From chiendarret at yahoo.com Sun Dec 2 01:27:16 2007 From: chiendarret at yahoo.com (Francesco Pietra) Date: Sun, 2 Dec 2007 01:27:16 -0800 (PST) Subject: [Chimera-users] Remove steric clashes Message-ID: <845458.24240.qm@web57613.mail.re1.yahoo.com> I would like to delete all water residues that are in steric clash with lipid residues. What I have is a single pdb file that includes both types of residues. Can't have the two as different models. Therefore I can't apply the zone tool that I know how to manage for two different models. The only alternative I can figure out is through the "Find Clashes,Contacts", writing a file for all WAT at a specified distance from the lipid residues and then manually deleting, or inventing a script for that (at <=0.6A there are 386 clashes). Hope to have missed an automatic tool from Chimera. If not, I suggest that as a most useful additional tool for cleaning systems. I dropped into the problem when at the first minimization, in view of MD, the system met segmentation fault after a few steps, with gradient decreasing by eight orders of magnitude along those few steps. Then I recognized not to have been careful enough before making the coordinate files for the MD suite. I should have not relied too much in the membrane builder and I had better spent time in checking for steric clashes. Thanks francesco pietra ____________________________________________________________________________________ Get easy, one-click access to your favorites. Make Yahoo! your homepage. http://www.yahoo.com/r/hs From meng at cgl.ucsf.edu Sun Dec 2 08:30:56 2007 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Sun, 2 Dec 2007 08:30:56 -0800 Subject: [Chimera-users] Remove steric clashes In-Reply-To: <845458.24240.qm@web57613.mail.re1.yahoo.com> References: <845458.24240.qm@web57613.mail.re1.yahoo.com> Message-ID: <6c1cd733b5b3025123733fd838c22b07@cgl.ucsf.edu> Hi Francesco, Zone selection does not require separate models. You can use any specifiers to indicate the atoms in the zone, for example open 1zik select solvent & protein z<4 (depending on what the waters are named you could use :wat or :.water instead of "solvent" and it sounds like you want to specify your lipids instead of protein... :popc or whatever those residues were named) Then you can "delete sel" or use Actions... Delete to delete the selection (warning: there is no undo except by reopening the starting structure). Find Clashes/Contacts could also be used to select the atoms, but remember it looks at "amount of VDW overlap" rather than "distance between atom centers" and there are more steps than the simple zone approach above. One of the options in Find Clashes/Contacts is to select the pairs of atoms. That would give water atom + lipid atom pairs in your case. Then subtract from the selection the lipid atoms. That would leave just selected water atoms. If you have hydrogens on the waters, promote the selection to the whole water residues. Then proceed as before to delete the selection. Here is a findclash example pretending I want to delete waters with 0.1 A VDW overlap with the protein in 1zik. open 1zik addh findclash solvent overlap .1 hbond 0 makePseudobonds false select true [that preceding findclash command is all one line!] ~sel ~ solvent sel up del sel You could do the same thing with the GUI and menus instead of commands. Best, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Dec 2, 2007, at 1:27 AM, Francesco Pietra wrote: > I would like to delete all water residues that are in steric clash > with lipid > residues. What I have is a single pdb file that includes both types of > residues. Can't have the two as different models. > > Therefore I can't apply the zone tool that I know how to manage for two > different models. > > The only alternative I can figure out is through the "Find > Clashes,Contacts", > writing a file for all WAT at a specified distance from the lipid > residues and > then manually deleting, or inventing a script for that (at <=0.6A > there are 386 > clashes). > > Hope to have missed an automatic tool from Chimera. If not, I suggest > that as a > most useful additional tool for cleaning systems. I dropped into the > problem > when at the first minimization, in view of MD, the system met > segmentation > fault after a few steps, with gradient decreasing by eight orders of > magnitude > along those few steps. Then I recognized not to have been careful > enough before > making the coordinate files for the MD suite. I should have not relied > too much > in the membrane builder and I had better spent time in checking for > steric > clashes. > > Thanks > francesco pietra From goddard at cgl.ucsf.edu Mon Dec 3 15:48:15 2007 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Mon, 03 Dec 2007 15:48:15 -0800 Subject: [Chimera-users] Question regarding Chimera usage In-Reply-To: <84998.66475.qm@web52408.mail.re2.yahoo.com> References: <84998.66475.qm@web52408.mail.re2.yahoo.com> Message-ID: <475495BF.7070809@cgl.ucsf.edu> Hi Navya, If you have a 3-button mouse you move the atomic model with the middle button. If that is not working then you probably have the mouse modes assigned differently. You can look at and change what the mouse buttons do with menu entry Features / Preferences category Mouse. Usually button 2 is assigned to translate in x and y (second column of table). It may not be assigned to that operation if you have used other tools like volume path tracer or volume subregion selection that reassign mouse button 2. Tom swetha davuluri wrote: > Hi, > > Thanks for your reply. I am trying to move the atomic model using the > mouse. But I can only rotate the model but not transitionally shift it > i.e. I am not able to move the model either up/down and sideways. Not > sure how to do this. Please let me know. > > Thank you, > Navya. > > ----- Original Message ---- > From: Tom Goddard > To: swethadn at yahoo.com > Cc: Chimera BB > Sent: Friday, November 30, 2007 9:27:37 AM > Subject: Re: [Chimera-users] Question regarding Chimera usage > > Hi Navya, > > The first step is to move the atomic model using the mouse close to > the correct location in the EM map. The Fit Model in Map tool will not > move the atomic model if its initial position lies outside the map. > Here are instructions on how to do the fitting. > > > http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#fitmodel > > Tom > > > > ------------------------------------------------------------------------ > Be a better pen pal. Text or chat with friends inside Yahoo! Mail. See > how. From meng at cgl.ucsf.edu Mon Dec 3 15:57:22 2007 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 3 Dec 2007 15:57:22 -0800 Subject: [Chimera-users] Question regarding Chimera usage In-Reply-To: <475495BF.7070809@cgl.ucsf.edu> References: <84998.66475.qm@web52408.mail.re2.yahoo.com> <475495BF.7070809@cgl.ucsf.edu> Message-ID: <1D2D3EE5-10B3-4F2C-8055-8C085BF65572@cgl.ucsf.edu> Hi Navya, At least a few years ago, we heard of problems with button 2 in certain Windows/Logitech MouseWare setups; a workaround is given here: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/ntmouse.html I don't know if it applies to your situation or not, or even to newer Windows/Logitech setups. Best, Elaine On Dec 3, 2007, at 3:48 PM, Tom Goddard wrote: > Hi Navya, > > If you have a 3-button mouse you move the atomic model with the > middle > button. If that is not working then you probably have the mouse modes > assigned differently. You can look at and change what the mouse > buttons > do with menu entry > > Features / Preferences > > category Mouse. Usually button 2 is assigned to translate in x and y > (second column of table). It may not be assigned to that operation if > you have used other tools like volume path tracer or volume subregion > selection that reassign mouse button 2. > > Tom From gregc at cgl.ucsf.edu Mon Dec 3 16:03:16 2007 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Mon, 3 Dec 2007 16:03:16 -0800 (PST) Subject: [Chimera-users] Question regarding Chimera usage In-Reply-To: <1D2D3EE5-10B3-4F2C-8055-8C085BF65572@cgl.ucsf.edu> References: <84998.66475.qm@web52408.mail.re2.yahoo.com> <475495BF.7070809@cgl.ucsf.edu> <1D2D3EE5-10B3-4F2C-8055-8C085BF65572@cgl.ucsf.edu> Message-ID: I had forgotton about that bug. For my more recent Logitech mouse, I had to reassign the scroll wheel button from "Universal Scroll" to "Generic Button" and the scrolling still works. Greg Couch UCSF Computer Graphics Lab On Mon, 3 Dec 2007, Elaine Meng wrote: > Hi Navya, > At least a few years ago, we heard of problems with button 2 in > certain Windows/Logitech MouseWare setups; a workaround is given here: > > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/ntmouse.html > > I don't know if it applies to your situation or not, or even to newer > Windows/Logitech setups. > Best, > Elaine > > > On Dec 3, 2007, at 3:48 PM, Tom Goddard wrote: > >> Hi Navya, >> >> If you have a 3-button mouse you move the atomic model with the >> middle >> button. If that is not working then you probably have the mouse modes >> assigned differently. You can look at and change what the mouse >> buttons >> do with menu entry >> >> Features / Preferences >> >> category Mouse. Usually button 2 is assigned to translate in x and y >> (second column of table). It may not be assigned to that operation if >> you have used other tools like volume path tracer or volume subregion >> selection that reassign mouse button 2. >> >> Tom > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > From zhiheng at caltech.edu Mon Dec 3 18:15:34 2007 From: zhiheng at caltech.edu (Zhiheng Yu) Date: Mon, 03 Dec 2007 18:15:34 -0800 Subject: [Chimera-users] how to export the volume data which is stored in the memory? Message-ID: <4754B846.70706@caltech.edu> Hi, I loaded some volume data (mrc files) into Chimera remotely from a network hard drive. Unfortunately, the network hard drive crashed so I can not access those mrc files anymore. But in Chimera which was started before the drive crash, I still have the volume data and am still able to manipulate them. Apparently, these are stored in the memory. Does anyone know how can I export these data onto a hard drive. I tried "save as" but there is an I/O error since the computer was simply trying to duplicate data from the crashed drive. Any suggestion is appreciated. Thanks, Zhiheng From goddard at cgl.ucsf.edu Mon Dec 3 19:07:15 2007 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Mon, 03 Dec 2007 19:07:15 -0800 Subject: [Chimera-users] how to export the volume data which is stored in the memory? In-Reply-To: <4754B846.70706@caltech.edu> References: <4754B846.70706@caltech.edu> Message-ID: <4754C463.6050803@cgl.ucsf.edu> Hi Zhiheng, Chimera keeps the map in memory if it is being displayed. You can see if your maps are in memory using the Chimera volume dialog menu entry Features / Data Display Options and pressing the data cache "Current use" button. If your map is displayed with step size > 1 then only a subsampled copy of the map is in memory (e.g. every other data plane). The fact that you get an IO error when trying to save the map from Chimera with volume dialog menu entry File / Save map as... suggests that the map is not all in memory and is trying to read the map in order to write the full resolution file. If you sent the Chimera traceback I could give a more definitive answer. There is no capability to write out just the subsampled part of the map which is in memory. Tom From vaiana at lanl.gov Mon Dec 3 19:51:11 2007 From: vaiana at lanl.gov (Andrea C. Vaiana) Date: Mon, 03 Dec 2007 20:51:11 -0700 Subject: [Chimera-users] occupancy with pdb trajectory In-Reply-To: <4754C463.6050803@cgl.ucsf.edu> References: <4754B846.70706@caltech.edu> <4754C463.6050803@cgl.ucsf.edu> Message-ID: <4754CEAF.30401@lanl.gov> Hello everyone, I am trying to calculate water occupancies from a pdb trajectory. The trajectory was generated with gromacs and loaded correctly in Chimera. I load the trajectory and it looks fine, I select the water molecules but I get this error log (below) when issuing the "calculate occupancy" command. Any clues as to what's wrong? I have osx 10.411 on a dual core mac book pro running Chimera 1.2470. BTW I also wasn't able to directly load the gromacs trajectory (tpr and trr), the bonds were all messed up from the third frame on. Any help would be appreciated Regards, Andrea AttributeError Exception in Tk callback Function: (type: ) Args: () Traceback (innermost last): File "/Applications/Chimera.app/Contents/Resources/lib/python2.4/site-packages/Pmw/Pmw_1_2/lib/PmwBase.py", line 1747, in __call__ return apply(self.func, args) File "/Applications/Chimera.app/Contents/Resources/share/chimera/baseDialog.py", line 238, in command getattr(s, buttonFuncName(txt))() File "/Applications/Chimera.app/Contents/Resources/share/chimera/baseDialog.py", line 452, in OK self.Apply() File "/Applications/Chimera.app/Contents/Resources/share/Movie/VolumeDialog.py", line 105, in Apply volumeName=name+" ["+atomType+"]") File "/Applications/Chimera.app/Contents/Resources/share/Movie/gui.py", line 356, in computeVolume self.model.LoadFrame(fn, makeCurrent=False) File "/Applications/Chimera.app/Contents/Resources/share/Trajectory/__init__.py", line 94, in LoadFrame crds = self._ensemble[frame] AttributeError: PdbTraj instance has no attribute '__getitem__' -- Andrea C. Vaiana Theoretical Biology and Biophysics Mail stop K710, T-10 Los Alamos, NM 87545 Los Alamos National Laboratory From menetret at bu.edu Tue Dec 4 12:53:10 2007 From: menetret at bu.edu (jean-francois menetret) Date: Tue, 4 Dec 2007 15:53:10 -0500 (EST) Subject: [Chimera-users] question about the model panel Message-ID: Is there is way to reorder the position of the models in the model panel ? (For example putting the mrc files on top and the pdb files at the bottom) Jean-Fran?ois M?n?tret, PhD Boston University School of Medicine Physiology and Biophysics Department 700 Albany Street W315 Boston, MA 02118 Email: menetret at bu.edu Mailing address: 715 Albany Street From meng at cgl.ucsf.edu Tue Dec 4 13:00:16 2007 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 4 Dec 2007 13:00:16 -0800 Subject: [Chimera-users] question about the model panel In-Reply-To: References: Message-ID: <1BE20745-73BF-4919-81F3-1DB18B5A60C0@cgl.ucsf.edu> Hi Jean-Francois, I believe the order is always numerical by model ID number. If you open the MRC files before the PDB files they will be listed first (as the default behavior is to use ascending model ID numbers as files are opened). Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Dec 4, 2007, at 12:53 PM, jean-francois menetret wrote: > > Is there is way to reorder the position of the models in the model > panel ? (For example putting the mrc files on top and the pdb files > at the bottom) > > Jean-Fran?ois M?n?tret, PhD > Boston University School of Medicine > Physiology and Biophysics Department > 700 Albany Street W315 > Boston, MA 02118 > Email: menetret at bu.edu > Mailing address: 715 Albany > Street_______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From jort at nmr.mpibpc.mpg.de Tue Dec 4 13:24:11 2007 From: jort at nmr.mpibpc.mpg.de (Julien Orts) Date: Tue, 4 Dec 2007 22:24:11 +0100 Subject: [Chimera-users] (no subject) Message-ID: <6F8C035A-192C-4AA6-B0A9-D5EC268B421A@nmr.mpibpc.mpg.de> Dear Chimera people, I would like to save a lot of pdb. I have for example 500 pdb. Each saved pdb file should contains 2 pdbs of these 500 pdbs. I can write a script for this but the command write does not work for more than two pdb. Is there any other way? thank you Julien From pett at cgl.ucsf.edu Tue Dec 4 14:04:59 2007 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Tue, 4 Dec 2007 14:04:59 -0800 Subject: [Chimera-users] occupancy with pdb trajectory In-Reply-To: <4754CEAF.30401@lanl.gov> References: <4754B846.70706@caltech.edu> <4754C463.6050803@cgl.ucsf.edu> <4754CEAF.30401@lanl.gov> Message-ID: <9CBB43E2-6A01-4FFD-B032-9313CD469111@cgl.ucsf.edu> Hi Andrea, I _believe_ this indicates that your frames aren't consecutively numbered. Is your PDB input a single file with multiple MODEL records. If so, are the numbers on these MODEL records consecutive? Chimera should probably handle non-consecutive numbering (at least when there's a regular "stride") but it doesn't yet. I'd also be interested in looking at your tpr/trr problem if you could get the files to me. How big are they? --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Dec 3, 2007, at 7:51 PM, Andrea C. Vaiana wrote: > Hello everyone, > > I am trying to calculate water occupancies from a pdb trajectory. The > trajectory was generated with gromacs and loaded correctly in > Chimera. I > load the trajectory and it looks fine, I select the water molecules > but > I get this error log (below) when issuing the "calculate occupancy" > command. Any clues as to what's wrong? I have osx 10.411 on a dual > core > mac book pro running Chimera 1.2470. > BTW I also wasn't able to directly load the gromacs trajectory (tpr > and > trr), the bonds were all messed up from the third frame on. > > Any help would be appreciated > > Regards, > Andrea > > > AttributeError Exception in Tk callback > Function: (type: ) > Args: () > Traceback (innermost last): > File > "/Applications/Chimera.app/Contents/Resources/lib/python2.4/site- > packages/Pmw/Pmw_1_2/lib/PmwBase.py", > line 1747, in __call__ > return apply(self.func, args) > File > "/Applications/Chimera.app/Contents/Resources/share/chimera/ > baseDialog.py", > line 238, in command > getattr(s, buttonFuncName(txt))() > File > "/Applications/Chimera.app/Contents/Resources/share/chimera/ > baseDialog.py", > line 452, in OK > self.Apply() > File > "/Applications/Chimera.app/Contents/Resources/share/Movie/ > VolumeDialog.py", > line 105, in Apply > volumeName=name+" ["+atomType+"]") > File > "/Applications/Chimera.app/Contents/Resources/share/Movie/gui.py", > line > 356, in computeVolume > self.model.LoadFrame(fn, makeCurrent=False) > File > "/Applications/Chimera.app/Contents/Resources/share/Trajectory/ > __init__.py", > line 94, in LoadFrame > crds = self._ensemble[frame] > AttributeError: PdbTraj instance has no attribute '__getitem__' > > > -- > > Andrea C. Vaiana > Theoretical Biology and Biophysics > Mail stop K710, T-10 > Los Alamos, NM 87545 > Los Alamos National Laboratory > > > > > > > > > > _______________________________________________ > 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 Tue Dec 4 14:51:33 2007 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 4 Dec 2007 14:51:33 -0800 Subject: [Chimera-users] (no subject) In-Reply-To: <6F8C035A-192C-4AA6-B0A9-D5EC268B421A@nmr.mpibpc.mpg.de> References: <6F8C035A-192C-4AA6-B0A9-D5EC268B421A@nmr.mpibpc.mpg.de> Message-ID: <5961425F-BB48-46C5-8DB1-026B12C762D0@cgl.ucsf.edu> Dear Julien, It is difficult to answer without knowing more about your situation, but I will describe what can be done in Chimera. The "write" command creates one PDB file containing atoms from one model ID number. If you opened your 500 structures from 500 separate PDB files, they will have 500 different model ID numbers (#0 #1 #2 ...), so "write" cannot be used to combine them. However, if you opened the 500 structures from a single PDB file, where MODEL/ENDMDL records are used to indicate the start and stop of each structure, they will be opened as submodels but with the same model ID number (#0.1 #0.2 #0.3 ...). For examples of this single- file input, see any NMR structure ensemble from the Protein DataBank, such as 1plx. In this single-file case, you can select any set of the submodels and write their coordinates to a single PDB file with "write" and the "selected" keyword: open 1plx select #0.1 #0.3 #0.5 write selected 0 1-3-5.pdb select #0.2 #0.25 write selected 0 2-25.pdb ... Disadvantages: (1) you still need to do a separate selection and write command for each pair; depending on how many pairs you planned to write, you might want to write a script to create the Chimera script. (2) the written files will still contain the MODEL and ENDMDL lines for submodels for which no atomic coordinates are included, which you might want to remove depending on what you are going to do with the files. The effect of not removing them is that when you open the file later in Chimera, it will still say there are 80 submodels (or whatever the total number you started with was) in the Model Panel even though some contain 0 atoms. The display will only show the coordinates you wanted, however. Given these issues, you might prefer to use your own scripts. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Dec 4, 2007, at 1:24 PM, Julien Orts wrote: > Dear Chimera people, > I would like to save a lot of pdb. I have for example 500 pdb. > Each saved pdb file should contains 2 pdbs of these 500 pdbs. > I can write a script for this but the command > write does not work for more than two pdb. > Is there any other way? > thank you > Julien From zhiheng at caltech.edu Tue Dec 4 10:26:16 2007 From: zhiheng at caltech.edu (Zhiheng Yu) Date: Tue, 04 Dec 2007 10:26:16 -0800 Subject: [Chimera-users] how to export the volume data which is stored in the memory? In-Reply-To: <4754C463.6050803@cgl.ucsf.edu> References: <4754B846.70706@caltech.edu> <4754C463.6050803@cgl.ucsf.edu> Message-ID: <47559BC8.4050803@caltech.edu> Hi Tom, Thanks for your prompt reply. All my maps are displayed with stepsize 1,1,1. I can rotate them, change contour level and do all sorts of manipulations as normal. But I can not save them. I attached the traceback as a file. Thanks for your help. Zhiheng Tom Goddard wrote: > Hi Zhiheng, > > Chimera keeps the map in memory if it is being displayed. You can > see if your maps are in memory using the Chimera volume dialog menu > entry Features / Data Display Options and pressing the data cache > "Current use" button. If your map is displayed with step size > 1 > then only a subsampled copy of the map is in memory (e.g. every other > data plane). > > The fact that you get an IO error when trying to save the map from > Chimera with volume dialog menu entry File / Save map as... suggests > that the map is not all in memory and is trying to read the map in > order to write the full resolution file. If you sent the Chimera > traceback I could give a more definitive answer. There is no > capability to write out just the subsampled part of the map which is > in memory. > > Tom > -------------- next part -------------- A non-text attachment was scrubbed... Name: traceback.log Type: text/x-log Size: 9887 bytes Desc: not available URL: From vaiana at lanl.gov Wed Dec 5 10:18:07 2007 From: vaiana at lanl.gov (Andrea C. Vaiana) Date: Wed, 05 Dec 2007 11:18:07 -0700 Subject: [Chimera-users] occupancy with pdb trajectory In-Reply-To: <9CBB43E2-6A01-4FFD-B032-9313CD469111@cgl.ucsf.edu> References: <4754B846.70706@caltech.edu> <4754C463.6050803@cgl.ucsf.edu> <4754CEAF.30401@lanl.gov> <9CBB43E2-6A01-4FFD-B032-9313CD469111@cgl.ucsf.edu> Message-ID: <4756EB5F.2000707@lanl.gov> Hi Eric, Thanks for the prompt reply. Yes, my pdb is a single file with multiple MODEL records. The numbers on the records are consecutive, so I guess that's not the problem. My original tpr + trr files are a total of ~25M (do you think your email can handle it?). The pdb file was >100M but I've tried on a smaller one (with only the first 4 frames of the run) and get the same error message. I guess email can handle the small pdb file (1M zipped), I will send this in a separate email. Let me know if/how I can send you the tpr/trr files. Andrea Eric Pettersen wrote: > Hi Andrea, > I _believe_ this indicates that your frames aren't consecutively > numbered. Is your PDB input a single file with multiple MODEL > records. If so, are the numbers on these MODEL records > consecutive? Chimera should probably handle non-consecutive numbering > (at least when there's a regular "stride") but it doesn't yet. > I'd also be interested in looking at your tpr/trr problem if you could > get the files to me. How big are they? > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > > -- Andrea C. Vaiana Theoretical Biology and Biophysics Mail stop K710, T-10 Los Alamos, NM 87545 Los Alamos National Laboratory From goddard at cgl.ucsf.edu Wed Dec 5 10:22:35 2007 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Wed, 05 Dec 2007 10:22:35 -0800 Subject: [Chimera-users] how to export the volume data which is stored in the memory? In-Reply-To: <47559BC8.4050803@caltech.edu> References: <4754B846.70706@caltech.edu> <4754C463.6050803@cgl.ucsf.edu> <47559BC8.4050803@caltech.edu> Message-ID: <4756EC6B.4090708@cgl.ucsf.edu> Hi Zhiheng, You must be using an older version of Chimera. Old versions read the original file even if the map was in memory when writing out the data. Maybe I can give you a script that will write the maps out from memory if you tell me what version of Chimera you are running (menu entry Help / About UCSF Chimera). Tom From goddard at cgl.ucsf.edu Wed Dec 5 11:19:37 2007 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Wed, 05 Dec 2007 11:19:37 -0800 Subject: [Chimera-users] how to export the volume data which is stored in the memory? In-Reply-To: <4756F0C3.8080004@caltech.edu> References: <4754B846.70706@caltech.edu> <4754C463.6050803@cgl.ucsf.edu> <47559BC8.4050803@caltech.edu> <4756EC6B.4090708@cgl.ucsf.edu> <4756F0C3.8080004@caltech.edu> Message-ID: <4756F9C9.2070906@cgl.ucsf.edu> Hi Zhiheng, Here is a script to write out the maps in memory using Chimera 1.2199. You open this script with menu entry File / Open... from the main Chimera window. It will write the files to /tmp. Of course be sure to check those files before closing Chimera. Tom Zhiheng Yu wrote: > Hi Tom, > > I got the following information: > > Beta Version 1 build 2199 2006/01/24 > Platform: linux 2. Windowing system:x11. > > Apparently, it is an older version. > > Thank you very much for your generous help. I really appreciate it. > > Zhiheng > > Tom Goddard wrote: >> Hi Zhiheng, >> >> You must be using an older version of Chimera. Old versions read >> the original file even if the map was in memory when writing out the >> data. Maybe I can give you a script that will write the maps out >> from memory if you tell me what version of Chimera you are running >> (menu entry Help / About UCSF Chimera). >> >> Tom >> -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: writemaps-2199.py URL: From pett at cgl.ucsf.edu Wed Dec 5 12:10:58 2007 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 5 Dec 2007 12:10:58 -0800 Subject: [Chimera-users] occupancy with pdb trajectory In-Reply-To: <4756EB5F.2000707@lanl.gov> References: <4754B846.70706@caltech.edu> <4754C463.6050803@cgl.ucsf.edu> <4754CEAF.30401@lanl.gov> <9CBB43E2-6A01-4FFD-B032-9313CD469111@cgl.ucsf.edu> <4756EB5F.2000707@lanl.gov> Message-ID: <988FF6E5-6D62-483F-B57F-E97490A0736A@cgl.ucsf.edu> Hi Andrea, It turns out that not all functions of MD Movie (such as occupancy calculation) were able to handle trajectories where the first coordinate set was numbered as zero -- as was the case with your file where the first MODEL was zero. I have fixed the code now and it should be available tomorrow from the "Daily Builds" link on the Chimera home page (check the date on the build to make sure the build worked -- the date on tomorrow's build should be Dec 5 since it will build this evening). If you want to do something before then your options are: 1) delete MODEL zero from your file 2) renumber the MODELs in your file 3) Change zero to the highest model number + 1 4) I can send you the changes to the MD Movie module (let me know) --Eric P.S. My mailer should be able to handle the tpr/trr combo. Give it a whirl. If it fails, let me know -- there are other transfer options. On Dec 5, 2007, at 10:18 AM, Andrea C. Vaiana wrote: > Hi Eric, > > Thanks for the prompt reply. Yes, my pdb is a single file with > multiple MODEL records. The numbers on the records are consecutive, > so I guess that's not the problem. My original tpr + trr files are > a total of ~25M (do you think your email can handle it?). The pdb > file was >100M but I've tried on a smaller one (with only the first > 4 frames of the run) and get the same error message. I guess email > can handle the small pdb file (1M zipped), I will send this in a > separate email. Let me know if/how I can send you the tpr/trr files. > > Andrea > > Eric Pettersen wrote: >> Hi Andrea, >> I _believe_ this indicates that your frames aren't consecutively >> numbered. Is your PDB input a single file with multiple MODEL >> records. If so, are the numbers on these MODEL records >> consecutive? Chimera should probably handle non-consecutive >> numbering (at least when there's a regular "stride") but it >> doesn't yet. >> I'd also be interested in looking at your tpr/trr problem if you >> could get the files to me. How big are they? >> >> --Eric >> >> Eric Pettersen >> UCSF Computer Graphics Lab >> http://www.cgl.ucsf.edu >> >> >> > > -- > > Andrea C. Vaiana > Theoretical Biology and Biophysics > Mail stop K710, T-10 > Los Alamos, NM 87545 > Los Alamos National Laboratory > > > > > > > > > From shengzhiya at nibs.ac.cn Fri Dec 7 01:55:22 2007 From: shengzhiya at nibs.ac.cn (shengzhiya at nibs.ac.cn) Date: Fri, 7 Dec 2007 17:55:22 +0800 (HKT) Subject: [Chimera-users] Writing alignment and RMSD out Message-ID: <4759188A.00008A.30913@mail7.corpease.net> Dear all, I would like to write both the sequence alignment and RMSD out after run ?mmaker?, but I do NOT want to do this interactively because I have a batch of structures to deal with. I found Eric?s python script: structAlign.py, which is gui-only, but I do not know how to extract RMSD from the Reply Log in gui mode. Any help would be appreciated. Thanks a lot! Btw, may I know how to run structAlign.py? Is there any command like ?chimera structAlign.py? and where should I put the input file structList? I can not run this script right now and here is the error message I got after run ?chimera structAlign.py?: Traceback (most recent call last): File "/home/sheng/local/bin/chimera/share/__main__.py", line 59, in ? value = chimeraInit.init(sys.argv) File "CHIMERA/share/chimeraInit.py", line 298, in init chimera.openModels.open(a, prefixableType=1) File "CHIMERA/share/chimera/__init__.py", line 1253, in open File "CHIMERA/share/chimera/__init__.py", line 746, in _openPython File "/home/sheng/local/bin/chimera/from_mailinglist/structAlign.py", line 18, in ? pdb1, pdb2, output = line.strip().split() ValueError: need more than 2 values to unpack Error while processing structAlign.py: ValueError: need more than 2 values to unpack (see reply log for Python traceback info) Best wishes, Zhiya -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Fri Dec 7 12:09:34 2007 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Fri, 7 Dec 2007 12:09:34 -0800 Subject: [Chimera-users] Writing alignment and RMSD out In-Reply-To: <4759188A.00008A.30913@mail7.corpease.net> References: <4759188A.00008A.30913@mail7.corpease.net> Message-ID: <93851F4E-0329-4828-935A-9899FCAD984E@cgl.ucsf.edu> Hi Zhiya, That error indicates that your "structList" file has a line that only has two fields, but three are required: pdb1, pdb2, output_file. E.g. a line like this: /mol/pdb/mn/pdb2mnr.ent /mol/pdb/en/pdb4enl.ent aligned.msf which would align the two named PDB files and write the alignment to aligned.msf. Now, there have been some improvements/changes in Chimera since the time that the structAlign.py script was written (2005). I've appended a revised version of the script that not only writes out the alignment, but writes out a second file with the RMSD (same name as the alignment file but with ".rmsd" appended). Since it seems that you didn't care about the Match->Align part of the original script, I cut that part out -- so the alignment is just what MatchMaker generates. --Eric -------------- next part -------------- A non-text attachment was scrubbed... Name: structAlign2.py Type: text/x-python-script Size: 1809 bytes Desc: not available URL: -------------- next part -------------- On Dec 7, 2007, at 1:55 AM, "" wrote: > Dear all, > > I would like to write both the sequence alignment and RMSD out > after run ?mmaker?, but I do NOT want to do this interactively > because I have a batch of structures to deal with. I found Eric?s > python script: structAlign.py, which is gui-only, but I do not know > how to extract RMSD from the Reply Log in gui mode. Any help would > be appreciated. Thanks a lot! > > Btw, may I know how to run structAlign.py? Is there any command > like ?chimera structAlign.py? and where should I put the input file > structList? I can not run this script right now and here is the > error message I got after run ?chimera structAlign.py?: > Traceback (most recent call last): > File "/home/sheng/local/bin/chimera/share/__main__.py", line 59, in ? > value = chimeraInit.init(sys.argv) > File "CHIMERA/share/chimeraInit.py", line 298, in init > chimera.openModels.open(a, prefixableType=1) > File "CHIMERA/share/chimera/__init__.py", line 1253, in open > File "CHIMERA/share/chimera/__init__.py", line 746, in _openPython > File "/home/sheng/local/bin/chimera/from_mailinglist/ > structAlign.py", line 18, in ? > pdb1, pdb2, output = line.strip().split() > ValueError: need more than 2 values to unpack > Error while processing structAlign.py: > ValueError: need more than 2 values to unpack > (see reply log for Python traceback info) > > > Best wishes, > Zhiya > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From shengzhiya at nibs.ac.cn Mon Dec 10 02:54:33 2007 From: shengzhiya at nibs.ac.cn (shengzhiya at nibs.ac.cn) Date: Mon, 10 Dec 2007 18:54:33 +0800 (HKT) Subject: [Chimera-users] Writing alignment and RMSD out In-Reply-To: <93851F4E-0329-4828-935A-9899FCAD984E@cgl.ucsf.edu> References: <4759188A.00008A.30913@mail7.corpease.net> <93851F4E-0329-4828-935A-9899FCAD984E@cgl.ucsf.edu> Message-ID: <475D1AE9.00002A.02186@mail7.corpease.net> Dear Eric, Thank you very much for your reply and I apologize for this late ?thank you?! I am out of town and can not touch the internet during the weekend. I still got several questions here. Would you please help me? 1. The significance of RMSD varies with the numbers of atom pairs, so maybe it makes more sense if I can write out the number of atom pairs at the same time. Is this possible? 