From kruggel at chemie.uni-hamburg.de Wed Apr 1 03:20:52 2009 From: kruggel at chemie.uni-hamburg.de (Sebastian Kruggel) Date: Wed, 01 Apr 2009 12:20:52 +0200 Subject: [Chimera-users] save reply log via command line? Message-ID: <49D34004.3060506@chemie.uni-hamburg.de> dear chimera team / users, i was looking for a way to save the content of the reply log to a text file via command line, because i wanted to embed and process some results given in the reply log in a small cmd/py-script without. thanks in advance, sebastian -- Sebastian Kruggel Institut f?r Pharmazie Bundesstr. 45 | Raum 112 (406) D 20146 Hamburg Tel +49 (0)40 42838-3626 (-3484) kruggel at chemie.uni-hamburg.de From brignole at scripps.edu Wed Apr 1 13:02:46 2009 From: brignole at scripps.edu (Edward Brignole) Date: Wed, 1 Apr 2009 13:02:46 -0700 Subject: [Chimera-users] write selected command Message-ID: <78D9C55D95B16B4192722DBCC37E42C5017BD2BB@EXCHV1.lj.ad.scripps.edu> Elaine and co, I have a mess of models that I'm opening, repositioning a ligand using match to various positions in each model. No problem there. For each model and ligand position I select the correct chains from that model with the repositioned ligand models but can't manage to save coordinates. Obviously there's the save pdb dialog but for all these models and ligands this will be more convenient scripted into chimera commands. I've got it all working except this: select #6:.a-p #8 #9 write selected relative 0 #6,8,9 /path/to/file.pdb ~select The part it doesn't like is the model_numbers and I've tried various permutations without success. The only way I can get it to work is if I only specify one model number. Can you please help me figure out how to phrase this command correctly? An example or two on that commands page might make the syntax easier to decipher. Thank you for your excellent program and support. Ed ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Edward Brignole NIH Kirschstein Postdoctoral Fellow Francisco Asturias Lab, CB227 Center for Integrative Molecular Biosciences The Scripps Research Institute www.scripps.edu/~brignole brignole at scripps.edu 443-653-2070 (cell) 858-784-8598 (lab) -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Wed Apr 1 13:11:01 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 1 Apr 2009 13:11:01 -0700 Subject: [Chimera-users] write selected command In-Reply-To: <78D9C55D95B16B4192722DBCC37E42C5017BD2BB@EXCHV1.lj.ad.scripps.edu> References: <78D9C55D95B16B4192722DBCC37E42C5017BD2BB@EXCHV1.lj.ad.scripps.edu> Message-ID: <531E7BE8-1B3B-485F-9718-11FDDE12321D@cgl.ucsf.edu> Hi Ed, The "write" command only allows you to save one model at a time. To save multiple models to one PDB file you have to use the GUI ("File... Save PDB" or "Actions... Write PDB"). Sorry about that, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Apr 1, 2009, at 1:02 PM, Edward Brignole wrote: > Elaine and co, > > I have a mess of models that I'm opening, repositioning a ligand > using match to various positions in each model. No problem there. > For each model and ligand position I select the correct chains from > that model with the repositioned ligand models but can't manage to > save coordinates. Obviously there's the save pdb dialog but for all > these models and ligands this will be more convenient scripted into > chimera commands. I've got it all working except this: > > select #6:.a-p #8 #9 > write selected relative 0 #6,8,9 /path/to/file.pdb > ~select > > The part it doesn't like is the model_numbers and I've tried > various permutations without success. The only way I can get it to > work is if I only specify one model number. > > Can you please help me figure out how to phrase this command > correctly? An example or two on that commands page might make the > syntax easier to decipher. > > Thank you for your excellent program and support. > > Ed > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Edward Brignole > NIH Kirschstein Postdoctoral Fellow > Francisco Asturias Lab, CB227 > Center for Integrative Molecular Biosciences > The