\ ... \Results_190809\dock001.pdb -or-: cd C:\Users\damien\ ... \Docking_Hex\Results_190809 open dock001.pdb The latter might be better if you are going to save files and would like them to go into that folder as well without specifying a big long path. > 2/ open Tools - Structure analysis - Sequence > 3/ select residues 203 to 227 chain A sel :203-227.A ":203-227.A" is the "atom specifier" for residues 203 to 227 of chain A. There is an extensive explanation of atom specifiers here: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/frameatom_spec.html > 4/ Actions Color Red color red sel > 5/ open Tools - Structure analysis - Sequence > 6/ select residues 54 to 87 chain A sel :54-87.A > 7/ Actions Color Magenta color magenta sel If the only reason you are making the selection is in order to color it magenta (i.e. you aren't going to do any other operations on it) then you could just cut out the selection step and: color magenta :54-87.A --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Wed Aug 19 11:49:29 2009 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 19 Aug 2009 11:49:29 -0700 Subject: [Chimera-users] Problems open Amber trajectory In-Reply-To: References: Message-ID: <81E1AEB8-2D91-480A-9946-61321628FB24@cgl.ucsf.edu> Hi Oliver, Chimera doesn't handle unwrapped trajectories. You will need to use the ptraj "image" command to prevent molecules from being split across box boundaries in your final trajectory. Perhaps the other errors will not occur with the re-imaged trajectory. If not, please let me know. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Aug 19, 2009, at 4:15 AM, Koch, O (Oliver) wrote: > Dear Chimera Team, > > I have a problem opening an AMBER trajectory using chimera v1.3 > (2000/12/09). > > When I look at the frames, they show this "spider web" phenomenon: > Connections between atoms that should not be there. > Furthermore, I got errors throughout the whole file: "Error: line > too long in:" > > I have a topology file and a coordinate file created using leap/ > ptraj from the Amber Tools 1.2. > I could look at the files using vmd with the options "Amber 7 parm" > for the topology file and "Amber coordinates with periodic box" for > the coordinate file. > Therefore, the files should not be corrupt, but, of course, I would > prefer to use Chimera for visualizing... > > Can you give me any advice how to open the files correctly? > > Thanks in advance. > > Kind regards, > Oliver > > Dr. Oliver Koch > BioChemInformatics Postdoctoral-Fellow > Intervet Innovation GmbH > Zur Propstei > 55270 Schwabenheim, Germany > > E-Mail: oliver.koch at sp.intervet.com > Phone: +49 (6130) 948 396 > Fax: +49 (6130) 948 517 > > Home http://www.intervet.com > > Sitz der Gesellschaft: Schwabenheim Amtsgericht Mainz, HRB 23 > 166 Gesch?ftsf?hrer: Dr. Peter Schmid > > -------------------------------------- > This message and any attachments are solely for the intended > recipient. > > If you are not the intended recipient, disclosure, copying, use or > distribution of the information included in this message is prohibited > > > > -- please immediately and permanently delete. > -------------------------------------- > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Wed Aug 19 13:45:50 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 19 Aug 2009 13:45:50 -0700 Subject: [Chimera-users] Script In-Reply-To: <40138F97-710A-42E9-9DF6-43951D4CE6E2@cgl.ucsf.edu> References: <4A8C01A0.4050906@fourmentinguilbert.org> <40138F97-710A-42E9-9DF6-43951D4CE6E2@cgl.ucsf.edu> Message-ID: <656BF1B6-73C5-4DF8-9C6B-00BFC3D02D19@cgl.ucsf.edu> Hi Damien, Eric's answer is perfect, I just wanted to add that you can try out each command by typing it into the Command Line (shown by choosing "Favorites... Command Line" from the menu). In other words, a Chimera command script is just a text file containing the same lines that could be entered at the Command Line. You can see a list of all commands by choosing "Help... User's Guide" from the menu and then clicking the "commands" link in the page that appears. That commands index also has a section near the bottom entitled "Chimera Command Files" with links to several example files. There are also many example commands in the tutorials (again under the Help menu). Another kind of script is Python code, which is sometimes needed if there is no Chimera command for what you want to do, or you need to loop through a large number of structures. Best, Elaine On Aug 19, 2009, at 11:22 AM, Eric Pettersen wrote: > Hi Damien, > You can use "open" with the full path to the file, or you can "cd" > to the folder and then just use the file's name. See below... > > On Aug 19, 2009, at 6:44 AM, Damien Larivi?re wrote: > >> Dear all, >> >> Sorry for this simple question : Is there an example of how to use a >> command in a script ? For example, the command "open" is described in >> the documentation but I confess (i'm not a programmer) that I do not >> understand how to use it for opening a pdb file in a specific >> directory >> : C:\Users\damien\Fondation\LifeExplorer\3D >> models\FtsZ_ring\Bond_Set\Docking_Hex\Results_190809\dock0001.pdb >> >> I would like to create a script that does : >> >> 1/ Open a PDB file (dock0001.pdb) > > Either: > open C:\Users\damien\ ... \Results_190809\dock001.pdb > > -or-: > cd C:\Users\damien\ ... \Docking_Hex\Results_190809 > open dock001.pdb > > The latter might be better if you are going to save files and would > like them to go into that folder as well without specifying a big > long path. > >> 2/ open Tools - Structure analysis - Sequence >> 3/ select residues 203 to 227 chain A > > sel :203-227.A > > ":203-227.A" is the "atom specifier" for residues 203 to 227 of > chain A. There is an extensive explanation of atom specifiers > here: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/ > frameatom_spec.html > >> 4/ Actions Color Red > > color red sel > >> 5/ open Tools - Structure analysis - Sequence >> 6/ select residues 54 to 87 chain A > > sel :54-87.A > >> 7/ Actions Color Magenta > > color magenta sel > > If the only reason you are making the selection is in order to > color it magenta (i.e. you aren't going to do any other operations > on it) then you could just cut out the selection step and: > > color magenta :54-87.A > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From gregc at cgl.ucsf.edu Wed Aug 19 13:53:22 2009 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Wed, 19 Aug 2009 13:53:22 -0700 (PDT) Subject: [Chimera-users] Moving atom labels In-Reply-To: References: Message-ID: On Fri, 7 Aug 2009, Greg Couch wrote: > On Thu, 6 Aug 2009, Michael Day wrote: > >> How does one change the position of atom labels? For small coordination >> complexes the default atom labels land on the atom and it would be nice to >> move them as a whole or individually so they are alongside the atom ball or >> anisotropic ellipsoid. >> >> Cheers, >> Mike > > In the next daily build, we will have interactive label moving, where you > can pick a label and drag it around, and if you hold down the shift key, > it will move in Z. It will default to the Control-button-3 mouse mode, > but can be reassigned using the mouse mode preferences. You will also be > able to change the label offsets using the command line, the "labeloffset > x y z atom-spec" and "rlabeloffset x y z atom-spec" commands to set the > offsets and "~labeloffset" and "~rlabeloffset" to reset them to the > default behavior of adjusting the offset with the representation. > > For users with existing saved preferences, you might need to turn label > dragging on by resetting the mouse mode preferences or by explicitly > assigning it to Control-button-3. There's no icon for it yet in the mouse > modes interface, but it will be the rightmost column for now. > > Since the label moving code is new, please send me feedback about how well > it works for you. > > - Greg In the next daily build, the labeloffset and rlabeloffset commands have been replaced with an offset argument to the label and rlabel commands: 'label' ['offset' ('default' | x,y,z)] atom-spec and likewise for rlabel. [] designates optional. (|) designates choices. '' designates literal text. x,y,z is three numbers separated by commas and no embedded spaces. The default offset resets to the default behavior, like ~labeloffset before. - Greg From tomguu at rice.edu Tue Aug 18 13:19:00 2009 From: tomguu at rice.edu (Tom Guu) Date: Tue, 18 Aug 2009 15:19:00 -0500 Subject: [Chimera-users] thanks In-Reply-To: References: <1CDF46F8044B482AA3F43289520C9DBC@TomPC> Message-ID: <5D018D3CE5D644CA82531FCE4B132DE0@TomPC> Hi Elaine, Thanks for both replies (last Friday and today). You and Tom Goddard are "life-saver," considering I had no prior knowledge on how to make animations. I am forever grateful for y'all's help. I eventually got the animations to work, at least for what I intended to show on the defense (things like zoom in, rocking, turning, etc). I LOVE chimera, and have so much appreciation for UCSF crew, who put in so much effort to make this terrific program. I will try out the surftransparency a bit later to see if the gradually disappearing command would work on our machine (well, instant disppearing of the EM map works, just not as cool). Again, thanks a bunch. ;-) Regards, Tom -----Original Message----- From: Elaine Meng [mailto:meng at cgl.ucsf.edu] Sent: Tuesday, August 18, 2009 3:08 PM To: tomguu at rice.edu Cc: chimera-users at cgl.ucsf.edu Subject: Re: [Chimera-users] surftransparency Hi Tom, It depends what version of Chimera you are using. In older versions it only works for molecular surfaces. In newer versions (daily builds from late June 2009 onwards) it works for the kind of surface you have and has a "frames" argument for scripting gradual changes. You might be looking at documentation that is not synchronized with your download. If you use the Help menu or "help" command, that will show documentation that goes with your downloaded version. If you go to the Web, it may be for a totally different version. It should work if you have a daily build from sometime in the last several weeks. Here is the latest documentation: You would just specify your surface by model number, for example "surftrans 100 #0 120" (change transparency of surface model #0 to completely transparent over 120 frames). 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 http://www.cgl.ucsf.edu/home/meng/index.html On Aug 14, 2009, at 2:17 PM, Tom Guu wrote: > Hi, > > I am trying to use the surftransparecy function on a EM-map (surface), > and don't seem to be able to get it to work. I read on the > documentation page, is this command specific for atoms and not for an > entire EM map? I know I can use show or hide for displaying EM map, > just wonder what other command can make the EM map gradually disappear > or appear. Thanks a bunch. > > Regards, > Tom From meng at cgl.ucsf.edu Thu Aug 20 09:49:24 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 20 Aug 2009 09:49:24 -0700 Subject: [Chimera-users] thanks In-Reply-To: <5D018D3CE5D644CA82531FCE4B132DE0@TomPC> References: <1CDF46F8044B482AA3F43289520C9DBC@TomPC> <5D018D3CE5D644CA82531FCE4B132DE0@TomPC> Message-ID: <4E2F2073-53A4-4CF4-BE74-2134F3629B76@cgl.ucsf.edu> Hi Tom, Thanks for your kind words -- I'm glad you were able to make the animations! Best wishes, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Aug 18, 2009, at 1:19 PM, Tom Guu wrote: > Hi Elaine, > Thanks for both replies (last Friday and today). You and Tom > Goddard are > "life-saver," considering I had no prior knowledge on how to make > animations. I am forever grateful for y'all's help. I eventually > got the > animations to work, at least for what I intended to show on the > defense > (things like zoom in, rocking, turning, etc). I LOVE chimera, and > have so > much appreciation for UCSF crew, who put in so much effort to make > this > terrific program. I will try out the surftransparency a bit later > to see if > the gradually disappearing command would work on our machine (well, > instant > disppearing of the EM map works, just not as cool). Again, thanks a > bunch. > ;-) > Regards, > Tom From damien.lariviere at fourmentinguilbert.org Thu Aug 20 11:23:40 2009 From: damien.lariviere at fourmentinguilbert.org (=?ISO-8859-1?Q?Damien_Larivi=E8re?