2. I think I need the alignment from Match->Align, which better represents the structure alignment. Sorry I kind of got stuck on the output problem, and forgot what I need in the first place. And I am curious about which residues are included in the ?core? regions and used for RMSD calculation after turning on the ?iterate? option. Can I see this from the Match->Align output? It seems that even if I choose the same cutoff in Match->Align as in iteration, the number of aligned residues is still not the same as the number of atom pairs in RMSD calculation. 3. Also, I am really sorry for not mention this in my first letter -- can I write the transformed PDB file out at the same time? I can only do this with a ?.com? file but not a python script. Thank you very much for your help! Have a nice day! Best wishes, Zhiya -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Mon Dec 10 14:54:50 2007 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 10 Dec 2007 14:54:50 -0800 Subject: [Chimera-users] Writing alignment and RMSD out In-Reply-To: <475D1AE9.00002A.02186@mail7.corpease.net> References: <4759188A.00008A.30913@mail7.corpease.net> <93851F4E-0329-4828-935A-9899FCAD984E@cgl.ucsf.edu> <475D1AE9.00002A.02186@mail7.corpease.net> Message-ID: Hi Zhiya, I've attached an enhanced version of the script that covers your additional needs. Changes are: 1) writes out # of residues pairs involved in RMSD 2) appends list of those residue pairs 3) does the Match->Align step and writes that alignment instead of MatchMaker alignment 4) writes out transformed version of second PDB 5) if alignment file is named xxx.msf, then RMSD file is xxx.rmsd (instead of xxx.msf.rmsd) and PDB file is xxx.pdb Note that in a Python script if you know how to do something with a Chimera command you can do the same thing in the script by using the "runCommand" function. So for instance if you look in the script you can see that I write the PDB file by using runCommand with an string argument that is the same as the "write" command that you would use at the Chimera command line to write the PDB file. Also, you may want change the script to use different values in the calls to the MatchMaker and Match->Align functions than what I used. For instance, the call to Match->Align uses a distance cutoff of 4.0 (same as the 2005 script) whereas the default cutoff nowadays is 5.0. In regards to Match->Align producing a different number of aligned columns than the MatchMaker "core" even with the same cutoff value, that is totally believable. You will get situations where loop residues happen to cross each other within the cutoff distance but those residues were not in the same column of the MatchMaker alignment [nor should they be really] and therefore could not be in it's final "core". --Eric -------------- next part -------------- A non-text attachment was scrubbed... Name: structAlign3.py Type: text/x-python-script Size: 2948 bytes Desc: not available URL: -------------- next part -------------- On Dec 10, 2007, at 2:54 AM, "" wrote: > Dear Eric, > > Thank you very much for your reply and I apologize for this late > ?thank you?! I am out of town and can not touch the internet during > the weekend. > > I still got several questions here. Would you please help me? > 1. The significance of RMSD varies with the numbers of atom pairs, > so maybe it makes more sense if I can write out the number of atom > pairs at the same time. Is this possible? > 2. I think I need the alignment from Match->Align, which better > represents the structure alignment. Sorry I kind of got stuck on > the output problem, and forgot what I need in the first place. And > I am curious about which residues are included in the ?core? > regions and used for RMSD calculation after turning on the > ?iterate? option. Can I see this from the Match->Align output? It > seems that even if I choose the same cutoff in Match->Align as in > iteration, the number of aligned residues is still not the same as > the number of atom pairs in RMSD calculation. > 3. Also, I am really sorry for not mention this in my first letter > -- can I write the transformed PDB file out at the same time? I can > only do this with a ?.com? file but not a python script. > > Thank you very much for your help! > > Have a nice day! > > Best wishes, > Zhiya > > From meng at cgl.ucsf.edu Mon Dec 10 15:31:27 2007 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 10 Dec 2007 15:31:27 -0800 Subject: [Chimera-users] Writing alignment and RMSD out In-Reply-To: References: <4759188A.00008A.30913@mail7.corpease.net> <93851F4E-0329-4828-935A-9899FCAD984E@cgl.ucsf.edu> <475D1AE9.00002A.02186@mail7.corpease.net> Message-ID: <4D49AE2B-4B23-46A8-B183-0ADF0868E91A@cgl.ucsf.edu> On Dec 10, 2007, at 2:54 PM, Eric Pettersen wrote: > In regards to Match->Align producing a different number of aligned > columns than the MatchMaker "core" even with the same cutoff value, > that is totally believable. You will get situations where loop > residues happen to cross each other within the cutoff distance but > those residues were not in the same column of the MatchMaker > alignment [nor should they be really] and therefore could not be in > it's final "core". Just wanted to add: I've found that with more difficult-to-align sequences (worst case is very low sequence identity and all-beta or all-alpha secondary structure), there may be incorrect segments in the initial MatchMaker alignment that are corrected in alignment from a subsequent Match- >Align step. The purpose of MatchMaker is to generate a correct superposition, and this is still successful in nearly all cases because the incorrect areas are pruned during fit iteration (only the correct columns are used to generate the final superposition). Match- >Align will then generate columns for all the superimposed parts, some of which were not used in the prior fitting step. Which alignment is better depends on the situation. For example, there could be different structures of the same protein where one loop moves a lot. The MatchMaker alignment will simply align the entire identical or nearly identical sequences, whereas Match->Align will not align the loops that are poorly superimposed in space. If you are comparing different structural matches, especially hard-to- align distantly related cases, it may be more appropriate to use the number of pairs in the Match->Align alignment rather than those values from MatchMaker. In our paper, for example, we reported the number of pairs and RMSDs from the Match->Align alignment, not the MatchMaker one: Tools for integrated sequence-structure analysis with UCSF Chimera: E.C. Meng, E.F. Pettersen, G.S. Couch, C.C. Huang, and T.E. Ferrin, BMC Bioinformatics 7, 339 (2006). http://www.biomedcentral.com/ 1471-2105/7/339 The drawback is that getting that RMSD value requires another round of fitting, this time on all positions in the Match->Align alignment (without iteration). This may have been more detail than you wanted! Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html From shengzhiya at nibs.ac.cn Mon Dec 10 20:38:55 2007 From: shengzhiya at nibs.ac.cn (shengzhiya at nibs.ac.cn) Date: Tue, 11 Dec 2007 12:38:55 +0800 (HKT) Subject: [Chimera-users] Writing alignment and RMSD out In-Reply-To: References: <4759188A.00008A.30913@mail7.corpease.net> <93851F4E-0329-4828-935A-9899FCAD984E@cgl.ucsf.edu> <475D1AE9.00002A.02186@mail7.corpease.net> Message-ID: <475E145F.000170.23957@mail7.corpease.net> Dear Eric and Elaine, Thank you so much for your help and advice! Best wishes, Zhiya -------------- next part -------------- An HTML attachment was scrubbed... URL: From chiendarret at yahoo.com Thu Dec 13 07:49:19 2007 From: chiendarret at yahoo.com (Francesco Pietra) Date: Thu, 13 Dec 2007 07:49:19 -0800 (PST) Subject: [Chimera-users] printing "zone" search Message-ID: <68307.93096.qm@web57606.mail.re1.yahoo.com> I am looking at the protein residues "responsible" for docking a single-residue ligand. select protein & :ligandname z<# works for various values of #. I would like to print the list of residues instead of having to detect them from the screen, which may lead to errors. Also, which section of the manual concerns RMSD? (I would like to calculate RMSD at various stages of DOCK6.1 and Amber9 MD for the above, i..e. how the ligand adapts and the protein follows it, or vice-versa). Thanks francesco pietra ____________________________________________________________________________________ Never miss a thing. Make Yahoo your home page. http://www.yahoo.com/r/hs From meng at cgl.ucsf.edu Thu Dec 13 09:17:23 2007 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 13 Dec 2007 09:17:23 -0800 Subject: [Chimera-users] printing "zone" search In-Reply-To: <68307.93096.qm@web57606.mail.re1.yahoo.com> References: <68307.93096.qm@web57606.mail.re1.yahoo.com> Message-ID: Hi Francesco, You can write out a list of what is selected with "Actions... Write List" or the coordinates of the selected atoms as a PDB file with "Actions... Write PDB". The dialog for writing a list lets you choose whether you want atoms or just residues listed, and the style to use, as explained here: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/menu.html#writespec There are several features (and corresponding parts of the documentation) that relate to RMSD. If you choose "Help... Search Documentation" from the menu and search for "rmsd" you get a list. From your description, you probably want to use the command "rmsd" - it calculates RMSD between two sets of atoms without moving/fitting them. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html Other things that relate to RMSD (see documentation if you need more details): - the "match" command, which fits the two specified sets of atoms and then reports the resulting RMSD - "matchmaker" command or MatchMaker tool, superimposes proteins and reports alpha-carbon RMSD for the residue pairs used in the fit - EnsembleMatch tool, which calculates all pairwise RMSD values for specified atoms within an ensemble of structures that contain identical atoms - MD Movie tool, which can calculate all pairwise RMSD values for selected atoms within frames of a trajectory I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Dec 13, 2007, at 7:49 AM, Francesco Pietra wrote: > I am looking at the protein residues "responsible" for docking a > single-residue > ligand. > > select protein & :ligandname z<# > > works for various values of #. I would like to print the list of > residues > instead of having to detect them from the screen, which may lead to > errors. > > Also, which section of the manual concerns RMSD? (I would like to > calculate > RMSD at various stages of DOCK6.1 and Amber9 MD for the above, > i..e. how the > ligand adapts and the protein follows it, or vice-versa). > > Thanks > francesco pietra From JeanDidier.Marechal at uab.cat Thu Dec 13 15:07:27 2007 From: JeanDidier.Marechal at uab.cat (Jean Didier Pie Marechal) Date: Fri, 14 Dec 2007 00:07:27 +0100 Subject: [Chimera-users] Morphing on small ligand Message-ID: <188dafce62e.4761c93f@uab.es> Hi everyone, I have a " small" ligand with two substantially different conformations. Just for interest: could we use the morphing module to generate intermediate conformations between those two structures? Cheers, JD Dr. Jean-Didier Mar?chal Professor Lector Unitat de Qu?mica F?sica Departament de Qu?mica Universitat Aut?noma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal at uab.es From meng at cgl.ucsf.edu Thu Dec 13 16:11:50 2007 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 13 Dec 2007 16:11:50 -0800 Subject: [Chimera-users] Morphing on small ligand In-Reply-To: <188dafce62e.4761c93f@uab.es> References: <188dafce62e.4761c93f@uab.es> Message-ID: <89167E5C-D370-4A5C-9781-40ED57CF0818@cgl.ucsf.edu> Hi JD, Currently the Morph Conformations tool is only applicable to alignable chains of residues such as proteins (and I think nucleic acids, although I haven't tried them). Best, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Dec 13, 2007, at 3:07 PM, Jean Didier Pie Marechal wrote: > Hi everyone, > > I have a " small" ligand with two substantially different > conformations. Just for interest: could we use the morphing module > to generate intermediate conformations between those two structures? > > Cheers, > JD > > > Dr. Jean-Didier Mar?chal > Professor Lector > Unitat de Qu?mica F?sica > Departament de Qu?mica > Universitat Aut?noma de Barcelona > Edifici C.n. > 08193 Cerdanyola (Barcelona) > Tel: +34.935814936 > e-mail: JeanDidier.Marechal at uab.es > > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From pavlovicz.7 at osu.edu Fri Dec 14 08:23:34 2007 From: pavlovicz.7 at osu.edu (Ryan) Date: Fri, 14 Dec 2007 11:23:34 -0500 Subject: [Chimera-users] printing "zone" search Message-ID: <16c560165960.16596016c560@osu.edu> I am actually currently interested in doing something similar to Francesco's previous question about writing out a list of residue names within a certain zone of a ligand -- however i would like to do this from a Python script. I tried to find the zone selection command to use in a script, but could not. Would it be easiest to just use the runCommand('z<') function to select a zone? Also, when the zone is selected, are the selected residue names stored in a list? If so, how can i access this list to print out the residue names into an output file of my own? Thanks a lot, ryan From vrr1 at columbia.edu Fri Dec 14 09:59:13 2007 From: vrr1 at columbia.edu (Vincent Racaniello) Date: Fri, 14 Dec 2007 12:59:13 -0500 Subject: [Chimera-users] edges Message-ID: When I display a protein as an edged ribbon, sometimes they have a black line on the edges, other times none. There seems to be no consistency in this behavior. The same also happens with surfaces. Is there a way to regulate this appearance? From meng at cgl.ucsf.edu Fri Dec 14 10:16:22 2007 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 14 Dec 2007 10:16:22 -0800 Subject: [Chimera-users] edges In-Reply-To: References: Message-ID: <9C1182B2-0563-42F4-AC12-015315A4C505@cgl.ucsf.edu> Hi Vincent, Maybe you are referring to "silhouette edges" - these are absolutely controllable, however, either by choosing a Preset that does or does not include them (from the Presets menu) or by opening the Effects tool (under Tools... Viewing Controls) and turning them on or off. http://www.cgl.ucsf.edu/home/meng/docs/UsersGuide/menu.html#menupresets http://www.cgl.ucsf.edu/home/meng/docs/UsersGuide/sideview.html#effects That seems the most likely to me. Otherwise, I have no idea why black edges might appear in the interactive Chimera display (graphics driver bug?). I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Dec 14, 2007, at 9:59 AM, Vincent Racaniello wrote: > When I display a protein as an edged ribbon, sometimes they have a > black line on the edges, other times none. There seems to be no > consistency in this behavior. The same also happens with surfaces. Is > there a way to regulate this appearance? From pett at cgl.ucsf.edu Fri Dec 14 11:26:53 2007 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Fri, 14 Dec 2007 11:26:53 -0800 Subject: [Chimera-users] printing "zone" search In-Reply-To: <16c560165960.16596016c560@osu.edu> References: <16c560165960.16596016c560@osu.edu> Message-ID: On Dec 14, 2007, at 8:23 AM, Ryan wrote: > I am actually currently interested in doing something similar to > Francesco's previous question about writing out a list of residue > names within a certain zone of a ligand -- however i would like to > do this from a Python script. > > I tried to find the zone selection command to use in a script, but > could not. Would it be easiest to just use the runCommand('z<') > function to select a zone? Using runCommand() would be by far the easiest and is what I would recommend. Nonetheless, there are alternatives. I've appended a script that finds all NZ atoms of lysines that are within 8 angstroms of an NZ of a different lysine. It calls into the underlying chimera.specifier.zone() function since it needs to do additional processing to exclude each lysine's own NZ atom when examining the zones for NZs within 8 angstroms. If efficiency is important (and it doesn't sound like it really is from your description) you would want to consider using the _closepoints module to quickly eliminate most atoms that aren't in the zone, but then you have to process the remainder to ensure that they meet the zone criteria (some remaining ones won't). Look at the start of the detectClash() function in DetectClash/__init__.py for an example. > Also, when the zone is selected, are the selected residue names > stored in a list? If so, how can i access this list to print out > the residue names into an output file of my own? chimera.selection.currentResidues() returns such a list. --Eric From pett at cgl.ucsf.edu Fri Dec 14 11:29:10 2007 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Fri, 14 Dec 2007 11:29:10 -0800 Subject: [Chimera-users] printing "zone" search In-Reply-To: References: <16c560165960.16596016c560@osu.edu> Message-ID: Of course, I forgot to actually attach the script I mentioned! -------------- next part -------------- A non-text attachment was scrubbed... Name: selLys.py Type: text/x-python-script Size: 643 bytes Desc: not available URL: From kenjang at gmail.com Fri Dec 14 13:24:21 2007 From: kenjang at gmail.com (Ken Jang) Date: Fri, 14 Dec 2007 16:24:21 -0500 Subject: [Chimera-users] Multi-scale models and BIOMT Message-ID: <26de96750712141324m67d8b8a2tde9860fcc6d2beae@mail.gmail.com> Hello, I work at Boston University working mostly with pili and helical reconstructions. Recently we have been trying to fit our subunit structures into maps generated from EM data. Because what we work with are helical in nature, we use BIOMT symmetry since it is the easiest to generate using readily available data. We wanted to see just how close our subunits get and wanted to use the MSC or Color Zone commands, but we have run into a problem with the Multi-Scale Models command. Since we are using the same BIOMT data, we assumed that Multi-Scale Models would use the same origin and orientation. This appears to be the case if we don't move the subunit structure after opening it, but after we move the subunit, the generated models don't seem to be in any relavent orientation. I have attached two pictures, both from the same view, and one showing the placement of the subunits using the 'sym' command and the other showing the surface models using Multi-Scale models. Both cases were generated off the same selected subunit. Any advice or clarification on how to use Mult-Scale Models and BIOMT information would be greatly appreciated. Be seeing you- Ken Jang -and all places are alike to me -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: sym_subunits.png Type: image/png Size: 1139157 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Multiscale_models_surfaces.png Type: image/png Size: 1124496 bytes Desc: not available URL: From goddard at cgl.ucsf.edu Fri Dec 14 14:30:00 2007 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Fri, 14 Dec 2007 14:30:00 -0800 Subject: [Chimera-users] Multi-scale models and BIOMT In-Reply-To: <26de96750712141324m67d8b8a2tde9860fcc6d2beae@mail.gmail.com> References: <26de96750712141324m67d8b8a2tde9860fcc6d2beae@mail.gmail.com> Message-ID: <476303E8.5010509@cgl.ucsf.edu> Hi Ken, Here's what's going on. You have BIOMT matrices in your PDB file that specify the rotations and translations that operate in the coordinate system of the EM map. This is just what the Chimera "sym" command expects. The multiscale model tool though assumes that the BIOMT matrices act in the coordinate system of the PDB atoms. It knows nothing about the volume. The trouble is that you've moved the PDB model relative to the map using "Fit model in map". So the coordinate frame for the PDB atoms is no longer aligned with the coordinate frame of the EM map. In some cases this is what you want. For example if your BIOMT matrices said how to make an icosahedral virus from a monomeric subunit, you'd want it still to make the correct icosahedron if you first fit the monomer into a density map. But in your case it isn't so nice since your BIOMT matrices are defined relative to the map coordinates. Here's the fix. Fit your PDB model into the map, then use File / Save PDB..., turn on the "Save relative to mymap.mrc" option and save the new PDB. Put the BIOMT matrices in that PDB file that has already been fit into the map and multiscale will work with it. Tom From pavlovicz.7 at osu.edu Fri Dec 14 16:55:39 2007 From: pavlovicz.7 at osu.edu (Ryan) Date: Fri, 14 Dec 2007 19:55:39 -0500 Subject: [Chimera-users] printing "zone" search Message-ID: <17bf4817f850.17f85017bf48@osu.edu> Hi Eric, thanks for your help. I'm getting closer to achieving the results i'd like. So i've been able to properly select the residues within a specified radius of my ligand, but am a little confused as to how Chimera handles the selection list. If i try: print chimera.selection.currentResidues() i get a list like this: > [<_chimera.Residue object at 0x578d2020>, <_chimera.Residue object at 0x578cbfb0>, ... ] but if i try: for x in chimera.selection.currentResidues(): print x i get output that is much closer to what i'm looking for: > #0:499 > #0:496 > ... What is the reason for the difference between these two forms of output that seem to be accessing the same list? Also, is there a way i can get more detailed output with residue names and numbers, such as ['#0:TYR499','#0:TRP496',...]? Sorry if these questions are answered elsewhere, but i could not find the answers online. Is there a document out there that can teach me how to better master the Chimera Python modules for scripting? I'm no Python expert -- i've so far only been learning things as i need them. Thanks again, ryan From pett at cgl.ucsf.edu Fri Dec 14 23:16:02 2007 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Fri, 14 Dec 2007 23:16:02 -0800 Subject: [Chimera-users] printing "zone" search In-Reply-To: <17bf4817f850.17f85017bf48@osu.edu> References: <17bf4817f850.17f85017bf48@osu.edu> Message-ID: <44880b27156e43be457b64c624e7099c@cgl.ucsf.edu> Hi Ryan, The difference is that when you print a list, the residues in the list are shown with repr(). When you print a residue directly, it is shown with str(). Quoting the Python Tutorial, the difference between str() and repr() is: "The str() function is meant to return representations of values which are fairly human-readable, while repr() is meant to generate representations which can be read by the interpreter..." Since there is no representation of a Residue object that can be directly read by the interpreter, you get the output you saw when printing the list. The result of str() when you directly print the residue is controlled by the "Atomspec display style" preference in the General preferences category (Favorites->Preferences). It seems you have that preference set to "command-line specifier". If you change it to "simple" instead you will get output like "LYS 12.A" etc. Alternatively you could use the chimeraLabel function, e.g.: print chimera.misc.chimeraLabel(r, style="simple") Programmer documentation for Chimera is considerably less complete than user documentation. My best advice is to read through some of the Programmer's Examples (http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/ index.html) and look through the Programmer's FAQ (http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html). If you know that some Chimera tool does something similar to what you want then browse through its source code. If you don't know Python that well you might want to work through the Python Tutorial if you have time (http://www.python.org/doc/current/tut/tut.html). And feel free to ask questions; we're happy to help. --Eric On Dec 14, 2007, at 4:55 PM, Ryan wrote: > Hi Eric, thanks for your help. I'm getting closer to achieving the > results i'd like. > > So i've been able to properly select the residues within a specified > radius of my ligand, but am a little confused as to how Chimera > handles the selection list. If i try: > > print chimera.selection.currentResidues() > > i get a list like this: > >> [<_chimera.Residue object at 0x578d2020>, <_chimera.Residue object at >> 0x578cbfb0>, ... ] > > but if i try: > > for x in chimera.selection.currentResidues(): > print x > > i get output that is much closer to what i'm looking for: > >> #0:499 >> #0:496 >> ... > > What is the reason for the difference between these two forms of > output that seem to be accessing the same list? Also, is there a way > i can get more detailed output with residue names and numbers, such as > ['#0:TYR499','#0:TRP496',...]? > > Sorry if these questions are answered elsewhere, but i could not find > the answers online. Is there a document out there that can teach me > how to better master the Chimera Python modules for scripting? I'm no > Python expert -- i've so far only been learning things as i need them. > Thanks again, > > ryan > From bshaanan at bgu.ac.il Sat Dec 15 13:00:16 2007 From: bshaanan at bgu.ac.il (Boaz Shaanan) Date: Sat, 15 Dec 2007 21:00:16 GMT Subject: [Chimera-users] crystallographic symmops and lattice translations in Chimera Message-ID: Hi, Since the question was raised before, I think I know the answer to my first question about lattice translations but let me verify: 1) Chimera can apply crystallographic symmetry operations to the model as they're listed in the pdb file but it won't apply lattice translations, or in other words, won't display molecules in neighbouring unit cells. Am I correct ? maybe you can surprize me me on this and prove me wrong ? 2) Is it possible to draw the unit cell boundaries after reading in the pdb or should I read in a dummy pdb with coordinates of the unit cell vertices ? Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan? -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at cgl.ucsf.edu Sat Dec 15 16:29:31 2007 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Sat, 15 Dec 2007 16:29:31 -0800 Subject: [Chimera-users] crystallographic symmops and lattice translations in Chimera In-Reply-To: References: Message-ID: <4764716B.2030101@cgl.ucsf.edu> Hi Boaz, Chimera can apply lattice translations in a variety of ways, though there isn't currently a simple flexible command for this. The Multiscale tool (menu Tools / Higher-Order Structure) can make a 3 by 3 by 3 array of unit cells, and you can drag to select and delete unwanted monomers. The Unit Cell tool (same menu) can translate the unit cell origin (values 0-1) and reposition all asym units to have their centers in the cell. That only allows translation by a fraction of a unit cell. The Crystal Coordinates script on the experimental features web page can write out PDB files for a block of unit cells. That has to be downloaded separately: http://www.cgl.ucsf.edu/chimera/experimental/experimental.html Another trick is you could open two copies of your PDB translate one by one unit cell length along x with a command line "move x 123.5" then apply the Unit Cell tool to both copies. You'd have to get the unit cell size in x by looking at the CRYST1 record in the PDB file. The Unit Cell tool has a button "Outline unit cell" that displays an outline box for the unit cell of a chosen PDB model. Tom From bshaanan at bgu.ac.il Sun Dec 16 02:54:17 2007 From: bshaanan at bgu.ac.il (Boaz Shaanan) Date: Sun, 16 Dec 2007 10:54:17 GMT Subject: [Chimera-users] crystallographic symmops and lattice translationsin Chimera In-Reply-To: <4764716B.2030101@cgl.ucsf.edu> References: <4764716B.2030101@cgl.ucsf.edu> Message-ID: Hi Tom, Thanks so much ! You did surprize me indeed with Chimera capabilities that I wasn't aware of. I'll try your suggestions very soon. Cheers, Boaz P.S. We have a Nature Chemical Biology paper coming up soon with some Chimera pictures in it (and in the supplementary online material). I'll send the pdf's once it's online. ----- Original Message ----- From: Tom Goddard Date: Sunday, December 16, 2007 2:29 Subject: Re: [Chimera-users] crystallographic symmops and lattice translationsin Chimera To: Boaz Shaanan Cc: chimera-users at cgl.ucsf.edu > Hi Boaz, > > Chimera can apply lattice translations in a variety of > ways, though > there isn't currently a simple flexible command for this. > The > Multiscale tool (menu Tools / Higher-Order Structure) can make a > 3 by 3 > by 3 array of unit cells, and you can drag to select and delete > unwanted > monomers. The Unit Cell tool (same menu) can translate the > unit cell > origin (values 0-1) and reposition all asym units to have their > centers > in the cell. That only allows translation by a fraction of > a unit > cell. The Crystal Coordinates script on the experimental > features web > page can write out PDB files for a block of unit cells. > That has to be > downloaded separately: > > > http://www.cgl.ucsf.edu/chimera/experimental/experimental.html > Another trick is you could open two copies of your PDB translate > one by > one unit cell length along x with a command line "move x 123.5" > then > apply the Unit Cell tool to both copies. You'd have to get > the unit > cell size in x by looking at the CRYST1 record in the PDB file. > > The Unit Cell tool has a button "Outline unit cell" that > displays an > outline box for the unit cell of a chosen PDB model. > > Tom > > Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan? -------------- next part -------------- An HTML attachment was scrubbed... URL: From moocow at mindless.com Mon Dec 17 05:12:55 2007 From: moocow at mindless.com (Moo Cow) Date: Mon, 17 Dec 2007 08:12:55 -0500 Subject: [Chimera-users] setting pdb path for local mirror Message-ID: <20071217131255.1E299164288@ws1-4.us4.outblaze.com> Sorry for an easy question. Chimera has a hook to use a local mirror of the PDB (preferences-PDB) I am too thick to see what path to give it. If you have the PDB, you have the top level /blah/blah/pdb the structure directory /blah/blah/pdb/data/structures/all and the divided directory /blah/blah/pdb/data/structures/divided/pdb When a non-python reader looks at the code (__init__.py), it seems to be trying out the divided directory IDcode = IDcode.lower() subpath = IDcode[1:3] + os.sep + "pdb" + IDcode + ".ent" pdbDir = systemPDBdir() if pdbDir is not None: ..... but this does not look correct. The PDB divided path would want subpath IDcode[1:2] to get the subdirectory "pt" from a file like "5pti" Many thanks and sorry for a seemingly daft question. -- Got No Time? Shop Online for Great Gift Ideas! http://mail.shopping.com/?linkin_id=8033174 From best at biochem.mpg.de Mon Dec 17 05:50:35 2007 From: best at biochem.mpg.de (Christoph Best) Date: Mon, 17 Dec 2007 14:50:35 +0100 Subject: [Chimera-users] setting pdb path for local mirror In-Reply-To: <20071217131255.1E299164288@ws1-4.us4.outblaze.com> References: <20071217131255.1E299164288@ws1-4.us4.outblaze.com> Message-ID: <18278.32427.145216.122741@random.tigertiger.de> Moo Cow writes: > When a non-python reader looks at the code (__init__.py), it > seems to be trying out the divided directory > > IDcode = IDcode.lower() > subpath = IDcode[1:3] + os.sep + "pdb" + IDcode + ".ent" Python has a "special" way of writing indices: The subsequence is formed excluding the final index, so s[1:3] means the second and third character of s (indices 1 and 2), but excluding the fourth at index 3. -Christoph -- | Christoph Best http://www.rzg.mpg.de/~cbest | Max-Planck-Institut fuer Biochemie, Munich, Germany +49-89-8578 2634 From abbas at scripps.edu Fri Dec 14 16:36:29 2007 From: abbas at scripps.edu (Abbas) Date: Fri, 14 Dec 2007 16:36:29 -0800 Subject: [Chimera-users] Transparent background Message-ID: <4A7AD72C-711E-435A-8A46-449F0C24B725@scripps.edu> Hi, One feature I really appreciated about chimera was the ability to make pictures without a background, however recently i realized this is not possible anymore I checked out under the effects dialog under tools>viewing controls and it give me an error saying this wasn't supported. I haven't changed my computer since i first started using chimera I have updated to the latest version of chimera available for OSX 10.4, I wonder if this is the cause of the problem. I would really like to have pictures without backgrounds like I used to, I know PyMol lets you do it, but I dislike this program. In any case I would greatly appreciate any help/pointers on this issue. Thanks in advance. abbas. From pmg7 at lineone.net Sun Dec 16 09:28:31 2007 From: pmg7 at lineone.net (Peter Girard) Date: Sun, 16 Dec 2007 17:28:31 -0000 Subject: [Chimera-users] Problem with Chimera under Windows XP Message-ID: <00bd01c84009$1637fb30$f17c0056@DELL9300> I am running release 2304 of Chimera under Windows XP with service pack 2 on a Dell Inspiron 9300 laptop. The image disappears from the screen for no apparent reason. With the structures I am currently working on, this has become frequent and often occurs after just a few seconds when I click anywhere in the Chimera window. I have found that if I use Model Panel, I can get the picture back by clicking the 'Shown' box to remove the tick mark, then clicking it again to re-insert the tick. But the picture soon disappears again. Occasionally, it doesn't disappear completely, but part of it collapses, or spurious long lines appear. I had the same problem with a previous release, 2184, and was disappointed that upgrading didn't fix it. I can find no mention of anything similar in the documentation or email archive. Can anyone suggest a possible cause? Peter Girard (University of Nottingham, UK) -------------- next part -------------- An HTML attachment was scrubbed... URL: From minimayas at gmail.com Mon Dec 17 00:34:20 2007 From: minimayas at gmail.com (maya shcushan) Date: Mon, 17 Dec 2007 10:34:20 +0200 Subject: [Chimera-users] Loading .dx maps to chimera Message-ID: <001301c84087$a6772d50$0b01a8c0@NirBNB5> Dear sir, I am trying to load a .dx file (electrostatic potential) onto a molecule in chimera. I successfully loaded the map onto a the molecule's surface. The problem is the potentials I get look differently than the original map. That is, the potentials appear different in the visualization tool of PMV, the program which generated the .dx file I tried to e-load on chimera. Thanks, Maya Schushan, Tel-Aviv university, Israel. -------------- next part -------------- An HTML attachment was scrubbed... URL: From gregc at cgl.ucsf.edu Mon Dec 17 09:43:42 2007 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Mon, 17 Dec 2007 09:43:42 -0800 (PST) Subject: [Chimera-users] Transparent background In-Reply-To: <4A7AD72C-711E-435A-8A46-449F0C24B725@scripps.edu> References: <4A7AD72C-711E-435A-8A46-449F0C24B725@scripps.edu> Message-ID: On Fri, 14 Dec 2007, Abbas wrote: > Hi, > One feature I really appreciated about chimera was the ability to > make pictures without a background, however recently i realized this > is not possible anymore I checked out under the effects dialog under > tools>viewing controls and it give me an error saying this wasn't > supported. I haven't changed my computer since i first started using > chimera I have updated to the latest version of chimera available for > OSX 10.4, I wonder if this is the cause of the problem. > I would really like to have pictures without backgrounds like I used > to, I know PyMol lets you do it, but I dislike this program. In any > case I would greatly appreciate any help/pointers on this issue. > Thanks in advance. abbas. Transparent backgrounds depend on the graphics card capabilities reported by OpenGL. On Mac OS X, Apple decided not to support background transparency (nor full window antialiasing) for OpenGL/X11 applications, so to use that feature you would have to use the Aqua version of chimera. Unfortunately, the chimera's cross-platform user interface toolkit, Tk, while improving for Aqua, has gotton worse for chimera, so you'll have to use an old version of chimera for Aqua to get transparent backgrounds. You can also file a bug report with Apple to help them decide to spend the time to fix it (OpenGL "destination alpha" and multisampling not supported in X11). Greg Couch UCSF Computer Graphics Lab From goddard at cgl.ucsf.edu Mon Dec 17 09:59:29 2007 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Mon, 17 Dec 2007 09:59:29 -0800 Subject: [Chimera-users] Loading .dx maps to chimera In-Reply-To: <001301c84087$a6772d50$0b01a8c0@NirBNB5> References: <001301c84087$a6772d50$0b01a8c0@NirBNB5> Message-ID: <4766B901.6080700@cgl.ucsf.edu> Hi Maya, Perhaps you could send screen shots of the PMV and Chimera windows showing the electrostatic potential to give us a better idea of what you mean by "look different". Maybe it is a problem aligning the map with the molecule. Tom From meng at cgl.ucsf.edu Mon Dec 17 10:00:24 2007 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 17 Dec 2007 10:00:24 -0800 Subject: [Chimera-users] Loading .dx maps to chimera In-Reply-To: <001301c84087$a6772d50$0b01a8c0@NirBNB5> References: <001301c84087$a6772d50$0b01a8c0@NirBNB5> Message-ID: <69721FA0-3939-4F89-B7E2-6EA7FF25112D@cgl.ucsf.edu> Dear Maya, I don't know much about the display in PMV, but I will assume that in both programs you are coloring a surface by electrostatic potential. Possible reasons for differences in appearance: (1) the default display settings may simply be different between the two programs, that is, what values are mapped to what colors. In Chimera's Electrostatic Surface Coloring tool, the default is red (10% transparent) at -10, white (50% transparent) at 0, blue (10% transparent) at +10. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/ surfcolor.html (2) the surfaces may be different. Chimera shows a solvent-excluded surface (probe contact + reentrant), where maybe PMV is showing a solvent-accessible surface (where the probe center goes). Even if both programs are showing the solvent-excluded surface, the atomic VDW radii used to calculate the surface and the vertex density of the surface likely differ. Another variable is the probe radius, although most programs use 1.4 angstroms as the default. These differences do not mean that either program is wrong. However, in Chimera you can adjust the color/value mapping with Electrostatic Surface Coloring (under Tools... Surface/Binding Analysis), and surface vertex density and probe radius in the molecular surface attributes panel (choose Favorites... Model Panel, and in the Model Panel choose the surface model on the left and click "attributes" on the right). You can also change atomic VDW radii, although that is more trouble, and we have been careful about using good values. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/ representation.html#surfaces http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/msmsattrib.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vdwrad.html Currently Chimera does not calculate a solvent-accessible surface. If PMV does calculate this type of surface and can write it out in GRASP surface format, you could then read it into Chimera. Finally, you could show a "pseudo" solvent-accessible surface in Chimera by increasing all radii by 1.4 (one probe radius) and then using a probe small as possible, as described in this previous message to chimera- users: http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-March/001425.html I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Dec 17, 2007, at 12:34 AM, maya shcushan wrote: > Dear sir, > > I am trying to load a .dx file (electrostatic potential) onto a > molecule in chimera. > > I successfully loaded the map onto a the molecule?s surface. > > The problem is the potentials I get look differently than the > original map. That is, the potentials appear different in the > visualization tool of PMV, the program which generated the .dx file > I tried to e-load on chimera. > > Thanks, > > Maya Schushan, > > Tel-Aviv university, Israel. From gregc at cgl.ucsf.edu Mon Dec 17 10:17:35 2007 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Mon, 17 Dec 2007 10:17:35 -0800 (PST) Subject: [Chimera-users] Problem with Chimera under Windows XP In-Reply-To: <00bd01c84009$1637fb30$f17c0056@DELL9300> References: <00bd01c84009$1637fb30$f17c0056@DELL9300> Message-ID: On Sun, 16 Dec 2007, Peter Girard wrote: > I am running release 2304 of Chimera under Windows XP with service pack > 2 on a Dell Inspiron 9300 laptop. The image disappears from the screen > for no apparent reason. With the structures I am currently working on, > this has become frequent and often occurs after just a few seconds when > I click anywhere in the Chimera window. > > I have found that if I use Model Panel, I can get the picture back by > clicking the 'Shown' box to remove the tick mark, then clicking it again > to re-insert the tick. But the picture soon disappears again. > Occasionally, it doesn't disappear completely, but part of it collapses, > or spurious long lines appear. > > I had the same problem with a previous release, 2184, and was > disappointed that upgrading didn't fix it. I can find no mention of > anything similar in the documentation or email archive. Can anyone > suggest a possible cause? > > Peter Girard > (University of Nottingham, UK) I am 99.99999% sure that this is not a chimera bug. This is most likely a graphics driver bug, but it could also be a hardware bug or a BIOS bug. So you should first update the graphics driver. There is also a newer BIOS, A05, that "addresses some NMI and blue screen issues seen by some customers using intensive 3D applications and games." And please update your chimera as well to 1.2470. Good luck, Greg Couch UCSF Computer Graphics Lab From pintilie at mit.edu Mon Dec 17 10:32:00 2007 From: pintilie at mit.edu (Greg Pintilie) Date: Mon, 17 Dec 2007 13:32:00 -0500 Subject: [Chimera-users] Problem with Chimera under Windows XP In-Reply-To: References: <00bd01c84009$1637fb30$f17c0056@DELL9300> Message-ID: I do have similar problems on my Windows XP laptop with Nvidia graphics card. I've come to accept it as a graphics card/driver problem, and the reason I'm pretty sure this is so is that the scripts I run reliably replicate the problem on my laptop, but when I run the same scripts on a computer with a different graphics card and same version of Chimera the problem disapears. It tends to happen when displaying very complex models; one possible scenario is that the geometry overfills the graphics card memory and the graphics driver doesn't handle it properly, but really who knows what is going on inside the driver. So possible advice is to reduce the complexity of the models if possible, or try using a different computer and see if you have the same problem. Greg On Dec 17, 2007 1:17 PM, Greg Couch wrote: > > On Sun, 16 Dec 2007, Peter Girard wrote: > > > I am running release 2304 of Chimera under Windows XP with service pack > > 2 on a Dell Inspiron 9300 laptop. The image disappears from the screen > > for no apparent reason. With the structures I am currently working on, > > this has become frequent and often occurs after just a few seconds when > > I click anywhere in the Chimera window. > > > > I have found that if I use Model Panel, I can get the picture back by > > clicking the 'Shown' box to remove the tick mark, then clicking it again > > to re-insert the tick. But the picture soon disappears again. > > Occasionally, it doesn't disappear completely, but part of it collapses, > > or spurious long lines appear. > > > > I had the same problem with a previous release, 2184, and was > > disappointed that upgrading didn't fix it. I can find no mention of > > anything similar in the documentation or email archive. Can anyone > > suggest a possible cause? > > > > Peter Girard > > (University of Nottingham, UK) > > I am 99.99999% sure that this is not a chimera bug. This is most likely a > graphics driver bug, but it could also be a hardware bug or a BIOS bug. > So you should first update the graphics driver. There is also a newer > BIOS, A05, that "addresses some NMI and blue screen issues seen by some > customers using intensive 3D applications and games." And please update > your chimera as well to 1.2470. > > Good luck, > > Greg Couch > UCSF Computer Graphics Lab > _______________________________________________ > 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 Mon Dec 17 10:33:17 2007 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 17 Dec 2007 10:33:17 -0800 Subject: [Chimera-users] Problem with Chimera under Windows XP In-Reply-To: <00bd01c84009$1637fb30$f17c0056@DELL9300> References: <00bd01c84009$1637fb30$f17c0056@DELL9300> Message-ID: <1A5BB976-920A-4234-A039-D3B5826D3031@cgl.ucsf.edu> While not addressing this specific issue, I wanted to mention we have a page on "graphics driver bugs observed in Chimera." This page includes general tips as well as specific problems that have been encountered: http://www.cgl.ucsf.edu/chimera/graphics/graphicsbugs.html From pett at cgl.ucsf.edu Mon Dec 17 11:22:25 2007 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 17 Dec 2007 11:22:25 -0800 Subject: [Chimera-users] setting pdb path for local mirror In-Reply-To: <20071217131255.1E299164288@ws1-4.us4.outblaze.com> References: <20071217131255.1E299164288@ws1-4.us4.outblaze.com> Message-ID: <07288BCC-A843-4ACF-A403-21CBBBFED43F@cgl.ucsf.edu> Hi, The file "pdbDir" in the same directory as __init__.py defines what directory to look in for a PDB mirror distribution. If you change the contents of that file to: pdbDir = " /blah/blah/pdb/data/structures/divided/pdb" then Chimera will find your mirror distribution. The trouble is that if you install a new version of Chimera then that file will be overwritten. So I've just committed a change to Chimera so that if you have a file named "pdbDir" in ~/.chimera/chimera then that file will be used instead of the one inside the Chimera distribution. So if you get tomorrow's daily build it will have that change in it. The "system PDB mirror finding" needs to be improved somehow so that a system administrator can specify where the mirror is and not have to have individual users place files in their home directories to specify it. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Dec 17, 2007, at 5:12 AM, Moo Cow wrote: > Sorry for an easy question. > Chimera has a hook to use a local mirror of the PDB (preferences-PDB) > I am too thick to see what path to give it. If you have the PDB, > you have the top level > /blah/blah/pdb > the structure directory > /blah/blah/pdb/data/structures/all > and the divided directory > /blah/blah/pdb/data/structures/divided/pdb > > When a non-python reader looks at the code (__init__.py), it > seems to be trying out the divided directory > > IDcode = IDcode.lower() > subpath = IDcode[1:3] + os.sep + "pdb" + IDcode + ".ent" > pdbDir = systemPDBdir() > if pdbDir is not None: > ..... > but this does not look correct. The PDB divided path would want > subpath IDcode[1:2] > to get the subdirectory "pt" from a file like "5pti" > > Many thanks and sorry for a seemingly daft question. > > > -- > Got No Time? Shop Online for Great Gift Ideas! > http://mail.shopping.com/?linkin_id=8033174 > > _______________________________________________ > 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 pett at cgl.ucsf.edu Mon Dec 17 11:56:39 2007 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 17 Dec 2007 11:56:39 -0800 Subject: [Chimera-users] other/5067 (error adding hydrogens) In-Reply-To: <200712171941.lBHJfiLn2069545@guanine.cgl.ucsf.edu> References: <200712171941.lBHJfiLn2069545@guanine.cgl.ucsf.edu> Message-ID: <72159237-86C8-4D5E-BB58-32F681C004CA@cgl.ucsf.edu> Hi Jean-Francois, I have seen this error reported, but only very rarely (maybe once a year at most). Is there any chance you can tell me how to reproduce it? --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From jkhilmer at gmail.com Mon Dec 17 12:35:25 2007 From: jkhilmer at gmail.com (Jonathan Hilmer) Date: Mon, 17 Dec 2007 13:35:25 -0700 Subject: [Chimera-users] Chimera-users Digest, Vol 56, Issue 14 In-Reply-To: References: Message-ID: <81277ce10712171235g2525da58u67f67b66292916ea@mail.gmail.com> Ryan, Try this as a way to figure out what you can do with an object: dir(chimera.selection.currentResidues()[0]) In the above command I've indexed the list of selections to return just one object, and the dir() function will return a list of names defined by the currentResidues module. It should contain something like the following: ... 