Scripps Research Institute > www.scripps.edu/~brignole > > brignole at scripps.edu > 443-653-2070 (cell) > 858-784-8598 (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 Wed Apr 1 13:26:43 2009 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 1 Apr 2009 13:26:43 -0700 Subject: [Chimera-users] write selected command In-Reply-To: <531E7BE8-1B3B-485F-9718-11FDDE12321D@cgl.ucsf.edu> References: <78D9C55D95B16B4192722DBCC37E42C5017BD2BB@EXCHV1.lj.ad.scripps.edu> <531E7BE8-1B3B-485F-9718-11FDDE12321D@cgl.ucsf.edu> Message-ID: Other possibilities include using the "combine" command to combine models 6, 8, and 9 into a single model (with model 0 as the 'refMol') and then use the write command on that (omitting 'relative 0'), or writing the models to separate files and using 'system cat file1 file2 file3 > file4' to combine them (though there would be END records between the models that way). --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Apr 1, 2009, at 1:11 PM, Elaine Meng wrote: > Hi Ed, > The "write" command only allows you to save one model at a time. > > > To save multiple models to one PDB file you have to use the GUI > ("File... Save PDB" or "Actions... Write PDB"). > > > Sorry about that, > Elaine > ----- > Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > http://www.cgl.ucsf.edu/home/meng/index.html > > On Apr 1, 2009, at 1:02 PM, Edward Brignole wrote: > >> Elaine and co, >> >> I have a mess of models that I'm opening, repositioning a ligand >> using match to various positions in each model. No problem there. >> For each model and ligand position I select the correct chains from >> that model with the repositioned ligand models but can't manage to >> save coordinates. Obviously there's the save pdb dialog but for all >> these models and ligands this will be more convenient scripted into >> chimera commands. I've got it all working except this: >> >> select #6:.a-p #8 #9 >> write selected relative 0 #6,8,9 /path/to/file.pdb >> ~select >> >> The part it doesn't like is the model_numbers and I've tried >> various permutations without success. The only way I can get it to >> work is if I only specify one model number. >> >> Can you please help me figure out how to phrase this command >> correctly? An example or two on that commands page might make the >> syntax easier to decipher. >> >> Thank you for your excellent program and support. >> >> Ed >> >> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >> Edward Brignole >> NIH Kirschstein Postdoctoral Fellow >> Francisco Asturias Lab, CB227 >> Center for Integrative Molecular Biosciences >> The Scripps Research Institute >> www.scripps.edu/~brignole >> >> brignole at scripps.edu >> 443-653-2070 (cell) >> 858-784-8598 (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 brignole at scripps.edu Wed Apr 1 13:32:18 2009 From: brignole at scripps.edu (Edward Brignole) Date: Wed, 1 Apr 2009 13:32:18 -0700 Subject: [Chimera-users] write selected command References: <78D9C55D95B16B4192722DBCC37E42C5017BD2BB@EXCHV1.lj.ad.scripps.edu> <531E7BE8-1B3B-485F-9718-11FDDE12321D@cgl.ucsf.edu> Message-ID: <78D9C55D95B16B4192722DBCC37E42C5017BD2C0@EXCHV1.lj.ad.scripps.edu> Great suggestion, I'll just use cat and strip the END lines. Since I want to then use these with morph conformations will I also have to resequence the atom id's? Ed ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Edward Brignole NIH Kirschstein Postdoctoral Fellow Francisco Asturias Lab, CB227 Center for Integrative Molecular Biosciences The Scripps Research Institute www.scripps.edu/~brignole brignole at scripps.edu 443-653-2070 (cell) 858-784-8598 (lab) -----Original Message----- From: Eric Pettersen [mailto:pett at cgl.ucsf.edu] Sent: Wed 4/1/2009 1:26 PM To: Edward Brignole Cc: chimera-users at cgl.ucsf.edu BB Subject: Re: [Chimera-users] write selected command Other possibilities include using the "combine" command to combine models 6, 8, and 9 into a single model (with model 0 as the 'refMol') and then use the write command on that (omitting 'relative 0'), or writing the