=) Date: Thu, 20 Aug 2009 20:23:40 +0200 Subject: [Chimera-users] Script In-Reply-To: <40138F97-710A-42E9-9DF6-43951D4CE6E2@cgl.ucsf.edu> References: <4A8C01A0.4050906@fourmentinguilbert.org> <40138F97-710A-42E9-9DF6-43951D4CE6E2@cgl.ucsf.edu> Message-ID: <4A8D94AC.2030105@fourmentinguilbert.org> Hi Eric and Elaine, Thank you very much for your answers ! I was blocked in fact by the "cd command" that does not work on my machine for opening a file. I reported the bug this morning. So, I have used Eric's suggestions and it works very well. I am not a python programmer (but I know Matlab well enough). So in Chimera I would like to open successive pdb files (dock000i.pdb with i = 1 to 20) and perform some actions on each one and then close each session that are previously saved in a Chimera session. The loop "for" in Matlab starts with "for i = 1:20" then the block of actions and ends with "end". What's about in Python programming ? I suggest the following but I know it can't work: for i = 1 to 20 open C:\Users\damien\Fondation\LifeExplorer\3D models\FtsZ_ring\Bond_Set\Docking_Hex\Results_190809\dock\dock000i.pdb color orange red :38-227.A color blue :228-356.A color magenta :203-227.A color green :261-271.A color green :297-307.A save C:\Users\damien\Fondation\LifeExplorer\3D models\FtsZ_ring\Bond_Set\Docking_Hex\Results_190809\dock\dock000i.py close session end Many thanks for your help Damien Eric Pettersen a ?crit : > Hi Damien, > You can use "open" with the full path to the file, or you can "cd" to > the folder and then just use the file's name. See below... > > On Aug 19, 2009, at 6:44 AM, Damien Larivi?re wrote: > >> Dear all, >> >> Sorry for this simple question : Is there an example of how to use a >> command in a script ? For example, the command "open" is described in >> the documentation but I confess (i'm not a programmer) that I do not >> understand how to use it for opening a pdb file in a specific directory >> : C:\Users\damien\Fondation\LifeExplorer\3D >> models\FtsZ_ring\Bond_Set\Docking_Hex\Results_190809\dock0001.pdb >> >> I would like to create a script that does : >> >> 1/ Open a PDB file (dock0001.pdb) > > Either: > open C:\Users\damien\ ... \Results_190809\dock001.pdb > > -or-: > cd C:\Users\damien\ ... \Docking_Hex\Results_190809 > open dock001.pdb > > The latter might be better if you are going to save files and would > like them to go into that folder as well without specifying a big long > path. > >> 2/ open Tools - Structure analysis - Sequence >> 3/ select residues 203 to 227 chain A > > sel :203-227.A > > ":203-227.A" is the "atom specifier" for residues 203 to 227 of chain > A. There is an extensive explanation of atom specifiers > here: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/frameatom_spec.html > >> 4/ Actions Color Red > > color red sel > >> 5/ open Tools - Structure analysis - Sequence >> 6/ select residues 54 to 87 chain A > > sel :54-87.A > >> 7/ Actions Color Magenta > > color magenta sel > > If the only reason you are making the selection is in order to color > it magenta (i.e. you aren't going to do any other operations on it) > then you could just cut out the selection step and: > > color magenta :54-87.A > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > From pett at cgl.ucsf.edu Thu Aug 20 16:02:45 2009 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Thu, 20 Aug 2009 16:02:45 -0700 Subject: [Chimera-users] Script In-Reply-To: <4A8D94AC.2030105@fourmentinguilbert.org> References: <4A8C01A0.4050906@fourmentinguilbert.org> <40138F97-710A-42E9-9DF6-43951D4CE6E2@cgl.ucsf.edu> <4A8D94AC.2030105@fourmentinguilbert.org> Message-ID: <084BB068-3667-4FB4-A356-FDB92A0D30D6@cgl.ucsf.edu> On Aug 20, 2009, at 11:23 AM, Damien Larivi?re wrote: > Hi Eric and Elaine, > > Thank you very much for your answers ! > > I was blocked in fact by the "cd command" that does not work on my > machine for opening a file. I reported the bug this morning. I will be looking into that. > So, I have used Eric's suggestions and it works very well. > > I am not a python programmer (but I know Matlab well enough). So in > Chimera I would like to open successive pdb files (dock000i.pdb with > i = 1 to 20) and perform some actions on each one and then close > each session that are previously saved in a Chimera session. The > loop "for" in Matlab starts with "for i = 1:20" then the block of > actions and ends with "end". What's about in Python programming ? As Elaine mentioned, if you need to do looping you will need to resort to Python. There is a function in Chimera named runCommand which allows you to execute Chimera commands in Python, so that way you don't have to spend a lot of time figuring out the equivalent Python functions. This lets us write your script pretty easily in Python: > I suggest the following but I know it can't work: > > for i = 1 to 20 > open C:\Users\damien\Fondation\LifeExplorer\3D models\FtsZ_ring > \Bond_Set\Docking_Hex\Results_190809\dock\dock000i.pdb > color orange red :38-227.A > color blue :228-356.A > color magenta :203-227.A > color green :261-271.A > color green :297-307.A > save C:\Users\damien\Fondation\LifeExplorer\3D models\FtsZ_ring > \Bond_Set\Docking_Hex\Results_190809\dock\dock000i.py > close session > end from chimera import runCommand as rc for i in range(1, 21): rc(r"open C:\Users\damien\Fondation\LifeExplorer\3D models\FtsZ_ring \Bond_Set\Docking_Hex\Results_190809\dock\dock%04d.pdb" % i) rc("color orange red :38-227.A") rc("color blue :228-356.A") rc("color magenta :203-227.A") rc("color green :261-271.A") rc("color green :297-307.A") rc(r"save C:\Users\damien\Fondation\LifeExplorer\3D models\FtsZ_ring \Bond_Set\Docking_Hex\Results_190809\dock\dock%04d.pdb" % i) rc("close session") The script is really pretty self-explanatory except for a couple of tricky things. One is that the quoted strings that contained backslashes needed to be preceded by an 'r' (marking them as a "raw" string) to prevent Python from doing special backslash processing on the string. The other is getting the zero-padded version of 'i' into the open and save commands. This is accomplished with the special text %04d which means replace that text with a zero-padded 4-digit decimal integer. The "% i" after the string indicates that the variable 'i' should be used in the text replacement. Good luck! :-) --Eric Eric Pettersen UCSF Computer Graphics Lab From danielgurnon at depauw.edu Fri Aug 21 17:52:46 2009 From: danielgurnon at depauw.edu (Daniel Gurnon) Date: Fri, 21 Aug 2009 20:52:46 -0400 Subject: [Chimera-users] pause during a fly-by? Message-ID: <4A8F091F02000003000C2DB4@gwia-vs.depauw.edu> Hi all, I've been considering ways to use Chimera in the classes I teach, and I love the potential of the "fly"command for smoothly navigating between preset positions. But is it possible to pause in mid-flight? The pause command hasn't worked for me here. What I'm really looking for is a way to automate some features of a presentation (e.g., the camera position) while retaining interactivity. Making a quicktime movie is less than ideal, because although I could pause the movie if a question is asked, I couldn't, for example, use a clipping plane to strip away a surface to show an underlying backbone, and then smoothly resume the camera flight. Perhaps I should consider making a demo instead, where pauses are built in? Thanks Dan ____________________________ Daniel Gurnon, Ph. D. Assistant Professor of Chemistry DePauw University Greencastle, IN 46135 p: 765-658-6279 e: danielgurnon at depauw.edu From goddard at cgl.ucsf.edu Fri Aug 21 18:25:19 2009 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Fri, 21 Aug 2009 18:25:19 -0700 Subject: [Chimera-users] pause during a fly-by? In-Reply-To: <4A8F091F02000003000C2DB4@gwia-vs.depauw.edu> References: <4A8F091F02000003000C2DB4@gwia-vs.depauw.edu> Message-ID: <4A8F48FF.9050106@cgl.ucsf.edu> Hi Daniel, The demo capability in Chimera is designed to do what you want including rewind. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/demos/demos.html It doesn't allow pausing in the middle of a motion -- only between panels (maybe between individual commands associated with a panel - not sure). But the idea is that the duration of motion in each panel would be short. We haven't made many demos and this tool may be pretty rough around the edges. The trouble with the pause command or Shift-Escape to pause/resume a script is that the fly command returns immediately after you invoke it. It sets up playing the motion which then happens after the command returns. Normally that motion could be halted with the command "freeze". This works with other motion commands "reset", "roll", "move", and it should work with "fly" but doesn't yet work for "fly". In any case, it simply terminates the motion and there is no way to restart it, so that won't do what you want. There is no mechanism to pause the playback in these motion commands, though maybe "pause" and the Shift-Escape key should be made to do that. Currently those mechanisms just block running of additional commands I believe. I wonder whether pause/resume would be adequate for teaching purposes. Seems very likely to me that you will need rewind. By the time a student asks a question the motion is already past the relevant section. We don't have any rewind capability in the motion commands or in general scripts, only the demo tool, and even there I think can be tricky to make it work. Tom -------- Original Message -------- Subject: [Chimera-users] pause during a fly-by? From: Daniel Gurnon To: chimera-users at cgl.ucsf.edu Date: 8/21/09 5:52 PM > Hi all, > I've been considering ways to use Chimera in the classes I teach, and I love the potential of the "fly"command for smoothly navigating between preset positions. But is it possible to pause in mid-flight? The pause command hasn't worked for me here. What I'm really looking for is a way to automate some features of a presentation (e.g., the camera position) while retaining interactivity. Making a quicktime movie is less than ideal, because although I could pause the movie if a question is asked, I couldn't, for example, use a clipping plane to strip away a surface to show an underlying backbone, and then smoothly resume the camera flight. Perhaps I should consider making a demo instead, where pauses are built in? > > Thanks > Dan > > ____________________________ > > Daniel Gurnon, Ph. D. > Assistant Professor of Chemistry > DePauw University > Greencastle, IN 46135 > From meng at cgl.ucsf.edu Sat Aug 22 11:07:33 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Sat, 22 Aug 2009 11:07:33 -0700 Subject: [Chimera-users] pause during a fly-by? In-Reply-To: <4A8F48FF.9050106@cgl.ucsf.edu> References: <4A8F091F02000003000C2DB4@gwia-vs.depauw.edu> <4A8F48FF.9050106@cgl.ucsf.edu> Message-ID: Hi Daniel, You might consider writing your script with a series of "reset" commands rather than "fly" -- the difference is that fly considers the trajectory to be taken after the next position, so that the whole thing looks smoother. If A,B,C,D are saved positions, schematically: fly A -> B -> C -> D where the approach to C is already being considered before arriving at B, versus reset -> A; wait reset -> B; wait ... where each reset command can specify number of frames (does not have to be instantaneous) The wait commands prevent the movement commands from overlapping execution. Shift-Esc will pause the script after the current command is done. If it is in the middle of a reset to C, it will go that far and then stop at C. Then it can be resumed with another Shift-Esc. That is not as precise as what you had asked about (instantaneously pausing), but more precise than after an entire fly command finishes. A demo is inherently a series of commands, and doesn't allow pausing in the middle of a command, so "reset" is probably also needed in that case. It is the only way I can think of in Chimera where you can just press a button to go back to a previous state. Easy for the user, but... Demo issues: - you would need to start the demo by opening a session with your saved positions, unless you know how to generate those positions by a series of commands - the "go back" feature automatically takes care of positions, but the demo creator is responsible for figuring out any other commands needed to revert to the previous state (any displaying/undisplaying, changing colors, styles). It can be more confusing than it sounds! You can see the "guts" of a demo by choosing it from the Tools... Demos menu (starting to play it back) but then choosing "File... Open in Editor" from the demo panel. Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Aug 21, 2009, at 6:25 PM, Tom Goddard wrote: > Hi Daniel, > > The demo capability in Chimera is designed to do what you want > including rewind. > > > http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/demos/ > demos.html > > It doesn't allow pausing in the middle of a motion -- only between > panels (maybe between individual commands associated with a panel - > not > sure). But the idea is that the duration of motion in each panel > would > be short. We haven't made many demos and this tool may be pretty > rough > around the edges. > > The trouble with the pause command or Shift-Escape to pause/resume a > script is that the fly command returns immediately after you invoke > it. > It sets up playing the motion which then happens after the command > returns. Normally that motion could be halted with the command > "freeze". This works with other motion commands "reset", "roll", > "move", and it should work with "fly" but doesn't yet work for "fly". > In any case, it simply terminates the motion and there is no way to > restart it, so that won't do what you want. There is no mechanism to > pause the playback in these motion commands, though maybe "pause" and > the Shift-Escape key should be made to do that. Currently those > mechanisms just block running of additional commands I believe. > > I wonder whether pause/resume would be adequate for teaching > purposes. Seems very likely to me that you will need rewind. By the > time a student asks a question the motion is already past the relevant > section. We don't have any rewind capability in the motion > commands or > in general scripts, only the demo tool, and even there I think can be > tricky to make it work. > > Tom > > > -------- Original Message -------- > Subject: [Chimera-users] pause during a fly-by? > From: Daniel Gurnon > To: chimera-users at cgl.ucsf.edu > Date: 8/21/09 5:52 PM >> Hi all, >> I've been considering ways to use Chimera in the classes I teach, >> and I love the potential of the "fly"command for smoothly >> navigating between preset positions. But is it possible to pause >> in mid-flight? The pause command hasn't worked for me here. What >> I'm really looking for is a way to automate some features of a >> presentation (e.g., the camera position) while retaining >> interactivity. Making a quicktime movie is less than ideal, >> because although I could pause the movie if a question is asked, I >> couldn't, for example, use a clipping plane to strip away a >> surface to show an underlying backbone, and then smoothly resume >> the camera flight. Perhaps I should consider making a demo >> instead, where pauses are built in? >> >> Thanks >> Dan >> >> ____________________________ >> >> Daniel Gurnon, Ph. D. >> Assistant Professor of Chemistry >> DePauw University >> Greencastle, IN 46135 >> > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From kruggel at chemie.uni-hamburg.de Mon Aug 24 04:43:01 2009 From: kruggel at chemie.uni-hamburg.de (Sebastian Kruggel) Date: Mon, 24 Aug 2009 13:43:01 +0200 Subject: [Chimera-users] problem with the scripting of rms deviations Message-ID: <4A927CC5.70307@chemie.uni-hamburg.de> Dear Chimera team and users, I tried to write a small chimera / python script to calculate rmsd to the crystal structure for a bunch of docked ligands and transform the values in a nice csv - because fred22 doesn't do this for me... The core function rms2ref is the one calculating the rmsd, than I save the reply log and afterwards transform this text file. Things worked out fine BUT than I started the script several times, and I got different orders in my list every time. Because I want to assign rmsd values to scores etc it is essential to keep the order provided in the sdf/mol2. I thought about problems with the format but the problem exists with mol2 and sdf files. Than I thought, chimera would change the order in opening the multimolecule files - but saving the #1.1 molecule and opening it in a new session showed - even more strange - that the molecule is exactly the same every time. So there is only the possibility that either the calculation of the rmsd or the order of the list (extraction of the replyLog.txt) doesn't work - which I *really* don't understand at all... Here is a small example where the rmsds-list has different orders every time I start the script... ############################## from chimera import runCommand from chimera.tkgui import saveReplyLog def rms2ref(ref, pose, no): runCommand('open %s; open %s' % (ref, pose)) i = 1 while i <= no: # only hetatms are included --> ~@/element=h runCommand('sel #1.%i & ~@/element=h' % i) runCommand('rmsd #0 sel') i += 1 rms2ref('lig_cryst.pdb', 'poses.sdf', 10) # generate output from replyLog.txt saveReplyLog('replyLog.txt') rmsds = [] for i in open('replyLog.txt').readlines(): if i.startswith('RMSD between'): rmsds.append(i.split()[-2]) print rmsds ############################## Maybe anybody can help me and tell me about the probably stupid mistake I am making - would be really great! I attached the lig_cryst.pdb and poses.sdf files just in case that anybody wants to try out ;-) Best regards and thanks in advance, Sebastian -- Sebastian Kruggel Institut f?r Pharmazie Bundesstr. 45 | Raum 112 (406) D 20146 Hamburg Tel: +49 (0)40 42838-3626 (-3484) mail: kruggel at chemie.uni-hamburg.de http://www.chemie.uni-hamburg.de/pha/phachem/lemcke/mitarbeiter.html -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: rmsExample.py URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: lig_cryst.pdb Type: chemical/x-pdb Size: 2511 bytes Desc: not available URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: poses.sdf URL: From fangshu at mail.nih.gov Mon Aug 24 08:57:41 2009 From: fangshu at mail.nih.gov (Fang, Shunming (NIH/NIDDK) [C]) Date: Mon, 24 Aug 2009 11:57:41 -0400 Subject: [Chimera-users] Help about install Chimera Message-ID: <1CE762DD5EADD04CA6BF4D2B260CDAA702D7E69B6B@NIHMLBX08.nih.gov> Hello, There, I just install the latest version of Chimera in my Fedora 11 machine. When I tested it after I installed it, it just show segmentation fault. I don't know why. The chimera version is chimera-1.3-linux.exe (32bit). my mahchine is 64bit. When I install this 32bit chimera, I also install all package it required. I really appreciate your help, Shunming From thomas.mitterfellner at tugraz.at Mon Aug 24 09:04:48 2009 From: thomas.mitterfellner at tugraz.at (Dipl.-Ing. Thomas Mitterfellner) Date: Mon, 24 Aug 2009 18:04:48 +0200 Subject: [Chimera-users] Ignored settings In-Reply-To: <4A5B7B09.4080902@cgl.ucsf.edu> References: <50346.133.1.134.198.1247452353.squirrel@acs-webmail.ucsd.edu> <4A5B7B09.4080902@cgl.ucsf.edu> Message-ID: <4A92BA20.4080806@tugraz.at> Hello! The recent chimera builds seem to ignore my standard molecule settings (ball and stick defaults to stick only) and the files to be read at startup. I normally read in a file with my custom colordefs, but when I set that, close chimera and open it again, this setting is lost. Is this a known issue, or is it just with my installation? Thanks for any hints, Thomas From pett at cgl.ucsf.edu Mon Aug 24 10:46:09 2009 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 24 Aug 2009 10:46:09 -0700 Subject: [Chimera-users] Ignored settings In-Reply-To: <4A92BA20.4080806@tugraz.at> References: <50346.133.1.134.198.1247452353.squirrel@acs-webmail.ucsd.edu> <4A5B7B09.4080902@cgl.ucsf.edu> <4A92BA20.4080806@tugraz.at> Message-ID: Hi Thomas, We recently changed Chimera so that molecules are initially displayed in a fashion very similar to the "Interactive 1 (ribbons)" preset rather than wireframe. This behavior is controlled by a new "smart initial display" New Molecule preference, which defaults to true. When that preference is true, many of the other preferences in that category are overridden*. So to get back to the behavior you had before, set "smart initial display" to false. Perhaps this is also the issue with you problem with colordefs, but I don't completely understand your description of that. Are we talking about Command Line startup files? Do you mean that you put a file in the list of Command Line file to read at startup and it's not in the list the next time you start Chimera? (You did click the 'Save' button, right?) --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu * all other prefs are overridden except for those dealing with initial model color, metal complexes, Mol2 model naming, line width, and ball/ stick scale. On Aug 24, 2009, at 9:04 AM, Dipl.-Ing. Thomas Mitterfellner wrote: > Hello! > The recent chimera builds seem to ignore my standard molecule settings > (ball and stick defaults to stick only) and the files to be read at > startup. I normally read in a file with my custom colordefs, but > when I > set that, close chimera and open it again, this setting is lost. > Is this a known issue, or is it just with my installation? -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Mon Aug 24 10:57:01 2009 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 24 Aug 2009 10:57:01 -0700 Subject: [Chimera-users] Ignored settings In-Reply-To: References: <50346.133.1.134.198.1247452353.squirrel@acs-webmail.ucsd.edu> <4A5B7B09.4080902@cgl.ucsf.edu> <4A92BA20.4080806@tugraz.at> Message-ID: On Aug 24, 2009, at 10:46 AM, Eric Pettersen wrote: > Are we talking about Command Line startup files? Do you mean that > you put a file in the list of Command Line file to read at startup > and it's not in the list the next time you start Chimera? (You did > click the 'Save' button, right?) Actually, if this is what you're describing then it is a known issue, namely ticket #7483 in our Trac database (http://socrates2.cgl.ucsf.edu/trac/chimera/ticket/7483 ). I believe it is in fact using your file, it's just not showing it in the list of files (which of course makes it hard to delete!). I will add you to the list of recipients for that Trac ticket, so you will be notified when it's fixed. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From gregc at cgl.ucsf.edu Mon Aug 24 11:29:17 2009 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Mon, 24 Aug 2009 11:29:17 -0700 (PDT) Subject: [Chimera-users] Help about install Chimera In-Reply-To: <1CE762DD5EADD04CA6BF4D2B260CDAA702D7E69B6B@NIHMLBX08.nih.gov> References: <1CE762DD5EADD04CA6BF4D2B260CDAA702D7E69B6B@NIHMLBX08.nih.gov> Message-ID: On Mon, 24 Aug 2009, Fang, Shunming (NIH/NIDDK) [C] wrote: > Hello, There, I just install the latest version of Chimera in my Fedora > 11 machine. When I tested it after I installed it, it just show > segmentation fault. I don't know why. The chimera version is > chimera-1.3-linux.exe (32bit). my mahchine is 64bit. When I install this > 32bit chimera, I also install all package it required. I really > appreciate your help, Shunming Two things: 32-bit verus 64-bit builds of chimera: As you noticed, the new 64-bit distributions of Linux do not include, by default, many of the 32-bit packages needed to run chimera. Since the list, and names, of missing packages varies by Linux distribution, we're going to drop the suggestion that people run the 32-bit version to save memory. It's not worth the trouble for most users. Fedora 11: If chimera is going to work at all, you need to use a daily build or the latest snapshot. However, it still might not work. Fedora 11 significantly altered how OpenGL (3D graphics) acceleration is incorporated into the kernel and by default uses open-source drivers for the various graphics cards and chipsets. While this is an overall improvement, there are lots of rough edges. For instance, if you have an ATI graphics card, the chimera daily build works with the default driver, but ATI's driver fails to install (it is documented to only be tested on Red Hat Enterprise Linux, SuSE, and Ubuntu, not Fedora). And if you have a NVidia graphics card, the open-source driver crashes chimera when you try to show a surface or ribbons (and ribbons are the new chimera default), but the closed source version from NVidia works great. I don't know about Intel graphics options, but I do know that one of the primary reasons that the Fedora 11 changes were made were to speed up Intel graphics performance, so if it works, it will be faster :-). Bottom line: If you want to use chimera, you're better off staying away from bleeding edge Linux distributions like Fedora 11. But it can work if you try hard enough. Good luck, Greg From goddard at cgl.ucsf.edu Mon Aug 24 11:49:34 2009 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Mon, 24 Aug 2009 11:49:34 -0700 Subject: [Chimera-users] Interactive Chimera demonstrations for teaching In-Reply-To: <4A8F48FF.9050106@cgl.ucsf.edu> References: <4A8F091F02000003000C2DB4@gwia-vs.depauw.edu> <4A8F48FF.9050106@cgl.ucsf.edu> Message-ID: <4A92E0BE.1020204@cgl.ucsf.edu> Hi Dan, If you haven't already, you should check out the two demos (cox inhibitors, hormone-receptor complex) in the Chimera Tools / Demos menu. These were made by Elaine Meng. If you look at pane 7 of the cox demo there are some html-style links "sticks" and "spheres" that allow you to change rendering options. You can also use the normal Chimera menus and tinker with the rendering and view point and the demo will usually revert to the normal depiction when you go to the next pane. Whether it does or not depends on how thorough the commands that define the demo are about setting all the display styles in case the user has fiddled. Going from panes 4 to 5 there is some motion of the molecules. But then pressing the back button jumps immediately to the preceding positions -- it does not show the motion in reverse. It may be easy to make the back button reverse the motion. In general the back operation has to be given as a series of commands that the demo creator knows will undo the forward step. You could put in the backwards motion commands. I have never made a demo so I am guessing. We are interested in improving Chimera for interactive teaching. Our thinking when developing the demo editor was more geared towards showing a researcher new to Chimera some of the Chimera capabilities. Creating these demos does not require programming knowledge, but rather a good knowledge of the Chimera commands. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/framecommand.html Before you team up with some computer science people, I think the steps should be: 1) study the two demos included in Chimera, and the commands used in those demos, 2) try making a simple demo from your own material, 3) talk with us about the problems you find. I think you'll encounter two problems, first that some needed commands don't exist, and second that the demo editor and player are clunky (it hasn't been used much to our knowledge). Both of these things we can work with you to improve -- possibly with pretty quick turn-around time (days/weeks). Tom -------- Original Message -------- Subject: Re: [Chimera-users] pause during a fly-by? From: Daniel Gurnon To: goddard at cgl.ucsf.edu Date: 8/22/09 9:24 AM > Thanks Tom. I'll try making some demos. From the ones I've seen, rewinding the demo is more like "reset", i.e., any motion won't be reversed but instead the model(s) will be reset to their position and rendering from the previous step. But it should provide much of what I need. > > Over the past few months, I've been learning Autodesk Maya and talking with Gael McGill and some of the others out there that do molecular animation. While I think animation software like Maya can be a very powerful teaching tool (especially when you need to model things for which there is no 3D data set), the finished movies lack interactivity. Ideally I want modules that automate some of the learning experience (fetching a structure, rendering to highlight appropriate features, taking the viewer on a fly-by tour of the system) while also leaving the participant free to pause and explore the scene on their own. The demos in Chimera are pretty close to what I want actually, but there are a few things I'd change if I could...motion rewinding is one, but it would also be useful to add buttons enabling the user to change rendering options at each demo stop-point without the risk of screwing up the rest of the demo. It would also be nice to instantly reset the demo to the current point if you made a change you want to undo. In a nutshell, I want to design modules that any student or any teacher could use with minimal time invested in learning Chimera. I really think Chimera has a lot of potential for teaching, but the learning curve associated with the program makes it tough for the inexperienced to get the most out of the Chimera's interactive capabilities. > > Do you think it would be feasible (and a good idea) for me to team up with some computer scientists at my school and work on retooling the demo editor with the goal of designing several student-friendly, interactive modules? I have a lot of experience with teaching, but none with programming, so I know what I want...I just don't know if it's possible. Any advice you can offer is much appreciated! > > Dan > -------- Original Message -------- Subject: Re: [Chimera-users] pause during a fly-by? From: Tom Goddard To: Daniel Gurnon Date: 8/21/09 6:25 PM > Hi Daniel, > > The demo capability in Chimera is designed to do what you want > including rewind. > > > http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/demos/demos.html > > It doesn't allow pausing in the middle of a motion -- only between > panels (maybe between individual commands associated with a panel - not > sure). But the idea is that the duration of motion in each panel would > be short. We haven't made many demos and this tool may be pretty rough > around the edges. > > The trouble with the pause command or Shift-Escape to pause/resume a > script is that the fly command returns immediately after you invoke it. > It sets up playing the motion which then happens after the command > returns. Normally that motion could be halted with the command > "freeze". This works with other motion commands "reset", "roll", > "move", and it should work with "fly" but doesn't yet work for "fly". > In any case, it simply terminates the motion and there is no way to > restart it, so that won't do what you want. There is no mechanism to > pause the playback in these motion commands, though maybe "pause" and > the Shift-Escape key should be made to do that. Currently those > mechanisms just block running of additional commands I believe. > > I wonder whether pause/resume would be adequate for teaching > purposes. Seems very likely to me that you will need rewind. By the > time a student asks a question the motion is already past the relevant > section. We don't have any rewind capability in the motion commands or > in general scripts, only the demo tool, and even there I think can be > tricky to make it work. > > Tom > > > -------- Original Message -------- > Subject: [Chimera-users] pause during a fly-by? > From: Daniel Gurnon > To: chimera-users at cgl.ucsf.edu > Date: 8/21/09 5:52 PM > >> Hi all, >> I've been considering ways to use Chimera in the classes I teach, and I love the potential of the "fly"command for smoothly navigating between preset positions. But is it possible to pause in mid-flight? The pause command hasn't worked for me here. What I'm really looking for is a way to automate some features of a presentation (e.g., the camera position) while retaining interactivity. Making a quicktime movie is less than ideal, because although I could pause the movie if a question is asked, I couldn't, for example, use a clipping plane to strip away a surface to show an underlying backbone, and then smoothly resume the camera flight. Perhaps I should consider making a demo instead, where pauses are built in? >> >> Thanks >> Dan >> >> ____________________________ >> >> Daniel Gurnon, Ph. D. >> Assistant Professor of Chemistry >> DePauw University >> Greencastle, IN 46135 >> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Mon Aug 24 14:40:02 2009 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 24 Aug 2009 14:40:02 -0700 Subject: [Chimera-users] problem with the scripting of rms deviations In-Reply-To: <4A927CC5.70307@chemie.uni-hamburg.de> References: <4A927CC5.70307@chemie.uni-hamburg.de> Message-ID: <79E7C7FA-DC95-46F3-A7AC-8B5DF2EB2205@cgl.ucsf.edu> Hi Sebastian, Between Chimera and your script, there are a couple of problems with the RMSD calculation. The executive summary of the solution is: explicitly list the atoms being matched in the RMSD calculation, i.e.: rmsd #0 at pg@pb at o1b@o2b... #1.1 at p3@p2 at o6@o10... To figure out the names that Chimera assigned to your SDF molecules, you will have to open one and look at it. The above approach explicitly ignores the hydrogens, so you can skip that in your script. I would imagine that you might want to skip matching the oxygens of the terminal phosphate as well since that phosphate freely rotates and it's impossible to know which oxygen should match with which. So, the problems are: 1) Chimera doesn't do a connectivity analysis of the atoms in the rmsd command to figure out which to match with which. In cases where the atoms aren't explicitly specified, it orders them by name (if the same name then by input order). The names given to the atoms in the SDF file is completely different from those in the PDB file. 2) When you do "set operations" like intersect (&) and union (|), Chimera may lose track of the ordering of the atoms. Chimera should do a better job of maintaining the ordering with intersection (and I will work on that) nonetheless commands like "rmsd #0 #1" or "rmsd #0:12 #1:1" will work (assuming the names of the atoms match) whereas more complicated commands involving intersection, union, or filtering by attribute values may not. I'll be opening a ticket in our Trac bug database for maintaining better ordering on intersection, with you on the cc list. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Aug 24, 2009, at 4:43 AM, Sebastian Kruggel wrote: > Dear Chimera team and users, > > I tried to write a small chimera / python script to calculate rmsd > to the crystal structure for a bunch of docked ligands and transform > the values in a nice csv - because fred22 doesn't do this for me... > > The core function rms2ref is the one calculating the rmsd, than I > save the reply log and afterwards transform this text file. > > Things worked out fine BUT than I started the script several times, > and I got different orders in my list every time. Because I want to > assign rmsd values to scores etc it is essential to keep the order > provided in the sdf/mol2. I thought about problems with the format > but the problem exists with mol2 and sdf files. Than I thought, > chimera would change the order in opening the multimolecule files - > but saving the #1.1 molecule and opening it in a new session showed > - even more strange - that the molecule is exactly the same every > time. So there is only the possibility that either the calculation > of the rmsd or the order of the list (extraction of the > replyLog.txt) doesn't work - which I *really* don't understand at > all... > > Here is a small example where the rmsds-list has different orders > every time I start the script... > > > ############################## > from chimera import runCommand > from chimera.tkgui import saveReplyLog > > def rms2ref(ref, pose, no): > runCommand('open %s; open %s' % (ref, pose)) > i = 1 > while i <= no: > # only hetatms are included --> ~@/element=h > runCommand('sel #1.