'addAtom', 'atomNames', 'atoms', 'atomsMap', 'bondedTo', 'count', 'findAtom', 'findRangeAtoms', 'getDefaultRibbonStyle', 'hasRibbon', 'id', 'isHelix', 'isHet', 'isSheet', 'isStrand', 'isTurn', 'kdHydrophobicity', 'label', 'labelColor', 'labelOffset', 'molecule', 'numAtoms', 'oslChildren', 'oslIdent', 'oslLevel', 'oslParents', 'oslTestAbbr', 'removeAtom', 'ribbonBinormals', 'ribbonCenters', 'ribbonColor', 'ribbonData', 'ribbonDisplay', 'ribbonDrawMode', 'ribbonFindStyle', 'ribbonFindStyleType', 'ribbonFindXSection', 'ribbonNormals', 'ribbonResidueClass', 'ribbonStyle', 'ribbonXSection', 'selLevel', 'type' If you try: chimera.selection.currentResidues()[0].type it will return a string with the 3-letter aa code, and the other options displayed by dir() will output useful things such as more strings, lists, or other objects that can be likewise explored. Try this combination: mySel = chimera.selection.currentResidues()[0] print "%s, %s" % (mySel.oslIdent(), mySel.type) On my test structure it returns '#0:127.A, ARG'. The second line is equivalent to 'print str(mySel.oslIdent() + ", " + mySel.type)', but the formatting I used in the above example helps to keep things clean if you have a complicated output that needs to have a specific format. There are some more advanced features of that approach detailed here: http://www.python.org/doc/1.5/tut/node45.html Jonathan > Date: Fri, 14 Dec 2007 19:55:39 -0500 > From: Ryan > Subject: Re: [Chimera-users] printing "zone" search > To: chimera-users at cgl.ucsf.edu > Message-ID: <17bf4817f850.17f85017bf48 at osu.edu> > Content-Type: text/plain; charset=us-ascii > > Hi Eric, thanks for your help. I'm getting closer to achieving the results i'd like. > > So i've been able to properly select the residues within a specified radius of my ligand, but am a little confused as to how Chimera handles the selection list. If i try: > > print chimera.selection.currentResidues() > > i get a list like this: > > > [<_chimera.Residue object at 0x578d2020>, <_chimera.Residue object at 0x578cbfb0>, ... ] > > but if i try: > > for x in chimera.selection.currentResidues(): > print x > > i get output that is much closer to what i'm looking for: > > > #0:499 > > #0:496 > > ... > > What is the reason for the difference between these two forms of output that seem to be accessing the same list? Also, is there a way i can get more detailed output with residue names and numbers, such as ['#0:TYR499','#0:TRP496',...]? > > Sorry if these questions are answered elsewhere, but i could not find the answers online. Is there a document out there that can teach me how to better master the Chimera Python modules for scripting? I'm no Python expert -- i've so far only been learning things as i need them. Thanks again, > > ryan From chiendarret at yahoo.com Tue Dec 18 06:25:44 2007 From: chiendarret at yahoo.com (Francesco Pietra) Date: Tue, 18 Dec 2007 06:25:44 -0800 (PST) Subject: [Chimera-users] rmsd cluster analysis Message-ID: <828413.2059.qm@web57605.mail.re1.yahoo.com> Is it feasible to command a cluster analysis from rmsd? I would like to group for likeliness snapshots from MD with respect to, say, the structure from which MD was started. Thanks francesco pietra ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ From meng at cgl.ucsf.edu Tue Dec 18 09:31:15 2007 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 18 Dec 2007 09:31:15 -0800 Subject: [Chimera-users] rmsd cluster analysis In-Reply-To: <828413.2059.qm@web57605.mail.re1.yahoo.com> References: <828413.2059.qm@web57605.mail.re1.yahoo.com> Message-ID: Hi Francesco, The MD Movie tool (which replays trajectories) can also calculate all- by-all pairwise RMSD values and show them as a grayscale map. In the map you can see which frames are similar to which, but the tool does not really perform clustering. MD Movie (see "RMSD Analysis" section): http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/ framemovie.html The "Trajectory and Ensemble Analysis" tutorial (part 2) uses this tool and shows an example RMSD map: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ ensembles2.html#part2 Perhaps the AMBER tutorials would be more useful in your situation. I believe tutorial B3 includes clustering: http://amber.scripps.edu/tutorials/ I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Dec 18, 2007, at 6:25 AM, Francesco Pietra wrote: > Is it feasible to command a cluster analysis from rmsd? I would > like to group > for likeliness snapshots from MD with respect to, say, the > structure from which > MD was started. > Thanks > francesco pietra From chiendarret at yahoo.com Tue Dec 18 09:46:03 2007 From: chiendarret at yahoo.com (Francesco Pietra) Date: Tue, 18 Dec 2007 09:46:03 -0800 (PST) Subject: [Chimera-users] rmsd cluster analysis In-Reply-To: Message-ID: <773205.86398.qm@web57613.mail.re1.yahoo.com> Elaine: I had carried out successfully all-by-all pairwise RMSD. Though, it does not help much comparing different ligands for the same protein. As to MMTSB, there are indications about the compilation that I do not understand yet. All in all, it seems to me that a tool for performing affinity analysis for ligands in explicit medium (ideally free energies) is not easily at hand. Hope I am wrong and someone comes with suggestions (I posted the problem of affinities in explicit medium yesterday to DOCK, so a suggestion might come from there too). Thanks francesco --- Elaine Meng wrote: > Hi Francesco, > The MD Movie tool (which replays trajectories) can also calculate all- > by-all pairwise RMSD values and show them as a grayscale map. In the > map you can see which frames are similar to which, but the tool does > not really perform clustering. > > MD Movie (see "RMSD Analysis" section): > http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/ > framemovie.html > > The "Trajectory and Ensemble Analysis" tutorial (part 2) uses this > tool and shows an example RMSD map: > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ > ensembles2.html#part2 > > Perhaps the AMBER tutorials would be more useful in your situation. > I believe tutorial B3 includes clustering: > http://amber.scripps.edu/tutorials/ > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu > UCSF Computer Graphics Lab and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > http://www.cgl.ucsf.edu/home/meng/index.html > > On Dec 18, 2007, at 6:25 AM, Francesco Pietra wrote: > > > Is it feasible to command a cluster analysis from rmsd? I would > > like to group > > for likeliness snapshots from MD with respect to, say, the > > structure from which > > MD was started. > > Thanks > > francesco pietra > ____________________________________________________________________________________ Looking for last minute shopping deals? Find them fast with Yahoo! Search. http://tools.search.yahoo.com/newsearch/category.php?category=shopping From jeandidier.marechal at uab.es Tue Dec 18 09:16:58 2007 From: jeandidier.marechal at uab.es (Jean-Didier =?ISO-8859-1?Q?Mar=E9chal?=) Date: Tue, 18 Dec 2007 18:16:58 +0100 Subject: [Chimera-users] Question regarding multiple mutant in the same chimera session Message-ID: <1197998219.13626.8.camel@asklipio> Hi, Is there a way to copy, in the same instance of chimera, a model X time? I'd like to generate different mutant of the same prot and have them stocked in the same session of chimera. Cheers, JD -- Dr. Jean-Didier Mar?chal Assistant Professor Computational Bioorganic and Bioinorganic Chemistry @Transmet Unitat de Qu?mica F?sica Departament de Qu?mica Universitat Aut?noma de Barcelona 08193 Bellaterra, Spain Tel: +34.(0)1935814936 Fax: +34.(0)1935812920 e-mail:jeandidier.marechal at uab.es From meng at cgl.ucsf.edu Tue Dec 18 10:39:01 2007 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 18 Dec 2007 10:39:01 -0800 Subject: [Chimera-users] Question regarding multiple mutant in the same chimera session In-Reply-To: <1197998219.13626.8.camel@asklipio> References: <1197998219.13626.8.camel@asklipio> Message-ID: <45980DF5-B02A-4926-B024-A50F10B2F0F4@cgl.ucsf.edu> Hi JD, Currently there is no "copy model" feature for atomic coordinates (at least in the user interface... perhaps doable with a script). I usually just open the same input file several times and then manipulate the individual copies separately. Best, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Dec 18, 2007, at 9:16 AM, Jean-Didier Mar?chal wrote: > Hi, > Is there a way to copy, in the same instance of chimera, a model X > time? > I'd like to generate different mutant of the same prot and have them > stocked in the same session of chimera. > Cheers, > JD From jeandidier.marechal at uab.es Tue Dec 18 10:40:09 2007 From: jeandidier.marechal at uab.es (Jean-Didier =?ISO-8859-1?Q?Mar=E9chal?=) Date: Tue, 18 Dec 2007 19:40:09 +0100 Subject: [Chimera-users] Regarding getSequence Message-ID: <1198003209.13626.19.camel@asklipio> Hi again, I'd like to return the sequence of the protein I opened in chimera in the python shell. >From what I read through, I thought that chimera.getSequence could be used to do so. I was thinking in a simple script beginning with : import chimera s=chimera.getSequence(0,0) .. However the chimera.getSequence(0,0) comes back with: Traceback (most recent call last): File "", line 1, in ? chimera.getSequence(0, 0) File "CHIMERA/share/chimera/Sequence.py", line 614, in getSequence File "CHIMERA/share/chimera/Sequence.py", line 656, in getSequences AttributeError: 'int' object has no attribute 'residues' and chimera.getSequence(0,A) with Traceback (most recent call last): File "", line 1, in ? chimera.getSequence(0,A) NameError: name 'A' is not defined Did I understand correctly the role of getSequence? if yes, what would be the correct syntax please? Thanks a lot! All the best, JD -- Dr. Jean-Didier Mar?chal Assistant Professor Computational Bioorganic and Bioinorganic Chemistry @Transmet Unitat de Qu?mica F?sica Departament de Qu?mica Universitat Aut?noma de Barcelona 08193 Bellaterra, Spain Tel: +34.(0)1935814936 Fax: +34.(0)1935812920 e-mail:jeandidier.marechal at uab.es From pett at cgl.ucsf.edu Tue Dec 18 11:41:42 2007 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Tue, 18 Dec 2007 11:41:42 -0800 Subject: [Chimera-users] Regarding getSequence In-Reply-To: <1198003209.13626.19.camel@asklipio> References: <1198003209.13626.19.camel@asklipio> Message-ID: On Dec 18, 2007, at 10:40 AM, Jean-Didier Mar?chal wrote: > Hi again, > > I'd like to return the sequence of the protein I opened in > chimera in > the python shell. > >> From what I read through, I thought that chimera.getSequence could be > used to do so. > > I was thinking in a simple script beginning with : > import chimera > s=chimera.getSequence(0,0) > .. > > However the chimera.getSequence(0,0) comes back with: > > Traceback (most recent call last): > File "", line 1, in ? > chimera.getSequence(0, 0) > File "CHIMERA/share/chimera/Sequence.py", line 614, in getSequence > File "CHIMERA/share/chimera/Sequence.py", line 656, in getSequences > AttributeError: 'int' object has no attribute 'residues' > > and > > > chimera.getSequence(0,A) > > with > > Traceback (most recent call last): > File "", line 1, in ? > chimera.getSequence(0,A) > NameError: name 'A' is not defined > > > Did I understand correctly the role of getSequence? if yes, what would > be the correct syntax please? Hi JD, getSequence takes two arguments: a Molecule instance and a string containing a chain ID. It looks like you were trying to provide a model number and a chain ID of A. The chain needed to be a string and not just the bare letter A, which is interpreted as a variable named A by the Python interpreter (and which you undoubtedly haven't previously defined). You get a Molecule instance by using chimera.openModels.list to list Models and grab the one you want from that list. Something like: from chimera import openModels, Molecule m = openModels.list(id=0, modelTypes=[Molecule])[0] to get the Molecule open as model 0. Once you have the Molecule instance you don't even have to use getSequence, just: m.sequence("A") will return the Sequence object. --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 Tue Dec 18 15:01:59 2007 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Tue, 18 Dec 2007 15:01:59 -0800 Subject: [Chimera-users] rmsd cluster analysis In-Reply-To: <828413.2059.qm@web57605.mail.re1.yahoo.com> References: <828413.2059.qm@web57605.mail.re1.yahoo.com> Message-ID: <062471E1-1616-4B4B-9E6A-84A0192C8A21@cgl.ucsf.edu> There will be a EnsembleCluster tool in tomorrow's daily build for clustering NMR ensembles (totally undocumented at this point). We are still discussing how to integrate its capabilities into the MD Movie tool. I wouldn't expect anything to appear in the MD Movie tool for a couple of weeks at least. --Eric On Dec 18, 2007, at 6:25 AM, Francesco Pietra wrote: > Is it feasible to command a cluster analysis from rmsd? I would > like to group > for likeliness snapshots from MD with respect to, say, the > structure from which > MD was started. > > Thanks > francesco pietra > > > > ______________________________________________________________________ > ______________ > Be a better friend, newshound, and > know-it-all with Yahoo! Mobile. Try it now. http:// > mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ > > _______________________________________________ > 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 Tue Dec 18 15:05:23 2007 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 18 Dec 2007 15:05:23 -0800 Subject: [Chimera-users] Question regarding multiple mutant in the same chimera session In-Reply-To: <1197998219.13626.8.camel@asklipio> References: <1197998219.13626.8.camel@asklipio> Message-ID: Hi JD, There is another way I didn't think of earlier, if you want to "clone" a model after making several changes instead of having to make the same changes to each copy. Open the structure, make the changes, save a session. Then, repeatedly open the session, which will put additional copies of the first model in successive model numbers if you answer "No" when prompted whether the existing model(s) should be closed. However, if you will be doing H-bond or clash detection either independently or within swapaa or Rotamers, I recommend against stacking the structures, as that will affect the calculations. The same problem applies to opening the same PDB file multiple times. Best, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Dec 18, 2007, at 9:16 AM, Jean-Didier Mar?chal wrote: > Hi, > > Is there a way to copy, in the same instance of chimera, a model X > time? > I'd like to generate different mutant of the same prot and have them > stocked in the same session of chimera. > > Cheers, > JD > From meng at cgl.ucsf.edu Tue Dec 18 15:30:18 2007 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 18 Dec 2007 15:30:18 -0800 Subject: [Chimera-users] Question regarding multiple mutant in the same chimera session In-Reply-To: References: <1197998219.13626.8.camel@asklipio> Message-ID: <903D086C-56FF-4E0C-8011-46D32FE4EE51@cgl.ucsf.edu> Correction: it is possible to make H-bond detection ignore other models - the GUIs and commands have options to do that. AddH is always affected by all other models, however. Findclash is always affected by all other models unless you designate only atoms within the same model and indicate they should only be checked for clashes among themselves. Elaine On Dec 18, 2007, at 3:05 PM, Elaine Meng wrote: > Hi JD, > There is another way I didn't think of earlier, if you want to > "clone" a model after making several changes instead of having to > make the same changes to each copy. > > Open the structure, make the changes, save a session. Then, > repeatedly open the session, which will put additional copies of the > first model in successive model numbers if you answer "No" when > prompted whether the existing model(s) should be closed. > > However, if you will be doing H-bond or clash detection either > independently or within swapaa or Rotamers, I recommend against > stacking the structures, as that will affect the calculations. The > same problem applies to opening the same PDB file multiple times. > From ksvinaykumar at gmail.com Tue Dec 18 23:51:33 2007 From: ksvinaykumar at gmail.com (Vinay Kumar) Date: Wed, 19 Dec 2007 13:21:33 +0530 Subject: [Chimera-users] superimpose --matchmaker. Message-ID: Hi all, There have been a few posts previously regarding superimposing of molecules. using matchmaker would work for a pdb file. I was curious if small molecules (ligands) could be matched. I did check out the documentation and the command match. But what i am not sure abt is, in wht format should the input file for a small molecule be?? could someone suggest!! regards, Vinay From meng at cgl.ucsf.edu Wed Dec 19 09:57:02 2007 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 19 Dec 2007 09:57:02 -0800 Subject: [Chimera-users] superimpose --matchmaker. In-Reply-To: References: Message-ID: Hi Vinay, The important thing for matchmaker is not the input format, but the type of structure: peptide/protein or nucleic acid chains are handled. These could be read from PDB, mmCIF, or Mol2 formats if described as chains of amino acid or nucleic acid residues (i.e. not one giant residue). For "match," it also does not matter much what input format you use. Once the structure is read in, it is treated basically the same way. It is better if the atoms have unique names, however (e.g. C1 C2 C3 ... instead of all "C"), since then you can use the atom names with the "match" command. The most commonly used formats (PDB, Mol2, CIF/mmCIF, MDL MOL/SDF) all accommodate unique atom names. Even if the structures don't have unique atom names, it may be possible to specify the atoms for the "match" command in some other way, such as by picking them from the graphics window. If you specify by picking (Ctrl-left button click by default), be careful to pick the atoms in the correct order, as described in the "match" man page: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html Finally, sometimes you can get away with just using the residue name (e.g. "match #1:fad #0:fad"), but usually that will not work well because the atoms are in a different order, or even if they are in identical order and chemical correspondence, the names could be reversed from what would give the best match in space. A simple example is two Asp residues, where you might get a better RMSD by matching OD1/OD2 and OD2/OD1 instead of OD1/OD1 and OD2/OD2. OD1 and OD2 are chemically indistinguishable but named differently. That may have been more detail than you wanted. 