models to separate files and using 'system cat file1 file2 file3 > file4' to combine them (though there would be END records between the models that way). --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Apr 1, 2009, at 1:11 PM, Elaine Meng wrote: > Hi Ed, > The "write" command only allows you to save one model at a time. > > > To save multiple models to one PDB file you have to use the GUI > ("File... Save PDB" or "Actions... Write PDB"). > > > Sorry about that, > Elaine > ----- > Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > http://www.cgl.ucsf.edu/home/meng/index.html > > On Apr 1, 2009, at 1:02 PM, Edward Brignole wrote: > >> Elaine and co, >> >> I have a mess of models that I'm opening, repositioning a ligand >> using match to various positions in each model. No problem there. >> For each model and ligand position I select the correct chains from >> that model with the repositioned ligand models but can't manage to >> save coordinates. Obviously there's the save pdb dialog but for all >> these models and ligands this will be more convenient scripted into >> chimera commands. I've got it all working except this: >> >> select #6:.a-p #8 #9 >> write selected relative 0 #6,8,9 /path/to/file.pdb >> ~select >> >> The part it doesn't like is the model_numbers and I've tried >> various permutations without success. The only way I can get it to >> work is if I only specify one model number. >> >> Can you please help me figure out how to phrase this command >> correctly? An example or two on that commands page might make the >> syntax easier to decipher. >> >> Thank you for your excellent program and support. >> >> Ed >> >> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >> Edward Brignole >> NIH Kirschstein Postdoctoral Fellow >> Francisco Asturias Lab, CB227 >> Center for Integrative Molecular Biosciences >> The Scripps Research Institute >> www.scripps.edu/~brignole >> >> brignole at scripps.edu >> 443-653-2070 (cell) >> 858-784-8598 (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 pett at cgl.ucsf.edu Wed Apr 1 14:02:11 2009 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 1 Apr 2009 14:02:11 -0700 Subject: [Chimera-users] write selected command In-Reply-To: <78D9C55D95B16B4192722DBCC37E42C5017BD2C0@EXCHV1.lj.ad.scripps.edu> References: <78D9C55D95B16B4192722DBCC37E42C5017BD2BB@EXCHV1.lj.ad.scripps.edu> <531E7BE8-1B3B-485F-9718-11FDDE12321D@cgl.ucsf.edu> <78D9C55D95B16B4192722DBCC37E42C5017BD2C0@EXCHV1.lj.ad.scripps.edu> Message-ID: Hi Ed, If the purpose of the combination is to use Morph Conformations, then I think you're in for a world of hurt unless you use the 'combine' method. One problem with the 'cat' method is the serial numbers as you surmised. If you have any non-standard residues that require CONECT records then the serial numbers will be a real issue. Another problem is that if you have any chains in models 8 and 9 that duplicate the ones you're using from #6 (a-p) or duplicate each other then Morph Conformations will probably fall over. 'combine' will rename chains that are in conflict and renumber problem residues. 'write' with the combined model will produce unique serial numbers. So your previous commands: select #6:.a-p #8 #9 write selected relative 0 #6,8,9 /path/to/file.pdb ~select could instead be: sel #6:.a-p sel invert sel del sel combine #6,8,9 refMol 0 modelId 7 write #7 /path/to/file.pdb BTW, you have to use a daily build to get the 'modelId' part of the 'combine' command. If your models #8 and 9 are just small molecules then you may be able to get away with the 'cat' method by stripping CONECT records in addition to END records -- making Chimera come up with the connectivity itself (though if the residues had the same number and chain ID as other residues...). --Eric On Apr 1, 2009, at 1:32 PM, Edward Brignole wrote: > Great suggestion, I'll just use cat and strip the END lines. Since I > want to then use these with morph conformations will I also have to > resequence the atom id's? > > Ed > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Edward