%i & ~@/element=h' % i) > runCommand('rmsd #0 sel') > i += 1 > > rms2ref('lig_cryst.pdb', 'poses.sdf', 10) > > # generate output from replyLog.txt > > saveReplyLog('replyLog.txt') > > rmsds = [] > for i in open('replyLog.txt').readlines(): > if i.startswith('RMSD between'): > rmsds.append(i.split()[-2]) > > print rmsds > ############################## > > > Maybe anybody can help me and tell me about the probably stupid > mistake I am making - would be really great! I attached the > lig_cryst.pdb and poses.sdf files just in case that anybody wants to > try out ;-) -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Mon Aug 24 17:45:45 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 24 Aug 2009 17:45:45 -0700 Subject: [Chimera-users] Interactive Chimera demonstrations for teaching In-Reply-To: <4A92E0BE.1020204@cgl.ucsf.edu> References: <4A8F091F02000003000C2DB4@gwia-vs.depauw.edu> <4A8F48FF.9050106@cgl.ucsf.edu> <4A92E0BE.1020204@cgl.ucsf.edu> Message-ID: <55850832-FA5C-4E10-B7EB-B33D0A79B745@cgl.ucsf.edu> Hello, In case it may be helpful, here is my general workflow in making the Demos distributed with Chimera (in the Tools... Demos menu): - create a Chimera command script for the whole forward process. I just create it in a text editor and then keep opening it over and over after making adjustments. I find this to be much easier than trying to use the Demo Editor at this stage. Remember to use "wait" to prevent overlapping execution of movement commands. Sometimes overlapping execution is OK, but in my experience it sometimes leads to different resulting positions on different runs of the same script. - decide which commands to string together in single lines, separated by semicolons (to avoid displaying the intermediate states, since the display just gets updated at the end of a line). This is really done in parallel with the above, so I'm still text-editing that Chimera command file. - decide how to chunk it up into panels, then enter these sets of commands in the Demo Editor, as well as the accompanying text that will show up in the Demo dialog. - figure out and enter "undo" commands for each panel. You only have to do this if you want the Back button to work. - add any fancy extras such as links that execute commands (like the options to show as sticks or spheres, or show residues from just one protein or another in the COX demo). Sometimes it can be a challenge to make sure the "undo" commands will work no matter which of these things the user chooses to execute. I'm sure there are other equally valid but different ways to go about this, so feel free to choose your own path! Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco From oshiroc at pharmgkb.org Wed Aug 26 14:48:50 2009 From: oshiroc at pharmgkb.org (Connie Oshiro) Date: Wed, 26 Aug 2009 14:48:50 -0700 Subject: [Chimera-users] is there a way... Message-ID: Elaine, et al-- I have a chimera session that was saved a while back (xxx.py). I can open it and view it in chimera. Question: Is there a way to extract/recontruct the commands that were used to create the view that I have? In this case, all commands were executed on the command line. The history file doesn't go back far enough. I took a look at the python file and didn't find midas/chimera commands. For example, I know I used "rainbow", with some options for the colors, but I don't see "rainbow" in the .py file. thanks for any info. connie -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Wed Aug 26 15:55:50 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 26 Aug 2009 15:55:50 -0700 Subject: [Chimera-users] is there a way... In-Reply-To: References: Message-ID: <03B1B1D7-E5BF-46B7-99C3-21C0994EF0C3@cgl.ucsf.edu> Hi Connie, A session saves the state, but not how the state was achieved. The command history is saved in your preferences file. You can change the number of commands that is saved (Favorites... Preference, Command Line category), but that has to be done proactively. Once something has fallen off the back end of the history, it is gone, sorry. Depending on what you are trying to do, you may want to take a look at the "mcopy" command. It copies settings from one molecule to another, but requires identical atom/residue names etc. 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 Aug 26, 2009, at 2:48 PM, Connie Oshiro wrote: > Elaine, et al-- > I have a chimera session that was saved a while back (xxx.py). I > can open it and view it in chimera. > Question: Is there a way to extract/recontruct the commands that > were used to create the view that I have? In this case, all > commands were executed on the command line. > > The history file doesn't go back far enough. > > I took a look at the python file and didn't find midas/chimera > commands. For example, I know I used "rainbow", with some options > for the colors, but I don't see "rainbow" in the .py file. > > thanks for any info. > connie From case at biomaps.rutgers.edu Thu Aug 27 05:00:09 2009 From: case at biomaps.rutgers.edu (case) Date: Thu, 27 Aug 2009 08:00:09 -0400 Subject: [Chimera-users] extending DNA for a figure In-Reply-To: References: Message-ID: <20090827120009.GE60416@biomaps.rutgers.edu> > On Aug 13, 2009, at 12:00 AM, Janet G Yang wrote: > > > I would like to make a > > figure showing the structure of the nucleosome with some extra DNA > > docked in at the edges.... Sorry to come in late to this, but you might want to consider the w3dna server from Wilma Olson's group: http://w3dna.rutgers.edu It has a lot of procedures to construct models of DNA and DNA/protein interactions, and the Olson group is particularly interested in nucleosomes. This is not a "Chimera solution", but could be an approach to generate the coordinates you need, that could then be loaded to make the figure you describe. ...regards...dave case From kmikals at ufl.edu Thu Aug 27 07:58:49 2009 From: kmikals at ufl.edu (MIKALS,KYLE A) Date: Thu, 27 Aug 2009 10:58:49 -0400 (EDT) Subject: [Chimera-users] Image not appearing Message-ID: <882780468.257851251385129555.JavaMail.osg@osgjas04.cns.ufl.edu> I made a code to make movie and two of the molecules are not appearing in the saved output images. I put in the code where to save them so if something went wrong. This is the code I made and models 18 and 14 display in the window while the code is running, but not in the saved images. I have no idea what is going wrong. Any ideas? Here is my code below. # start capturing frames, in .png format movie record fformat png raytrace true directory /msg/users/kmikals/Chimera_Files #Created Label saying AAV Capsid Assembly 2dlabels create lab1 text 'AAV Capsid Assembly' color khaki size 28 xpos .2 ypos .94 visibility show scale 1.008 50 #Starts action once previous command is complete wait modeldisplay#0 wait 5 turn y -1 35 wait 30 modeldisplay#17 turn y -.6 20 wait 30 modeldisplay#18 wait 30 turn y +1.4 35 wait 30 modeldisplay#3 ~modeldisplay#0 ~modeldisplay#17 ~modeldisplay#18 wait 30 scale 0.992 50 wait 15 turn y -1 65 wait 9 modeldisplay#4 wait 9 turn y -1 35 modeldisplay#5 wait 9 turn y -1 65 modeldisplay#10 wait 9 modeldisplay#9 wait 9 turn y -1 65 modeldisplay#14 wait 9 modeldisplay#11 wait 9 turn y -0.5 30 modeldisplay#12 wait 9 turn y -1 65 modeldisplay#13 wait 9 modeldisplay#6 turn y -1 65 wait 9 modeldisplay#7 wait 9 modeldisplay#8 2dlabels delete lab1 #hide_all_molecules ~modeldisplay#3 ~modeldisplay#4 ~modeldisplay#5 ~modeldisplay#6 ~modeldisplay#7 ~modeldisplay#8 ~modeldisplay#9 ~modeldisplay#10 ~modeldisplay#11 ~modeldisplay#12 ~modeldisplay#13 ~modeldisplay#14 wait 20 scale 0.987 modeldisplay#16 turn y -.3 20 wait turn x -.75 35 wait 30 turn x .75 35 wait 30 turn x -.38 35 wait turn y -1 35 wait 30 turn y 2 180 wait turn x 2 180 wait # stop recording frames movie stop # write status information to reply log movie status # encode a movie in mp4 format from recorded frames movie encode mformat mp4 output /msg/users/kmikals/Chimera_Files -- MIKALS,KYLE A Biochemistry University of Florida From goddard at cgl.ucsf.edu Thu Aug 27 11:18:30 2009 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Thu, 27 Aug 2009 11:18:30 -0700 Subject: [Chimera-users] Image not appearing In-Reply-To: <882780468.257851251385129555.JavaMail.osg@osgjas04.cns.ufl.edu> References: <882780468.257851251385129555.JavaMail.osg@osgjas04.cns.ufl.edu> Message-ID: <4A96CDF6.8030506@cgl.ucsf.edu> Hi Kyle, This problem is mysterious. Never saw anything like it. Do the missing models #18 and #14 appear in the movie if you don't use raytracing? It could be a raytracing error. If you run just part of your script without movie recording up to the point where model 18 is displayed, then try File / Save Image and enable raytracing, does that raytraced image show model 18? Are models 18 and 14 atomic models? What display style? stick? sphere? ribbon? wire? Are any of the models 0 - 18 transparent? Chimera has trouble with more than one transparent model, although I would not expect that to be a problem raytracing a movie. By the way the "modeldisplay#N" commands should have a space before the "#". The command is "modeldisplay" and "#N" is the argument. I am amazed that works without a space, but I tested and it does work and I don't think that is related to your missing models. Tom -------- Original Message -------- Subject: [Chimera-users] Image not appearing From: MIKALS,KYLE A To: chimera-users at cgl.ucsf.edu Date: 8/27/09 7:58 AM > I made a code to make movie and two of the molecules are not > appearing in the saved output images. I put in the code where to > save them so if something went wrong. > > This is the code I made and models 18 and 14 display in the window > while the code is running, but not in the saved images. I have no > idea what is going wrong. Any ideas? Here is my code below. > > # start capturing frames, in .png format > movie record fformat png raytrace true directory > /msg/users/kmikals/Chimera_Files > #Created Label saying AAV Capsid Assembly > > 2dlabels create lab1 text 'AAV Capsid Assembly' color khaki size > 28 xpos .2 ypos .94 visibility show > > scale 1.008 50 > > #Starts action once previous command is complete > > wait > > modeldisplay#0 > wait 5 > > turn y -1 35 > > wait 30 > > modeldisplay#17 > turn y -.6 20 > > > wait 30 > > modeldisplay#18 > wait 30 > > turn y +1.4 35 > > wait 30 > > modeldisplay#3 > ~modeldisplay#0 > ~modeldisplay#17 > ~modeldisplay#18 > > wait 30 > > scale 0.992 50 > > wait 15 > > turn y -1 65 > > wait 9 > > modeldisplay#4 > > wait 9 > > turn y -1 35 > > modeldisplay#5 > > wait 9 > > turn y -1 65 > > modeldisplay#10 > > wait 9 > > modeldisplay#9 > > wait 9 > > turn y -1 65 > > modeldisplay#14 > > wait 9 > > modeldisplay#11 > > wait 9 > > turn y -0.5 30 > > modeldisplay#12 > > wait 9 > > turn y -1 65 > > modeldisplay#13 > > wait 9 > > modeldisplay#6 > turn y -1 65 > > wait 9 > > modeldisplay#7 > > wait 9 > > modeldisplay#8 > > 2dlabels delete lab1 > > #hide_all_molecules > > ~modeldisplay#3 > > ~modeldisplay#4 > > ~modeldisplay#5 > > ~modeldisplay#6 > > ~modeldisplay#7 > > ~modeldisplay#8 > > ~modeldisplay#9 > > ~modeldisplay#10 > > ~modeldisplay#11 > > ~modeldisplay#12 > > ~modeldisplay#13 > > ~modeldisplay#14 > wait 20 > > scale 0.987 > > modeldisplay#16 > turn y -.3 20 > wait > turn x -.75 35 > wait 30 > turn x .75 35 > wait 30 > turn x -.38 35 > wait > turn y -1 35 > wait 30 > turn y 2 180 > wait > turn x 2 180 > wait > # stop recording frames > movie stop > # write status information to reply log > movie status > # encode a movie in mp4 format from recorded frames > movie encode mformat mp4 output /msg/users/kmikals/Chimera_Files > > > > -- > MIKALS,KYLE A > Biochemistry > University of Florida > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From goddard at cgl.ucsf.edu Thu Aug 27 11:38:46 2009 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Thu, 27 Aug 2009 11:38:46 -0700 Subject: [Chimera-users] Enabling silhouette edges in a nogui script In-Reply-To: <3e4b67ca0908270722j10ecaf24if0ddfb8ec49df79f@mail.gmail.com> References: <3e4b67ca0907090832r4e46b826i5dfe81842b58685a@mail.gmail.com> <4A5779EB.2060407@cgl.ucsf.edu> <3e4b67ca0907110111q27b9ddaet423fe6ec2a5479ef@mail.gmail.com> <4A5B72E8.4010801@cgl.ucsf.edu> <3e4b67ca0907131219o114e2a26ldcc788c07869be83@mail.gmail.com> <4A724166.9020003@cgl.ucsf.edu> <3e4b67ca0908030402g3ae434eaqc792dee5634cb0ff@mail.gmail.com> <4A7A3F3B.9050103@cgl.ucsf.edu> <3e4b67ca0908060204p1d6c2479nd852a874562d7d8a@mail.gmail.com> <3e4b67ca0908270722j10ecaf24if0ddfb8ec49df79f@mail.gmail.com> Message-ID: <4A96D2B6.8070203@cgl.ucsf.edu> Hi Davide, There is a new command in Chimera 1.4 daily builds that lets you turn on silhouette edges and set their width set silhouette set silhouette_width 2 and to turn off silhouette edges ~set silhouette Here's the documentation http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/set.html You're right that the "ac" command to run keyboard shortcuts doesn't work in nogui mode. That is because of some sloppy code that tries to create the keyboard shortcut dialog if you use the "ac" command and dialogs cannot be created in nogui mode. I've added an entry to the Chimera request list to fix that. http://plato.cgl.ucsf.edu/trac/chimera/wiki/requests Tom -------- Original Message -------- Subject: Re: [chimera-dev] Generating images in chimera with the --nogui option From: Davide Ba? To: Tom Goddard Date: 8/27/09 7:22 AM > Tom, > > how are you? > > I'm just back from (good) holidays! Hope you had good holidays too :-) > > I've tried out the "shape tube" command and it works great. Just one > question. From the sample image you attached to your last email, it > seems to me that silhouettes are toggled on ('ac se'). Is that > true/possible via a command script? Chimera Keyboard Shortcuts > (Accelerators) do not work when called form within a script (Error while > sourcing chimera.cmd: Unrecognized command: "'ac") and I haven't found a > different way (maybe using the set command?) to toggle silhouettes on. > > Thanks againg for your support, > Davide > From chesketh at gmail.com Fri Aug 28 09:50:54 2009 From: chesketh at gmail.com (Christian Hesketh) Date: Fri, 28 Aug 2009 12:50:54 -0400 Subject: [Chimera-users] Exporting surfaces as vrml Message-ID: <598cf8520908280950g156cc9eblab55ca5359cace4a@mail.gmail.com> Hi there, I am trying to export molecular surfaces with varying transparencies to vrml, but the resultant model has a completely opaque surface. Is there anyway to export surfaces with transparent features to a 3D model? I would rather not work with x3d files as there don't seem to be any good 3D modeling programs that can accept this format. Thanks in advance, Christian -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at cgl.ucsf.edu Fri Aug 28 11:01:22 2009 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Fri, 28 Aug 2009 11:01:22 -0700 Subject: [Chimera-users] Exporting surfaces as vrml In-Reply-To: <598cf8520908280950g156cc9eblab55ca5359cace4a@mail.gmail.com> References: <598cf8520908280950g156cc9eblab55ca5359cace4a@mail.gmail.com> Message-ID: <4A981B72.4080802@cgl.ucsf.edu> Hi Christian, I'm not sure what version of Chimera you are using, but with the current daily build, the VRML export (File / Export Scene...) does include transparency of surfaces. I believe older Chimera versions (1.3, ...) also do this. I made a transparent red icosahedron and writing as vrml shape icos div 1 color 1,0,0,0.3 export format vrml ~/Desktop/test.vrml The resulting vrml text file does have the transparency information, and when I open it in Chimera it is transparent (although Chimera does not display transparency of VRML models correctly). So quite possibly the program you are using to read the VRML is ignoring the transparency. Tom -------- Original Message -------- Subject: [Chimera-users] Exporting surfaces as vrml From: Christian Hesketh To: chimera-users at cgl.ucsf.edu Date: 8/28/09 9:50 AM > Hi there, > I am trying to export molecular surfaces with varying transparencies > to vrml, but the resultant model has a completely opaque surface. Is > there anyway to export surfaces with transparent features to a 3D > model? I would rather not work with x3d files as there don't seem to > be any good 3D modeling programs that can accept this format. > Thanks in advance, > Christian > ------------------------------------------------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From gregc at cgl.ucsf.edu Fri Aug 28 11:46:12 2009 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Fri, 28 Aug 2009 11:46:12 -0700 (PDT) Subject: [Chimera-users] Exporting surfaces as vrml In-Reply-To: <4A981B72.4080802@cgl.ucsf.edu> References: <598cf8520908280950g156cc9eblab55ca5359cace4a@mail.gmail.com> <4A981B72.4080802@cgl.ucsf.edu> Message-ID: As you found out, VRML has limited support for transparency, and that is one reason why chimera's native export format is X3D. VRML's transparency is limited to a single value per shape, and X3D's transparency can vary within a shape. Tom's example only worked because the surface was of a single color. FYI, if you are just interested in molecular surfaces, it should be fairly easy to extract the information you need out of the X3D file and write it out in whatever format your modeling program needs. - Greg On Fri, 28 Aug 2009, Tom Goddard wrote: > Hi Christian, > > I'm not sure what version of Chimera you are using, but with the current > daily build, the VRML export (File / Export Scene...) does include > transparency of surfaces. I believe older Chimera versions (1.3, ...) also > do this. I made a transparent red icosahedron and writing as vrml > > shape icos div 1 color 1,0,0,0.3 > export format vrml ~/Desktop/test.vrml > > The resulting vrml text file does have the transparency information, and when > I open it in Chimera it is transparent (although Chimera does not display > transparency of VRML models correctly). So quite possibly the program you > are using to read the VRML is ignoring the transparency. > > Tom > > -------- Original Message -------- > Subject: [Chimera-users] Exporting surfaces as vrml > From: Christian Hesketh > To: chimera-users at cgl.ucsf.edu > Date: 8/28/09 9:50 AM >> Hi there, >> I am trying to export molecular surfaces with varying transparencies to >> vrml, but the resultant model has a completely opaque surface. Is there >> anyway to export surfaces with transparent features to a 3D model? I would >> rather not work with x3d files as there don't seem to be any good 3D >> modeling programs that can accept this format. >> Thanks in advance, >> Christian >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > > -------------- next part -------------- _______________________________________________ Chimera-users mailing list Chimera-users at cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From sergio.alberto.garay at gmail.com Fri Aug 28 12:53:42 2009 From: sergio.alberto.garay at gmail.com (Sergio Garay) Date: Fri, 28 Aug 2009 16:53:42 -0300 Subject: [Chimera-users] Problem building 3D structure from smile text ... Message-ID: <74e2c5910908281253l1602db10q54fc0a13b707a64@mail.gmail.com> Hi all I'm trying to build a 3D structure from this smile text: N[C@@H](C)C(=O)O But the program stops and doesn't respond to any key. The log window shows the next message: Exception in Tk callback Function: > (type: ) Args: () Traceback (innermost last): File "CHIMERA/lib/python2.5/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", line 1747, in __call__ None File "CHIMERA/share/BuildStructure/gui.py", line 632, in _placeAtoms None File "CHIMERA/share/BuildStructure/Smiles.py", line 15, in openSmiles None File "CHIMERA/share/BuildStructure/Smiles.py", line 21, in smiles2mol None File "CHIMERA/share/BuildStructure/SOAPpy/WSDL.py", line 61, in __init__ None File "CHIMERA/lib/python2.5/urllib.py", line 82, in urlopen return opener.open(url) File "CHIMERA/lib/python2.5/urllib.py", line 190, in open return getattr(self, name)(url) File "CHIMERA/lib/python2.5/urllib.py", line 325, in open_http h.endheaders() File "CHIMERA/lib/python2.5/httplib.py", line 860, in endheaders self._send_output() File "CHIMERA/lib/python2.5/httplib.py", line 732, in _send_output self.send(msg) File "CHIMERA/lib/python2.5/httplib.py", line 699, in send self.connect() File "CHIMERA/lib/python2.5/httplib.py", line 673, in connect self.sock.connect(sa) File "", line 1, in connect None : Am I doing something wrong? I am working with this chimera version: alpha version, build 2577, 2008/12/09 -- Dr. Sergio Garay Facultad de Bioquimica y Cs. Biol?gicas Universidad Nacional del Litoral Santa Fe - Argentina C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA Argentina Ph. +54 (342) 4575-213 Fax. +54 (342) 4575-221 -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Fri Aug 28 13:29:26 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 28 Aug 2009 13:29:26 -0700 Subject: [Chimera-users] Problem building 3D structure from smile text ... In-Reply-To: <74e2c5910908281253l1602db10q54fc0a13b707a64@mail.gmail.com> References: <74e2c5910908281253l1602db10q54fc0a13b707a64@mail.gmail.com> Message-ID: Hi Sergio, Normally if you want to report an error it is best to use "Help... Report a Bug" in the Chimera menu since that would automatically include information about your computer and Chimera version, and let you attach files. However, in this case I can immediately see the problem: you need a newer version of Chimera! You would need a version from July 3 or later, for example the August 20 snapshot: Explanation: The SMILES -> 3D structure conversion is done by a Web server provided by a group at Indiana University, and a few months ago they changed how this service is accessed. It was necessary to change Chimera to use the new, updated service. I tested the following command in the snapshot version just now, and it worked fine: open smiles:N[C@@H](C)C(=O)O Using this command is the same as entering the SMILES in the Build Structure dialog. I also checked doing it that way. I think you will be pleasantly surprised to see the many improvements we have made in Build Structure and in other tools, and the many new features that have been added to Chimera! Improvements between 1.3 and the snapshot (and you were using a version older than 1.3): 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 From aaksyuk at bio.purdue.edu Fri Aug 28 14:23:12 2009 From: aaksyuk at bio.purdue.edu (Anastasia A Aksyuk) Date: Fri, 28 Aug 2009 17:23:12 -0400 Subject: [Chimera-users] movie image resolution Message-ID: <4A984AC0.6040402@bio.purdue.edu> Hi, It is very easy to specify resolution for a saved image, but not for the images used to create a movie. Is there a way to generate a movie or a stack of images with higher resolution then a display screen? I seem to be limited to 1273x870. Thanks a lot, Anastasia From goddard at cgl.ucsf.edu Fri Aug 28 14:41:38 2009 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Fri, 28 Aug 2009 14:41:38 -0700 Subject: [Chimera-users] movie image resolution In-Reply-To: <4A984AC0.6040402@bio.purdue.edu> References: <4A984AC0.6040402@bio.purdue.edu> Message-ID: <4A984F12.9090105@cgl.ucsf.edu> Hi Anastasia, There is not an option to record movies larger than the Chimera window size. It wouldn't be difficult to add that. I've put it on the Chimera request list http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/requests If you want to go to some trouble you can do it now using the Chimera "perframe" command to save an image with the "copy" command for each frame, then run a movie encoder on the frames (could use ffmpeg included in the Chimera distribution) to make the movie file. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/perframe.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/copy.html Tom -------- Original Message -------- Subject: [Chimera-users] movie image resolution From: Anastasia A Aksyuk To: chimera-users at cgl.ucsf.edu Date: 8/28/09 2:23 PM > Hi, > It is very easy to specify resolution for a saved image, but not for the > images used to create a movie. > Is there a way to generate a movie or a stack of images with higher > resolution then a display screen? I seem to be limited to 1273x870. > Thanks a lot, > Anastasia > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > From gregc at cgl.ucsf.edu Fri Aug 28 14:52:55 2009 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Fri, 28 Aug 2009 14:52:55 -0700 (PDT) Subject: [Chimera-users] movie image resolution In-Reply-To: <4A984F12.9090105@cgl.ucsf.edu> References: <4A984AC0.6040402@bio.purdue.edu> <4A984F12.9090105@cgl.ucsf.edu> Message-ID: Note that there is a "windowsize" command in chimera to set the graphics window to a particular size. See: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/windowsize.html - Greg On Fri, 28 Aug 2009, Tom Goddard wrote: > Hi Anastasia, > > There is not an option to record movies larger than the Chimera window > size. It wouldn't be difficult to add that. I've put it on the Chimera > request list > > http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/requests > > If you want to go to some trouble you can do it now using the Chimera > "perframe" command to save an image with the "copy" command for each > frame, then run a movie encoder on the frames (could use ffmpeg included > in the Chimera distribution) to make the movie file. > > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/perframe.html > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/copy.html > > Tom > > > -------- Original Message -------- > Subject: [Chimera-users] movie image resolution > From: Anastasia A Aksyuk > To: chimera-users at cgl.ucsf.edu > Date: 8/28/09 2:23 PM >> Hi, >> It is very easy to specify resolution for a saved image, but not for the >> images used to create a movie. >> Is there a way to generate a movie or a stack of images with higher >> resolution then a display screen? I seem to be limited to 1273x870. >> Thanks a lot, >> Anastasia >> >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >> > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > From mikeday at caltech.edu Fri Aug 28 15:25:26 2009 From: mikeday at caltech.edu (Michael Day) Date: Fri, 28 Aug 2009 15:25:26 -0700 Subject: [Chimera-users] Centro-symmetric space groups Message-ID: <10F90B7A-E56C-41F9-B362-7643E30127B6@caltech.edu> How do you get Chimera to recognize centrosymmetric space groups. If I include the space group on the CRYST1 card of the PDB file all is well for non-centrosymmetric groups but when a center of symmetry enters the picture all bets are off. I'm using Tool->Higher-Order Structure->Unit cell For example adding the space group in column 56 of the PDB P1 as P 1 - all's good P-1 as P -1 - complete nonsense although it recognizes there are two symmetry elements P2 as P 1 2 1 - all's good P21 as P 1 21 1 - all's good P212121 as P 21 21 21 - no problem But; P21/c as P 1 21/c 1 - no recognized symmetry elements and no unit cell expansion. Cheers, Mike <<< ------------------------------------------------------------------------> >> Dr. Michael W. Day Director - X-ray Crystallography Lab & Molecular Observatory California Institute of Technology Mail Code 139-74 Pasadena, CA 91125 <>< <>< <>< <>< <>< <>< <>< <>< <>< <>< Beckman Institute, Room 116 Phone: (626) 395-2734 Fax: (626) 449-4159 e-mail: mikeday at caltech.edu <<< ------------------------------------------------------------------------> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at cgl.ucsf.edu Fri Aug 28 15:41:34 2009 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Fri, 28 Aug 2009 15:41:34 -0700 Subject: [Chimera-users] Centro-symmetric space groups In-Reply-To: <10F90B7A-E56C-41F9-B362-7643E30127B6@caltech.edu> References: <10F90B7A-E56C-41F9-B362-7643E30127B6@caltech.edu> Message-ID: <4A985D1E.300@cgl.ucsf.edu> Hi Mike, The space groups recognized by the Unit Cell tool are defined in the Chimera distribution in file chimera/share/Crystal/space_groups.py (On the Mac this is Chimera.app/Contents/Resources/share/Crystal/space_groups.py.) That is Python code and you can look at it in any text editor. Look at the table at the end of the file. A few years ago I made this file and I tried to include every space group listed in a Protein Databank entry though I may not have succeeded. Are the non-centrosymmetric groups used by the PDB? A fallback is to just specify exactly the symmetries that build the unit cell from the asymmetric unit using PDB REMARK 290 SMTRY records. Can be inconvenient, but if those symmetries are already present in a different PDB entry you can copy and paste them. More detail on Unit Cell is in the User's Guide. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/unitcell/unitcell.html If you have suggestions for how to improve it, tell me. I have to warn you that we've really focused on electron microscopy density map analysis in Chimera and our x-ray map capabilities are rough. Tom -------- Original Message -------- Subject: [Chimera-users] Centro-symmetric space groups From: Michael Day To: chimera-users at cgl.ucsf.edu Date: 8/28/09 3:25 PM > How do you get Chimera to recognize centrosymmetric space groups. > > If I include the space group on the CRYST1 card of the PDB file all is > well for non-centrosymmetric groups but when a center of symmetry > enters the picture all bets are off. > > I'm using Tool->Higher-Order Structure->Unit cell > > For example adding the space group in column 56 of the PDB > P1 as P 1 - all's good > P-1 as P -1 - complete nonsense although it recognizes there are two > symmetry elements > P2 as P 1 2 1 - all's good > P21 as P 1 21 1 - all's good > P212121 as P 21 21 21 - no problem > But; > P21/c as P 1 21/c 1 - no recognized symmetry elements and no unit cell > expansion. > > Cheers, > Mike > > <<< > ------------------------------------------------------------------------>>> > Dr. Michael W. Day > Director - X-ray Crystallography Lab & Molecular Observatory > California Institute of Technology > Mail Code 139-74 > Pasadena, CA 91125 > > <>< <>< <>< <>< <>< <>< <>< <>< <>< <>< -------------- next part -------------- An HTML attachment was scrubbed... URL: From sergio.alberto.garay at gmail.com Sat Aug 29 05:36:12 2009 From: sergio.alberto.garay at gmail.com (Sergio Garay) Date: Sat, 29 Aug 2009 09:36:12 -0300 Subject: [Chimera-users] Problem building 3D structure from smile text ...(Solved. Thanks) Message-ID: <74e2c5910908290536v20606a82p5b4783c15593c505@mail.gmail.com> Thank tou Alaine. The new chimera version works perfect! On Fri, Aug 28, 2009 at 5:29 PM, Elaine Meng wrote: > Hi Sergio, > Normally if you want to report an error it is best to use "Help... Report a > Bug" in the Chimera menu since that would automatically include information > about your computer and Chimera version, and let you attach files. > > However, in this case I can immediately see the problem: you need a newer > version of Chimera! > > You would need a version from July 3 or later, for example the August 20 > snapshot: > > > Explanation: The SMILES -> 3D structure conversion is done by a Web server > provided by a group at Indiana University, and a few months ago they changed > how this service is accessed. It was necessary to change Chimera to use the > new, updated service. > > I tested the following command in the snapshot version just now, and it > worked fine: > > open smiles:N[C@@H](C)C(=O)O > > Using this command is the same as entering the SMILES in the Build > Structure dialog. I also checked doing it that way. > > I think you will be pleasantly surprised to see the many improvements we > have made in Build Structure and in other tools, and the many new features > that have been added to Chimera! > > Improvements between 1.3 and the snapshot (and you were using a version > older than 1.3): > > > 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 > > > > -- Dr. Sergio Garay Facultad de Bioquimica y Cs. Biol?gicas Universidad Nacional del Litoral Santa Fe - Argentina C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA Argentina Ph. +54 (342) 4575-213 Fax. +54 (342) 4575-221 -------------- next part -------------- An HTML attachment was scrubbed... URL: From bala.biophysics at gmail.com Mon Aug 31 01:56:37 2009 From: bala.biophysics at gmail.com (Bala subramanian) Date: Mon, 31 Aug 2009 10:56:37 +0200 Subject: [Chimera-users] chimera latest build Message-ID: <288df32a0908310156j3a35cd59ief95fc076d1228af@mail.gmail.com> Friends, 1) I downloaded the chimera's today's build and tried to change the nucleic acid representation using..Depiction in Tools. I get the following error. Kindly write me what is going wrong ? TclError: unknown option -width TclError: unknown option -width File "CHIMERA/share/CGLtk/OptionMenu.py", line 15, in __init__ See reply log for Python traceback. Thanks, Bala -------------- next part -------------- An HTML attachment was scrubbed... URL: From analuiza at larces.uece.br Fri Aug 28 15:08:53 2009 From: analuiza at larces.uece.br (Ana Luiza) Date: Fri, 28 Aug 2009 19:08:53 -0300 Subject: [Chimera-users] 2D projections Message-ID: <9769b07f0908281508h691c905fj9085ad08c6e7ab75@mail.gmail.com> Hi, Is it possible to build 2D projections from a 3D surface in Chimera? Thanks, Ana Luiza. -------------- next part -------------- An HTML attachment was scrubbed... URL: From xzhang1999 at ucla.edu Mon Aug 31 10:10:48 2009 From: xzhang1999 at ucla.edu (Xing Zhang) Date: Mon, 31 Aug 2009 10:10:48 -0700 Subject: [Chimera-users] Cannot save the labels in Volume trace In-Reply-To: References: <391712D3-29D0-43A0-9DED-569B96685DFC@biochem.uthscsa.edu> Message-ID: <002201ca2a5d$fc76a700$f563f500$@edu> Dear All, I try to put stickers and balls in my EM density to trace secondary structures of protein. During this process, I put a number to label each of the secondary structures. However, these labels are all lost after I save this session and restore the session. Any suggestion to solve this problem would be greatly appreciated. Thanks. Xing From meng at cgl.ucsf.edu Mon Aug 31 11:02:33 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 31 Aug 2009 11:02:33 -0700 Subject: [Chimera-users] chimera latest build In-Reply-To: <288df32a0908310156j3a35cd59ief95fc076d1228af@mail.gmail.com> References: <288df32a0908310156j3a35cd59ief95fc076d1228af@mail.gmail.com> Message-ID: Hi Bala, Please use the Report Bug button on the error dialog instead of sending e-mail to this list. That would send us more information about what you are doing and what kind of computer you are on, and possibly allow us to reproduce the problem. I don't know what the problem is, but I also had a problem (a different one) with Nucleotides in the new daily build. I didn't have a problem with Nucleotides in the snapshot, so you may want to try the snapshot version instead: 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 Aug 31, 2009, at 1:56 AM, Bala subramanian wrote: > Friends, > > 1) I downloaded the chimera's today's build and tried to change the > nucleic acid representation using..Depiction in Tools. I get the > following error. Kindly write me what is going wrong ? > > TclError: unknown option -width > TclError: unknown option -width > > File "CHIMERA/share/CGLtk/OptionMenu.py", line 