8-) I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Dec 18, 2007, at 11:51 PM, Vinay Kumar wrote: > Hi all, > There have been a few posts previously regarding superimposing of > molecules. using matchmaker would work for a pdb file. I was curious > if small molecules (ligands) could be matched. I did check out the > documentation and the command match. But what i am not sure abt is, in > wht format should the input file for a small molecule be?? > could someone suggest!! > > regards, > Vinay From pmg7 at lineone.net Tue Dec 18 14:00:29 2007 From: pmg7 at lineone.net (Peter Girard) Date: Tue, 18 Dec 2007 22:00:29 -0000 Subject: [Chimera-users] Problem with Chimera under Windows XP References: <00bd01c84009$1637fb30$f17c0056@DELL9300> Message-ID: <006f01c841c1$6a34d500$45400352@DELL9300> Thanks for the suggestions (from Greg Couch, Elaine Meng, Greg Pintilie). It sounds like a graphics driver bug or hardware bug (I already had the A05 version of the BIOS). My graphics card is an 'ATI Mobility Radeon X300' and I found a slightly later driver on the Dell website (Sept 2005 rather than March 2005); and I've tried it but unfortunately the problem has not gone away. There don't seem to be any later drivers recommended by Dell for the Inspiron 9300; so perhaps I should contact Dell for advice. I haven't yet tried the other suggestions in the 'Graphics Driver Bugs' document, but will do so, as it looks likely I will have to live with this problem as well as possible. Thanks again for the help and suggestions. At least I know what sort of problem it is now. Peter Girard. ----- Original Message ----- From: "Greg Couch" To: "Peter Girard" Cc: Sent: Monday, December 17, 2007 6:17 PM Subject: Re: [Chimera-users] Problem with Chimera under Windows XP > On Sun, 16 Dec 2007, Peter Girard wrote: > >> I am running release 2304 of Chimera under Windows XP with service pack 2 >> on a Dell Inspiron 9300 laptop. The image disappears from the screen for >> no apparent reason. With the structures I am currently working on, this >> has become frequent and often occurs after just a few seconds when I >> click anywhere in the Chimera window. >> >> I have found that if I use Model Panel, I can get the picture back by >> clicking the 'Shown' box to remove the tick mark, then clicking it again >> to re-insert the tick. But the picture soon disappears again. >> Occasionally, it doesn't disappear completely, but part of it collapses, >> or spurious long lines appear. >> >> I had the same problem with a previous release, 2184, and was >> disappointed that upgrading didn't fix it. I can find no mention of >> anything similar in the documentation or email archive. Can anyone >> suggest a possible cause? >> >> Peter Girard >> (University of Nottingham, UK) > > I am 99.99999% sure that this is not a chimera bug. This is most likely a > graphics driver bug, but it could also be a hardware bug or a BIOS bug. So > you should first update the graphics driver. There is also a newer BIOS, > A05, that "addresses some NMI and blue screen issues seen by some > customers using intensive 3D applications and games." And please update > your chimera as well to 1.2470. > > Good luck, > > Greg Couch > UCSF Computer Graphics Lab From goddard at cgl.ucsf.edu Wed Dec 19 21:50:58 2007 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Wed, 19 Dec 2007 21:50:58 -0800 Subject: [Chimera-users] fitting models into maps In-Reply-To: <5258338D-D7D2-4491-AA48-5B96B3C9316B@msg.ucsf.edu> References: <5258338D-D7D2-4491-AA48-5B96B3C9316B@msg.ucsf.edu> Message-ID: <476A02C2.6090801@cgl.ucsf.edu> Hi Dan, The Chimera fit model in map tool doesn't give a correlation value. To get a correlation requires you have two maps to compare, so first a map needs to be calculated from the PDB model that matches the resolution of the experimental map. Although I'd like to have that in Chimera, it is not currently there. I have used the EMAN pdb2mrc program to compute the map. Then you can use the Chimera fit map in map tool to get a correlation value, or you could use fit model in map, then open the map calculated for the PDB and find the correlation for the orientation obtained for the PDB model. You're right that reported correlation values depend on some often unreported parameters. First there is the method used for producing a map from the PDB model. Then the correlation depends on the part of the volume used. I would guess this is typically the portion within a certain contour level of the PDB map. What contour level? Something like 1 standard deviation is not sensible since it depends on the size of the map (the extent of padding). Probably a contour level that encloses a given volume -- maybe the volume enclosed by the solvent excluded surface of the PDB model with a reasonable probe radius. Would be nice if Chimera automated this calculation starting from the fit model in map position -- some day, hopefully in 2008. Reporting average density value at the atom positions would only make sense if the map is normalized. Maybe reporting that value in standard deviations. But the standard deviation depends on how much empty volume surrounds the structure, so that is not very satisfactory. Chimera reports that number so you can compare different fits in the same map -- only relative values are meaningful. Another value I have seen reported is the number of atoms outside a certain contour level of the experimental map. The fit model in map tool reports that in the reply log (Favorites / Reply Log). Of course it depends on how you set the contour level. Again if you set that as some number of standard deviations that depends on the map size. Alternatively you could set the contour level so the experimental map encloses the expected volume. Menu entry Tools / Volume Data / Measure Volume and Area can help set such a contour level. Seems correlation is the most meaningful number. You can calculate the standard deviation of a map from its mean in newer versions of Chimera with menu entry Tools / Volume Data / Volume Mean, SD, RMS. Tom Daniel Southworth wrote: > Tom: > > Hi. I'm a post-doc in David Agard's lab and I have a question about > the "fit model in map" function in chimera. I'm having some good > success fitting crystal structures into my low-resolution em maps > using this function once I get a global fit either by hand or using > situs. I'm wondering if there is any way to get a correlation value > out of the fits or how people typically report on their confidence of > the chimera fitting in publications? I know correlation values are > often different from program to program so perhaps the best measure is > to state the average map value? Any help would be great - thanks. > > Dan From paul.pillot at ac-nice.fr Mon Dec 17 10:17:56 2007 From: paul.pillot at ac-nice.fr (Paul Pillot) Date: Mon, 17 Dec 2007 19:17:56 +0100 Subject: [Chimera-users] [SPAM?] Re: Transparent background In-Reply-To: References: <4A7AD72C-711E-435A-8A46-449F0C24B725@scripps.edu> Message-ID: You can also render your images using PovRay with transparent backgroung as a setting Paul Le 17 d?c. 07 ? 18:43, Greg Couch a ?crit : > On Fri, 14 Dec 2007, Abbas wrote: > >> Hi, >> One feature I really appreciated about chimera was the ability to >> make pictures without a background, however recently i realized this >> is not possible anymore I checked out under the effects dialog under >> tools>viewing controls and it give me an error saying this wasn't >> supported. I haven't changed my computer since i first started using >> chimera I have updated to the latest version of chimera available for >> OSX 10.4, I wonder if this is the cause of the problem. >> I would really like to have pictures without backgrounds like I used >> to, I know PyMol lets you do it, but I dislike this program. In any >> case I would greatly appreciate any help/pointers on this issue. >> Thanks in advance. abbas. > > Transparent backgrounds depend on the graphics card capabilities > reported > by OpenGL. On Mac OS X, Apple decided not to support background > transparency (nor full window antialiasing) for OpenGL/X11 > applications, > so to use that feature you would have to use the Aqua version of > chimera. > Unfortunately, the chimera's cross-platform user interface toolkit, > Tk, > while improving for Aqua, has gotton worse for chimera, so you'll > have to > use an old version of chimera for Aqua to get transparent backgrounds. > You can also file a bug report with Apple to help them decide to spend > the time to fix it (OpenGL "destination alpha" and multisampling not > supported in X11). > > Greg Couch > UCSF Computer Graphics Lab > _______________________________________________ > 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 Thu Dec 20 11:13:11 2007 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Thu, 20 Dec 2007 11:13:11 -0800 Subject: [Chimera-users] [SPAM?] Re: Transparent background In-Reply-To: References: <4A7AD72C-711E-435A-8A46-449F0C24B725@scripps.edu> Message-ID: Paul sent me this in a separate mail, which seems relevant... I've just been able to raytrace with alpha channel by disabling the fog in the povray file. I don't know if it has always been necessary... if so, sorry for the trouble Paul --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Dec 17, 2007, at 10:17 AM, Paul Pillot wrote: > You can also render your images using PovRay with transparent > backgroung as a setting > Paul > > Le 17 d?c. 07 ? 18:43, Greg Couch a ?crit : > >> On Fri, 14 Dec 2007, Abbas wrote: >> >>> Hi, >>> One feature I really appreciated about chimera was the ability to >>> make pictures without a background, however recently i realized this >>> is not possible anymore I checked out under the effects dialog under >>> tools>viewing controls and it give me an error saying this wasn't >>> supported. I haven't changed my computer since i first started using >>> chimera I have updated to the latest version of chimera available >>> for >>> OSX 10.4, I wonder if this is the cause of the problem. >>> I would really like to have pictures without backgrounds like I used >>> to, I know PyMol lets you do it, but I dislike this program. In any >>> case I would greatly appreciate any help/pointers on this issue. >>> Thanks in advance. abbas. >> >> Transparent backgrounds depend on the graphics card capabilities >> reported >> by OpenGL. On Mac OS X, Apple decided not to support background >> transparency (nor full window antialiasing) for OpenGL/X11 >> applications, >> so to use that feature you would have to use the Aqua version of >> chimera. >> Unfortunately, the chimera's cross-platform user interface toolkit, >> Tk, >> while improving for Aqua, has gotton worse for chimera, so you'll >> have to >> use an old version of chimera for Aqua to get transparent >> backgrounds. >> You can also file a bug report with Apple to help them decide to >> spend >> the time to fix it (OpenGL "destination alpha" and multisampling not >> supported in X11). >> >> Greg Couch >> UCSF Computer Graphics Lab >> _______________________________________________ >> 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From gregc at cgl.ucsf.edu Thu Dec 20 11:19:51 2007 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Thu, 20 Dec 2007 11:19:51 -0800 (PST) Subject: [Chimera-users] [SPAM?] Re: Transparent background In-Reply-To: References: <4A7AD72C-711E-435A-8A46-449F0C24B725@scripps.edu> Message-ID: And just to follow this up. There was an alpha channel in the file, it's just all one (opaque). We will add documentation and/or a warning about not using fog if you want background transparency. - Greg On Thu, 20 Dec 2007, Eric Pettersen wrote: > Paul sent me this in a separate mail, which seems relevant... > > I've just been able to raytrace with alpha channel by disabling the > fog in the povray file. I don't know if it has always been > necessary... if so, sorry for the trouble > Paul > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > > On Dec 17, 2007, at 10:17 AM, Paul Pillot wrote: > >> You can also render your images using PovRay with transparent >> backgroung as a setting >> Paul >> >> Le 17 d?c. 07 ? 