Brignole > NIH Kirschstein Postdoctoral Fellow > Francisco Asturias Lab, CB227 > Center for Integrative Molecular Biosciences > The Scripps Research Institute > www.scripps.edu/~brignole > > brignole at scripps.edu > 443-653-2070 (cell) > 858-784-8598 (lab) > > > > -----Original Message----- > From: Eric Pettersen [mailto:pett at cgl.ucsf.edu] > Sent: Wed 4/1/2009 1:26 PM > To: Edward Brignole > Cc: chimera-users at cgl.ucsf.edu BB > Subject: Re: [Chimera-users] write selected command > > Other possibilities include using the "combine" command to combine > models 6, 8, and 9 into a single model (with model 0 as the 'refMol') > and then use the write command on that (omitting 'relative 0'), or > writing the models to separate files and using 'system cat file1 file2 > file3 > file4' to combine them (though there would be END records > between the models that way). > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > > On Apr 1, 2009, at 1:11 PM, Elaine Meng wrote: > > > Hi Ed, > > The "write" command only allows you to save one model at a time. > > > > > > To save multiple models to one PDB file you have to use the GUI > > ("File... Save PDB" or "Actions... Write PDB"). > > > > > > Sorry about that, > > Elaine > > ----- > > Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu > > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > > Department of Pharmaceutical Chemistry > > University of California, San Francisco > > http://www.cgl.ucsf.edu/home/meng/index.html > > > > On Apr 1, 2009, at 1:02 PM, Edward Brignole wrote: > > > >> Elaine and co, > >> > >> I have a mess of models that I'm opening, repositioning a ligand > >> using match to various positions in each model. No problem there. > >> For each model and ligand position I select the correct chains from > >> that model with the repositioned ligand models but can't manage to > >> save coordinates. Obviously there's the save pdb dialog but for all > >> these models and ligands this will be more convenient scripted into > >> chimera commands. I've got it all working except this: > >> > >> select #6:.a-p #8 #9 > >> write selected relative 0 #6,8,9 /path/to/file.pdb > >> ~select > >> > >> The part it doesn't like is the model_numbers and I've tried > >> various permutations without success. The only way I can get it to > >> work is if I only specify one model number. > >> > >> Can you please help me figure out how to phrase this command > >> correctly? An example or two on that commands page might make the > >> syntax easier to decipher. > >> > >> Thank you for your excellent program and support. > >> > >> Ed > >> > >> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > >> Edward Brignole > >> NIH Kirschstein Postdoctoral Fellow > >> Francisco Asturias Lab, CB227 > >> Center for Integrative Molecular Biosciences > >> The Scripps Research Institute > >> www.scripps.edu/~brignole > >> > >> brignole at scripps.edu > >> 443-653-2070 (cell) > >> 858-784-8598 (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 meng at cgl.ucsf.edu Wed Apr 1 15:37:22 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 1 Apr 2009 15:37:22 -0700 Subject: [Chimera-users] write selected command In-Reply-To: <78D9C55D95B16B4192722DBCC37E42C5017BD2BE@EXCHV1.lj.ad.scripps.edu> References: <78D9C55D95B16B4192722DBCC37E42C5017BD2BB@EXCHV1.lj.ad.scripps.edu> <735A4B07-65D0-4FDF-952B-2DC27107905B@cgl.ucsf.edu> <78D9C55D95B16B4192722DBCC37E42C5017BD2BE@EXCHV1.lj.ad.scripps.edu> Message-ID: Hi Ed, Are there conformational changes in this process, or do chains simply move as rigid bodies? I had thought there were conformational changes within chains, but now looking at your movie again, I'm not sure. If each rigid body is a separate model, you would simply save the different configurations of the entire set as named positions with the command "savepos". Then you can reset to successive named over a specified number of frames with "reset" or smoothly interpolate over multiple saved positions with "fly". There have been recent improvements including addition of "fly" so I'd recommend a