15, in __init__ > > See reply log for Python traceback. > > Thanks, > Bala From goddard at cgl.ucsf.edu Mon Aug 31 17:21:23 2009 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Mon, 31 Aug 2009 17:21:23 -0700 Subject: [Chimera-users] 2D projections In-Reply-To: <9769b07f0908281508h691c905fj9085ad08c6e7ab75@mail.gmail.com> References: <9769b07f0908281508h691c905fj9085ad08c6e7ab75@mail.gmail.com> Message-ID: <4A9C6903.7070007@cgl.ucsf.edu> Hi Ana, Do you want to project volume data or a surface? For volume data you can display a projection by using "solid" style rendering and set the transparency to 100% in the volume dialog brightness and transparency panel, and move the nodes on the volume histogram to create a linear ramp. This just provides an on-screen image that looks like a projection. Probably good to use orthographic projection too (menu Tools / Viewing Controls / Camera, projection -> orthographic) instead of perspective projection. Chimera is not able to create a 2d volume data sets which is the exact projection, but I'd like to add that. It is on the Chimera request list (entry 58). http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/requests Tom -------- Original Message -------- Subject: [Chimera-users] 2D projections From: Ana Luiza To: chimera-users at cgl.ucsf.edu Date: 8/28/09 3:08 PM > Hi, > > Is it possible to build 2D projections from a 3D surface in Chimera? > > Thanks, > Ana Luiza. > > > ------------------------------------------------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From goddard at cgl.ucsf.edu Mon Aug 31 17:25:54 2009 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Mon, 31 Aug 2009 17:25:54 -0700 Subject: [Chimera-users] Centro-symmetric space groups In-Reply-To: <4A985D1E.300@cgl.ucsf.edu> References: <10F90B7A-E56C-41F9-B362-7643E30127B6@caltech.edu> <4A985D1E.300@cgl.ucsf.edu> Message-ID: <4A9C6A12.2090307@cgl.ucsf.edu> Hi Mike, If there is a bug I want to fix it. Give me the example PDB and the correct answer, say from some other software -- best if it were another PDB file with the other asymmetric units in the unit cell. If that is difficult and image might suffice. I'm not clear on what you are saying is wrong. Do you mean the placement of the asymmetric units produced by the Unit Cell dialog for space group "P -1" is wrong? That would be pretty odd -- I'd expect many space groups to give wrong results if there was a bug. If that is the issue, you may be getting tripped up by the fact that the asymmetric units are placed according to the symmetries but then moved so that the center of each asymmetric unit being placed lies within the unit cell box having origin at the location given in the dialog. The purpose of this is to get a packed unit cell. Probably should have an option to disable that behavior so you just get exactly the standard symmetry placement. Tom -------- Original Message -------- Subject: Re: [Chimera-users] Centro-symmetric space groups From: Michael Day To: Tom Goddard Date: 8/31/09 4:45 PM > Tom, > > Thanks for the info! Especially the speedy response! The PDB definitely > allows centrosymmetric groups even though they never appear in proteins. > > Centrosymmetric space groups still get mangled. Your file appears to > have the right symmetry operators. I ran into this on a P-1 structure > that is a stack of planar molecules but when I expand the unit cell I > get some thing completely different. > > I've tried the PDB file with other viewers and I can get the correct > representation but I much prefer Chimera to everything else I've tried > (there's really no comparison). > > It seems one of the the most straightforward options would be to start > with CIF files because they have the symmetry operators in them and the > coordinates are the actual crystallographic coordinates and therefore > wouldn't need to be transformed/deorthogonalized. > > It may be a bug with your deorthogonalization routine. > > Cheers, > Mike > From goddard at cgl.ucsf.edu Mon Aug 31 17:53:52 2009 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Mon, 31 Aug 2009 17:53:52 -0700 Subject: [Chimera-users] Cannot save the labels in Volume trace In-Reply-To: <002201ca2a5d$fc76a700$f563f500$@edu> References: <391712D3-29D0-43A0-9DED-569B96685DFC@biochem.uthscsa.edu> <002201ca2a5d$fc76a700$f563f500$@edu> Message-ID: <4A9C70A0.4050304@cgl.ucsf.edu> Hi Xing, If you placed markers with the Volume Tracer dialog and use Features / Marker Note in that dialog to label the markers they will be saved in session files. I see that if you use Actions / Label / other... to label the markers then that is not saved in Chimera 1.3, and it is saved but not restored in Chimera 1.4, because the empty Marker Note overrides the label. I'll try to fix this for the upcoming Chimera 1.4 release, so that labels set with Actions / Label are treated the same as marker notes. For now, use the Volume Tracer dialog Features / Marker Note and it will be saved and restored from sessions. Thanks for reporting the problem. Tom -------- Original Message -------- Subject: [Chimera-users] Cannot save the labels in Volume trace From: Xing Zhang To: 'Chimera BB' Date: 8/31/09 10:10 AM > Dear All, > > I try to put stickers and balls in my EM density to trace secondary > structures of protein. During this process, I put a number to label each of > the secondary structures. However, these labels are all lost after I save > this session and restore the session. Any suggestion to solve this problem > would be greatly appreciated. Thanks. > > Xing > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From james.fethiere at umontreal.ca Mon Aug 31 17:34:00 2009 From: james.fethiere at umontreal.ca (James Fethiere) Date: Mon, 31 Aug 2009 20:34:00 -0400 Subject: [Chimera-users] menu commands in script In-Reply-To: References: <288df32a0908310156j3a35cd59ief95fc076d1228af@mail.gmail.com> Message-ID: <4A9C6BF8.7020704@umontreal.ca> Hi everybody, is there a command equivalent to the menu command: coulombic surface coloring. I need to include it in a movie script. Thanks James Elaine Meng wrote: > Hi Bala, > Please use the Report Bug button on the error dialog instead of > sending e-mail to this list. That would send us more information > about what you are doing and what kind of computer you are on, and > possibly allow us to reproduce the problem. > > I don't know what the problem is, but I also had a problem (a > different one) with Nucleotides in the new daily build. I didn't have > a problem with Nucleotides in the snapshot, so you may want to try the > snapshot version instead: > > > 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 Aug 31, 2009, at 1:56 AM, Bala subramanian wrote: > > >> Friends, >> >> 1) I downloaded the chimera's today's build and tried to change the >> nucleic acid representation using..Depiction in Tools. I get the >> following error. Kindly write me what is going wrong ? >> >> TclError: unknown option -width >> TclError: unknown option -width >> >> File "CHIMERA/share/CGLtk/OptionMenu.py", line 15, in __init__ >> >> See reply log for Python traceback. >> >> Thanks, >> Bala >> > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at cgl.ucsf.edu Mon Aug 31 18:14:28 2009 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Mon, 31 Aug 2009 18:14:28 -0700 Subject: [Chimera-users] Centro-symmetric space groups In-Reply-To: <4A9C6A12.2090307@cgl.ucsf.edu> References: <10F90B7A-E56C-41F9-B362-7643E30127B6@caltech.edu> <4A985D1E.300@cgl.ucsf.edu> <4A9C6A12.2090307@cgl.ucsf.edu> Message-ID: <4A9C7574.5080600@cgl.ucsf.edu> Hi Mike, Oops. The symmetries that invert coordinates don't work in the Unit Cell tool. This is because it sets the transformation matrix (rotation and shift) for the asymmetric unit copies but it can only handle proper rotations. Chimera is generally used for proteins which are handed (not symmetric under inversion) so such space groups generally don't occur for proteins. But of course for small molecules they can. I'll fix this soon, maybe later this week. I'll have to change atom coordinates instead of setting the transform matrix for the asymmetric unit copies. Tom -------- Original Message -------- Subject: Re: [Chimera-users] Centro-symmetric space groups From: Thomas Goddard To: Michael Day Date: 8/31/09 5:25 PM > Hi Mike, > > If there is a bug I want to fix it. Give me the example PDB and the > correct answer, say from some other software -- best if it were another > PDB file with the other asymmetric units in the unit cell. If that is > difficult and image might suffice. > > I'm not clear on what you are saying is wrong. Do you mean the > placement of the asymmetric units produced by the Unit Cell dialog for > space group "P -1" is wrong? That would be pretty odd -- I'd expect > many space groups to give wrong results if there was a bug. If that is > the issue, you may be getting tripped up by the fact that the asymmetric > units are placed according to the symmetries but then moved so that the > center of each asymmetric unit being placed lies within the unit cell > box having origin at the location given in the dialog. The purpose of > this is to get a packed unit cell. Probably should have an option to > disable that behavior so you just get exactly the standard symmetry > placement. > > Tom > > > -------- Original Message -------- > Subject: Re: [Chimera-users] Centro-symmetric space groups > From: Michael Day > To: Tom Goddard > Date: 8/31/09 4:45 PM > > > Tom, > > > > Thanks for the info! Especially the speedy response! The PDB definitely > > allows centrosymmetric groups even though they never appear in proteins. > > > > Centrosymmetric space groups still get mangled. Your file appears to > > have the right symmetry operators. I ran into this on a P-1 structure > > that is a stack of planar molecules but when I expand the unit cell I > > get some thing completely different. > > > > I've tried the PDB file with other viewers and I can get the correct > > representation but I much prefer Chimera to everything else I've tried > > (there's really no comparison). > > > > It seems one of the the most straightforward options would be to start > > with CIF files because they have the symmetry operators in them and the > > coordinates are the actual crystallographic coordinates and therefore > > wouldn't need to be transformed/deorthogonalized. > > > > It may be a bug with your deorthogonalization routine. > > > > Cheers, > > Mike > > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From goddard at cgl.ucsf.edu Mon Aug 31 18:29:03 2009 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Mon, 31 Aug 2009 18:29:03 -0700 Subject: [Chimera-users] Chimera works on Snow Leopard In-Reply-To: <0F7EC288-A229-4AEA-9C97-189226CC735F@cgl.ucsf.edu> References: <0F7EC288-A229-4AEA-9C97-189226CC735F@cgl.ucsf.edu> Message-ID: <4A9C78DF.5000709@cgl.ucsf.edu> Hi John, I tested Chimera 1.3 and 1.4 daily builds on Mac OS 10.6 (Snow Leopard). All the tests worked fine. I ran our test suite using the Aqua Mac Chimera 1.4 snapshot and it all passed. I tested Chimera 1.3 production releases Mac Aqua and Mac X11 by hand opening a few data sets (molecules and volume data) and doing some coloring and encountered no problems. Tom -------- Original Message -------- Subject: Re: Snow Leopard ? From: Elaine Meng To: John Gerlt Date: 8/27/09 9:12 AM > Hi John, > I don't know for certain, so I'm turning over the question to the rest > of the staff (cc'd on this message). To whomever answers: could > include response on chimera-users list if you think others will have the > same question... thanks! > Best, > Elaine > > > On Aug 27, 2009, at 9:08 AM, John Gerlt wrote: > >> Elaine, >> >> Apple is issuing OS 10.6 tomorrow. For reasons I don't understand, I >> like to be current. But, as I recall from the past, when I tried to >> be current and install a new OS (10.5?), Chimera would not work. Do >> you know if Chimera will work with 10.6? >> >> Thanks. >> >> John