18:43, Greg Couch a ?crit : >> >>> On Fri, 14 Dec 2007, Abbas wrote: >>> >>>> Hi, >>>> One feature I really appreciated about chimera was the ability to >>>> make pictures without a background, however recently i realized this >>>> is not possible anymore I checked out under the effects dialog under >>>> tools>viewing controls and it give me an error saying this wasn't >>>> supported. I haven't changed my computer since i first started using >>>> chimera I have updated to the latest version of chimera available for >>>> OSX 10.4, I wonder if this is the cause of the problem. >>>> I would really like to have pictures without backgrounds like I used >>>> to, I know PyMol lets you do it, but I dislike this program. In any >>>> case I would greatly appreciate any help/pointers on this issue. >>>> Thanks in advance. abbas. >>> >>> Transparent backgrounds depend on the graphics card capabilities >>> reported >>> by OpenGL. On Mac OS X, Apple decided not to support background >>> transparency (nor full window antialiasing) for OpenGL/X11 >>> applications, >>> so to use that feature you would have to use the Aqua version of >>> chimera. >>> Unfortunately, the chimera's cross-platform user interface toolkit, >>> Tk, >>> while improving for Aqua, has gotton worse for chimera, so you'll >>> have to >>> use an old version of chimera for Aqua to get transparent backgrounds. >>> You can also file a bug report with Apple to help them decide to spend >>> the time to fix it (OpenGL "destination alpha" and multisampling not >>> supported in X11). >>> >>> Greg Couch >>> UCSF Computer Graphics Lab >>> _______________________________________________ >>> 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 meng at cgl.ucsf.edu Thu Dec 20 15:58:31 2007 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 20 Dec 2007 15:58:31 -0800 Subject: [Chimera-users] rmsd cluster analysis Message-ID: <9598979A-3753-4D20-B9B5-2F6A2D08D0F1@cgl.ucsf.edu> Hi Francesco and others, People with MD trajectories can also use this new EnsembleCluster tool (available in the most recent daily builds) by: - viewing the whole trajectory with the "MD Movie" tool, or at least all the frames you want to cluster - from the MD Movie dialog menu, choosing File... Save PDB and saving "all frames" to a file - quitting from MD Movie and opening the new file with File... Open - choosing Tools... MD/Ensemble Analysis... EnsembleCluster, clicking the line that shows that new file, then OK I just tried this to make sure it works. The clustering calculation may take a while, but eventually another dialog with results should appear. This tool is still under development and may change, but this will at least allow users to try it on trajectory ensembles as well as NMR ensembles. Best, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html From huy.bui at mol.biol.ethz.ch Fri Dec 21 00:49:00 2007 From: huy.bui at mol.biol.ethz.ch (Bui Khanh Huy) Date: Fri, 21 Dec 2007 09:49:00 +0100 Subject: [Chimera-users] Gradient map In-Reply-To: <9598979A-3753-4D20-B9B5-2F6A2D08D0F1@cgl.ucsf.edu> Message-ID: Hi, I'm pretty newbie for Chimera. Anyone knows there is a function to display a density map as a gradient map? My purpose is: - Having one density map displayed as a surface rendering map - Having another different density map displayed as a gradient map only on the surface of the surface rendering map above. Thanks a lot, Huy From meng at cgl.ucsf.edu Fri Dec 21 07:54:19 2007 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 21 Dec 2007 07:54:19 -0800 Subject: [Chimera-users] Gradient map In-Reply-To: References: Message-ID: <90c3d9952f9bc81b7e7f2bf57f739052@cgl.ucsf.edu> Hi Huy, If I understand correctly, you want (1) a isosurface of the density map (2) colored by the gradient in that same map. (1) If you open the density map in Chimera, it will automatically start Volume Viewer, in which you can adjust the isosurface display (contour level(s), smoothing, etc.). More details on Volume Viewer: http://www.cgl.ucsf.edu/home/meng/docs/ContributedSoftware/ volumeviewer/framevolumeviewer.html (2) Then you can use Surface Color (listed under Tools... Volume Data in the main menu, or in the Volume Viewer Tools menu) to color that isosurface by the data gradient. You do not have to make a separate map with the gradient. In Surface Color, choose the option to use the "gradient norm" of the density map you already opened. Then you can adjust how colors should map to the gradient norm values. More details on Surface Color: http://www.cgl.ucsf.edu/home/meng/docs/ContributedSoftware/surfcolor/ surfcolor.html I hope this is what you had in mind. Best, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Dec 21, 2007, at 12:49 AM, Bui Khanh Huy wrote: > > Hi, > I'm pretty newbie for Chimera. Anyone knows there is a function to > display a density map as a gradient map? > > My purpose is: > - Having one density map displayed as a surface rendering map > - Having another different density map displayed as a gradient map only > on the surface of the surface rendering map above. > > Thanks a lot, > Huy From snoze.pa at gmail.com Sat Dec 22 12:16:31 2007 From: snoze.pa at gmail.com (snoze pa) Date: Sat, 22 Dec 2007 14:16:31 -0600 Subject: [Chimera-users] formal charge or net charge Message-ID: <10f848910712221216u67b98329m45407b711292173a@mail.gmail.com> Dear Chimera Users, Is it possible to calculate the net charge or formal charge of unknown residues using chimera. I have a large set of molecules for which i am trying to calculate the net charge on each molecule. Thanks in advance s -------------- next part -------------- An HTML attachment was scrubbed... URL: From huy.bui at mol.biol.ethz.ch Mon Dec 24 15:29:07 2007 From: huy.bui at mol.biol.ethz.ch (Bui Khanh Huy) Date: Tue, 25 Dec 2007 00:29:07 +0100 Subject: [Chimera-users] Gradient map References: <90c3d9952f9bc81b7e7f2bf57f739052@cgl.ucsf.edu> Message-ID: Hi Elaine, I tried what you told me, and it seems to work like what I expected. But I just want to confirm what I did is right as I don't fully understand the guide on the webpage you gave me. My question: I have volume A & B. I want to color the surface of volume A by the gradient of volume B. What I did: - I chose iso surface display of volume A using Volume Viewer. - Go to Tools/Volume Data/Surface Color, choose Color Surface A, using B gradient norm, then Color. Best regards, Huy ________________________________ Von: Elaine Meng [mailto:meng at cgl.ucsf.edu] Gesendet: Fr 12/21/2007 4:54 An: Bui Khanh Huy Cc: chimera-users at cgl.ucsf.edu Betreff: Re: [Chimera-users] Gradient map Hi Huy, If I understand correctly, you want (1) a isosurface of the density map (2) colored by the gradient in that same map. (1) If you open the density map in Chimera, it will automatically start Volume Viewer, in which you can adjust the isosurface display (contour level(s), smoothing, etc.). More details on Volume Viewer: http://www.cgl.ucsf.edu/home/meng/docs/ContributedSoftware/ volumeviewer/framevolumeviewer.html (2) Then you can use Surface Color (listed under Tools... Volume Data in the main menu, or in the Volume Viewer Tools menu) to color that isosurface by the data gradient. You do not have to make a separate map with the gradient. In Surface Color, choose the option to use the "gradient norm" of the density map you already opened. Then you can adjust how colors should map to the gradient norm values. More details on Surface Color: http://www.cgl.ucsf.edu/home/meng/docs/ContributedSoftware/surfcolor/ surfcolor.html I hope this is what you had in mind. Best, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Dec 21, 2007, at 12:49 AM, Bui Khanh Huy wrote: > > Hi, > I'm pretty newbie for Chimera. Anyone knows there is a function to > display a density map as a gradient map? > > My purpose is: > - Having one density map displayed as a surface rendering map > - Having another different density map displayed as a gradient map only > on the surface of the surface rendering map above. > > Thanks a lot, > Huy From meng at cgl.ucsf.edu Mon Dec 24 16:57:07 2007 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 24 Dec 2007 16:57:07 -0800 Subject: [Chimera-users] Gradient map In-Reply-To: References: <90c3d9952f9bc81b7e7f2bf57f739052@cgl.ucsf.edu> Message-ID: Hi Huy, It sounds like you did exactly the right thing. The description in my previous message was slightly different because I thought you wanted the surface and gradient both from the same volume data. Best, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Dec 24, 2007, at 3:29 PM, Bui Khanh Huy wrote: > Hi Elaine, > > I tried what you told me, and it seems to work like what I > expected. But I just want to confirm what I did is right as I don't > fully understand the guide on the webpage you gave me. > > My question: I have volume A & B. I want to color the surface of > volume A by the gradient of volume B. > > What I did: > - I chose iso surface display of volume A using Volume Viewer. > - Go to Tools/Volume Data/Surface Color, choose Color Surface A, > using B gradient norm, then Color. > > Best regards, > Huy From pett at cgl.ucsf.edu Tue Dec 25 18:42:34 2007 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Tue, 25 Dec 2007 18:42:34 -0800 Subject: [Chimera-users] formal charge or net charge In-Reply-To: <10f848910712221216u67b98329m45407b711292173a@mail.gmail.com> References: <10f848910712221216u67b98329m45407b711292173a@mail.gmail.com> Message-ID: <02BCABDA-A512-4168-96B0-B85158ACECC9@cgl.ucsf.edu> Hi Snoze, For bulk calculations of charge, you are going to have to use a Python script. In particular you will need to use the estimateFormalCharge method from the AddCharge module. Here's an example script that works if the only molecule open in Chimera is the one you want to estimate the charge for: ---- from chimera import openModels, Molecule from AddCharge import estimateFormalCharge mol = openModels.list(modelTypes=[Molecule])[0] print estimateFormalCharge(mol.atoms) ---- You would run such a script (if you called the script charge.py) with: chimera --nogui --nostatus molecule.pdb charge.py The charge would be printed on standard output. I would recommend you use at least Chimera 1.2470, and the latest daily build if possible if that works for you. You might want to avoid the overhead of starting Chimera for each molecule by opening them all in one instance of Chimera, in which case the script would be something like: ---- from chimera import openModels, Molecule from AddCharge import estimateFormalCharge for mol in openModels.list(modelTypes=[Molecule]): print mol.name, estimateFormalCharge(mol.atoms) ---- The charge estimation in Chimera works reasonably well, most usually failing when the molecular geometry is poor --causing atom types to be mistyped (e.g. a deprotonated alcohol mistaken for a carbonyl due to the bond length being very short). Therefore you might want to sanity check the charge estimation by adding up the atomic numbers of the atoms and ensuring that when you add the estimated charge you get an even number. Something like: fc = estimateFormalCharge(mol.atoms) atomicSum = 0 for a in mol.atoms: atomicSum += a.element.number if (atomicSum + fc) % 2 == 0: print mol.name, fc else: print "BAD CHARGE ESTIMATE:", mol.name, fc --Eric Eric Pettersen UCSF Computer Graphics Lab On Dec 22, 2007, at 12:16 PM, snoze pa wrote: > Dear Chimera Users, > > Is it possible to calculate the net charge or formal charge of > unknown residues using chimera. I have a large set of molecules for > which i am trying to calculate the net charge on each molecule. > > Thanks in advance > s > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From shengzhiya at nibs.ac.cn Wed Dec 26 01:58:59 2007 From: shengzhiya at nibs.ac.cn (shengzhiya at nibs.ac.cn) Date: Wed, 26 Dec 2007 17:58:59 +0800 (HKT) Subject: [Chimera-users] Command for volume and area calculation Message-ID: <477225E3.0000DF.29901@mail7.corpease.net> Dear all, May I know if there is some command in chimera for measuring volume and area like in the menus: ?Tools?Surface/Binding Analysis?Measure Volume and Area?? Thanks in advance! Happy new year and have a nice holiday! Zhiya -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Wed Dec 26 11:51:36 2007 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 26 Dec 2007 11:51:36 -0800 Subject: [Chimera-users] Command for volume and area calculation In-Reply-To: <477225E3.0000DF.29901@mail7.corpease.net> References: <477225E3.0000DF.29901@mail7.corpease.net> Message-ID: Dear Zhiya, There is no Chimera command to measure surface area or surface- enclosed volume, but there are keyboard shortcuts (Accelerators) to perform these measurements on the currently selected surface(s). (1) turn on Accelerators (Tools... General Controls... Accelerators On) (2) select the surface(s) - for many kinds of surface (molecular, multiscale, etc.), simply use Ctrl-click to select, Shift-Ctrl-click to add to selection - the only way I was able to select a volume surface for these measurements was to use the Model Panel (under Favorites): choose the volume surface on the left side of the Model Panel, click the "select" button on the right (3) type the accelerator "ma" to measure area and "mv" to measure volume For details, see: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/accelerators/ accelerators.html http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/accelerators/ alist.html http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/accelerators/ alist.html#measure However, accelerators cannot be included in a Chimera command script, and you would still have to select the surface(s) interactively. In the future we hope to have the surface calculations more integrated and available with Chimera commands, but it has not been done yet. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Dec 26, 2007, at 1:58 AM, "" wrote: > Dear all, > > May I know if there is some command in chimera for measuring volume > and area like in the menus: ?Tools?Surface/Binding Analysis?Measure > Volume and Area?? Thanks in advance! > > Happy new year and have a nice holiday! > > Zhiya From shengzhiya at nibs.ac.cn Thu Dec 27 01:16:49 2007 From: shengzhiya at nibs.ac.cn (shengzhiya at nibs.ac.cn) Date: Thu, 27 Dec 2007 17:16:49 +0800 (HKT) Subject: [Chimera-users] Command for volum e and area calculation In-Reply-To: References: <477225E3.0000DF.29901@mail7.corpease.net> Message-ID: <47736D81.000178.14870@mail7.corpease.net> Dear Elaine, Thank you very much! Sure it helps! Best wishes, Zhiya -------------- next part -------------- An HTML attachment was scrubbed... URL: From dsouthwo at msg.ucsf.edu Thu Dec 20 10:47:13 2007 From: dsouthwo at msg.ucsf.edu (Daniel Southworth) Date: Thu, 20 Dec 2007 10:47:13 -0800 Subject: [Chimera-users] fitting models into maps In-Reply-To: <476A02C2.6090801@cgl.ucsf.edu> References: <5258338D-D7D2-4491-AA48-5B96B3C9316B@msg.ucsf.edu> <476A02C2.6090801@cgl.ucsf.edu> Message-ID: Thanks - this is very informative. I agree it sounds like getting a cc value from 'fit map into map' is probably the best way. When I generate the volume from the pdb with eman I'll just have the molecular weight set to a threshold of 1 and use that threshold when I run 'fit map into map'. I'll check in to using a std value as well to see if the numbers are any different. Thanks for your help. Dan On Dec 19, 2007, at 9:50 PM, Tom Goddard wrote: > Hi Dan, > > The Chimera fit model in map tool doesn't give a correlation > value. To get a correlation requires you have two maps to compare, > so first a map needs to be calculated from the PDB model that > matches the resolution of the experimental map. Although I'd like > to have that in Chimera, it is not currently there. I have used > the EMAN pdb2mrc program to compute the map. Then you can use the > Chimera fit map in map tool to get a correlation value, or you > could use fit model in map, then open the map calculated for the > PDB and find the correlation for the orientation obtained for the > PDB model. > > You're right that reported correlation values depend on some often > unreported parameters. First there is the method used for > producing a map from the PDB model. Then the correlation depends > on the part of the volume used. I would guess this is typically > the portion within a certain contour level of the PDB map. What > contour level? Something like 1 standard deviation is not sensible > since it depends on the size of the map (the extent of padding). > Probably a contour level that encloses a given volume -- maybe the > volume enclosed by the solvent excluded surface of the PDB model > with a reasonable probe radius. Would be nice if Chimera automated > this calculation starting from the fit model in map position -- > some day, hopefully in 2008. > > Reporting average density value at the atom positions would only > make sense if the map is normalized. Maybe reporting that value in > standard deviations. But the standard deviation depends on how > much empty volume surrounds the structure, so that is not very > satisfactory. Chimera reports that number so you can compare > different fits in the same map -- only relative values are meaningful. > > Another value I have seen reported is the number of atoms outside > a certain contour level of the experimental map. The fit model in > map tool reports that in the reply log (Favorites / Reply Log). Of > course it depends on how you set the contour level. Again if you > set that as some number of standard deviations that depends on the > map size. Alternatively you could set the contour level so the > experimental map encloses the expected volume. Menu entry Tools / > Volume Data / Measure Volume and Area can help set such a contour > level. > > Seems correlation is the most meaningful number. > > You can calculate the standard deviation of a map from its mean in > newer versions of Chimera with menu entry Tools / Volume Data / > Volume Mean, SD, RMS. > > Tom > > > Daniel Southworth wrote: >> Tom: >> >> Hi. I'm a post-doc in David Agard's lab and I have a question >> about the "fit model in map" function in chimera. I'm having some >> good success fitting crystal structures into my low-resolution em >> maps using this function once I get a global fit either by hand or >> using situs. I'm wondering if there is any way to get a >> correlation value out of the fits or how people typically report >> on their confidence of the chimera fitting in publications? I know >> correlation values are often different from program to program so >> perhaps the best measure is to state the average map value? Any >> help would be great - thanks. >> >> Dan >