recent daily build if it sounds like this approach is doable. The process would then be scripted in a Chimera command file rather than appearing as playback in MD Movie. Once the command file generates the desired movie content, you could put a "movie record" command at the top and "movie stop" and "movie encode" commands at the bottom. example command files: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/movies.html#examples I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html From pett at cgl.ucsf.edu Wed Apr 1 19:35:10 2009 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 1 Apr 2009 19:35:10 -0700 Subject: [Chimera-users] save reply log via command line? In-Reply-To: <49D34004.3060506@chemie.uni-hamburg.de> References: <49D34004.3060506@chemie.uni-hamburg.de> Message-ID: Hi Sebastian, One thing is that if you are running in nogui mode (i.e. with the startup command line argument "--nogui") then replies will come out on standard output, which you could redirect to a file. Otherwise you can save the contents of the reply log with this Python code: from chimera.tkgui import saveReplyLog saveReplyLog("savefilename") --Eric Eric Pettersen UCSF Computer Graphics Lab On Apr 1, 2009, at 3:20 AM, Sebastian Kruggel wrote: > dear chimera team / users, > > i was looking for a way to save the content of the reply log > to a text file via command line, because i wanted to embed > and process some results given in the reply log in a small > cmd/py-script without. > > thanks in advance, > sebastian > > > > -- > Sebastian Kruggel > Institut f?r Pharmazie > Bundesstr. 45 | Raum 112 (406) > D 20146 Hamburg > > Tel +49 (0)40 42838-3626 (-3484) > kruggel at chemie.uni-hamburg.de > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From bala.biophysics at gmail.com Thu Apr 2 01:06:59 2009 From: bala.biophysics at gmail.com (Bala subramanian) Date: Thu, 2 Apr 2009 10:06:59 +0200 Subject: [Chimera-users] calculating centroid of atoms Message-ID: <288df32a0904020106k28f6f320m3fa31cf8913f79cc@mail.gmail.com> Friends, I want to choose certains atoms and get the x,y,z coordinates of the center. Kindly write me how to do it in chimera. Bala -------------- next part -------------- An HTML attachment was scrubbed... URL: From dchen at caltech.edu Thu Apr 2 09:01:56 2009 From: dchen at caltech.edu (David Chenoweth) Date: Thu, 2 Apr 2009 09:01:56 -0700 Subject: [Chimera-users] calculating centroid of atoms In-Reply-To: <288df32a0904020106k28f6f320m3fa31cf8913f79cc@mail.gmail.com> References: <288df32a0904020106k28f6f320m3fa31cf8913f79cc@mail.gmail.com> Message-ID: <55F89313-CEF6-42E3-AD8F-95B5E834EB0D@caltech.edu> Hi Bala, I have been using the free program Mercury to calculate centroids. It allows you to pick any number of atoms, least-squares fit them to a plane, and calculate a centroid. I usually do this and then output the xyz coordinates and past them into a pdb file with a dummy atom name or you can assign the atoms to boron or something else not in your structure. You can then open your pdb files and use chimera to superimpose centroid atoms of multiple structures or make measurements and pictures. Mercury also allows you to least squares fit planes to atoms or points and measure angles between intersecting planes. These would be great analysis tools to add to Chimera! If you need any help or more info don't hesitate to email me. Cheers, Dave ********************************************** David M. Chenoweth California Institute of Technology Division of Chemistry and Chemical Engineering Mail Code: 164-30 1200 California Boulevard, 91125 Pasadena California, USA Phone: 626-395-6074 Email: dchen at caltech.edu ********************************************** On Apr 2, 2009, at 1:06 AM, Bala subramanian wrote: > Friends, > > I want to choose certains atoms and get the x,y,z coordinates of the > center. Kindly write me how to do it in chimera. > > Bala > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From tchiang at gallo.ucsf.edu Wed Apr 1 15:34:25 2009 From: tchiang at gallo.ucsf.edu (Terrance Chiang) Date: Wed, 1 Apr 2009 15:34:25 -0700 Subject: [Chimera-users] chimera help Message-ID: Hi, I am trying to show a structural change between two proteins that differ by one amino acid, is this possible with chimera? I was unable to display the transformation I desired, so I looked into other ways to show changes between two overall similar molecules. I found that it is possible to show a change in the surface between two similar molecules, but I am unable to utilize the function because it requires a different file format. I would like to do both... that is, to show the conformational change from one protein to another, as well as show the change in surface from one protein to another, but I keep hitting these road blocks. Any help would be highly appreciated! Thanks, Terrance Chiang -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Thu Apr 2 09:41:21 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 2 Apr 2009 09:41:21 -0700 Subject: [Chimera-users] chimera help In-Reply-To: References: Message-ID: <0AD47CF9-C96C-45E4-8388-ED1CC99CEA3B@cgl.ucsf.edu> Hi Terrance, I'm not sure what you were trying. You can just open the two structures and show them in any style you want, including molecular surfaces. I am assuming you already have the two structures. Chimera can "mutate" one amino acid to another, but other than choosing the best possible rotamer for the new amino acid, it will not predict structural changes caused by a mutation. If the structures are not already matched or superimposed, you can use MatchMaker to superimpose them, and if you use the MatchMaker option to show the sequence alignment, that will automatically show an RMSD histogram above the sequences (for 2 sequences, the bar height shows simply the CA-CA distance in each column). If you want the structures side by side rather than superimposed, you would first superimpose them and then translate one of them along the laboratory Y axis with the command "move" (or translate each one but in opposite directions, e.g. one to the left and one to the right). If you show surfaces (e.g. Actions... Surface... show) it is often too confusing to superimpose two structures, and the side-by-side approach may be better. You can color the surfaces by properties such as hydrophobicity (see Presets... Interactive 3 (hydrophobicity surface)) or Coulombic electrostatic potential (see Tools... Surface/Binding Analysis... Coulombic Surface Color -- for that you need a recent daily build). If you need more details on any of these I can point you to the relevant manual pages. There are also tutorials on structure analysis and comparison of related structures: I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Apr 1, 2009, at 3:34 PM, Terrance Chiang wrote: > Hi, > I am trying to show a structural change between two proteins that > differ by one amino acid, is this possible with chimera? > > I was unable to display the transformation I desired, so I looked > into other ways to show changes between two overall similar > molecules. I found that it is possible to show a change in the > surface between two similar molecules, but I am unable to utilize > the function because it requires a different file format. > > I would like to do both... that is, to show the conformational > change from one protein to another, as well as show the change in > surface from one protein to another, but I keep hitting these road > blocks. > > Any help would be highly appreciated! > > Thanks, > Terrance Chiang From pett at cgl.ucsf.edu Thu Apr 2 11:48:54 2009 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Thu, 2 Apr 2009 11:48:54 -0700 Subject: [Chimera-users] calculating centroid of atoms In-Reply-To: <288df32a0904020106k28f6f320m3fa31cf8913f79cc@mail.gmail.com> References: <288df32a0904020106k28f6f320m3fa31cf8913f79cc@mail.gmail.com> Message-ID: <895CAD07-94C3-4C35-BE3F-CC19C92D340B@cgl.ucsf.edu> Hi Bala, David had good suggestions, but if you just want the center with equal weights for each atom then you can use Chimera's 'cofr' command to get that if you're careful. For instance: cofr :10.a & aromatic ring will report the center of the aromatic ring in residue 10 of chain A to the status line and to the Reply Log. However, it reports it in lab coordinates, not model coordinates, so you have to be careful not to move your model after opening it -- so that the model and lab coordinates are the same. If you do move it, you should be able to use the "reset" command to get the coordinate systems back in sync. This presumes that you don't have other models open. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Apr 2, 2009, at 1:06 AM, Bala subramanian wrote: > Friends, > > I want to choose certains atoms and get the x,y,z coordinates of the > center. Kindly write me how to do it in chimera. > > Bala > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From matthewd at bcm.edu Thu Apr 2 13:23:26 2009 From: matthewd at bcm.edu (Matthew Dougherty) Date: Thu, 2 Apr 2009 15:23:26 -0500 Subject: [Chimera-users] PDB data In-Reply-To: References: <8BF26F03-EB20-4C44-AFEF-1071A1BCE40C@rosettadesigngroup.com> <39C5E804-B634-4207-9B7E-5D384690E97B@bcm.edu> Message-ID: <63F18FF4-7697-4202-9064-E9C87B9BF488@bcm.edu> I was writing some python code involving PDB data. looking at pre-existing code involving PDB: m = om.open(pdb_path, 'PDB')[0] rlist = m.residues for r in rlist: lc = 'monomer residue %d' % (r.id.position) if r.isHelix: lc += ' HELIX' elif r.isSheet: lc += ' SHEET' I was trying to track down the data structure for r/rlist, to see if there are any other parameters I could use besides isHelix, isSheet, and id.position. where would that be located in the Chimera package? thanks, Matt From matthewd at bcm.edu Thu Apr 2 13:37:30 2009 From: matthewd at bcm.edu (Matthew Dougherty) Date: Thu, 2 Apr 2009 15:37:30 -0500 Subject: [Chimera-users] reset/savepos In-Reply-To: References: <8BF26F03-EB20-4C44-AFEF-1071A1BCE40C@rosettadesigngroup.com> <39C5E804-B634-4207-9B7E-5D384690E97B@bcm.edu> Message-ID: <25DA8834-F0CF-444D-93B3-59269FF5CF88@bcm.edu> I have a chimera session file that is being passed around. Different users are using savepos with no common nomenclature for the view_name. How can I get a list of all view_names? thanks, Matt From matthewd at bcm.edu Thu Apr 2 13:52:52 2009 From: matthewd at bcm.edu (Matthew Dougherty) Date: Thu, 2 Apr 2009 15:52:52 -0500 Subject: [Chimera-users] save/reset/new PDB In-Reply-To: References: <8BF26F03-EB20-4C44-AFEF-1071A1BCE40C@rosettadesigngroup.com> <39C5E804-B634-4207-9B7E-5D384690E97B@bcm.edu> Message-ID: I am trying to incorporate a new pdb structure into an existing session file that has a number of savepos view_names. The new pdb file that is pretty much the same as the old pdb file, just a few side chains moved. So in reset default, they are pretty much sync'd up. when I try some of the other view_names, the new pdb structure does not match. Its as though the same transformations used in the old PDB structure are not being applied to the new PDB structure. How can I sync the new PDB structure to the various view_names? thanks, Matt From pett at cgl.ucsf.edu Thu Apr 2 14:00:57 2009 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Thu, 2 Apr 2009 14:00:57 -0700 Subject: [Chimera-users] reset/savepos In-Reply-To: <25DA8834-F0CF-444D-93B3-59269FF5CF88@bcm.edu> References: <8BF26F03-EB20-4C44-AFEF-1071A1BCE40C@rosettadesigngroup.com> <39C5E804-B634-4207-9B7E-5D384690E97B@bcm.edu> <25DA8834-F0CF-444D-93B3-59269FF5CF88@bcm.edu> Message-ID: <7EE3F51D-BC9C-4504-B875-5C38EE804C95@cgl.ucsf.edu> "reset list" will show the view names in the Reply Log. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Apr 2, 2009, at 1:37 PM, Matthew Dougherty wrote: > I have a chimera session file that is being passed around. > Different users are using savepos with no common nomenclature for the > view_name. > > How can I get a list of all view_names? > > thanks, Matt > _______________________________________________ > 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 Thu Apr 2 14:01:28 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 2 Apr 2009 14:01:28 -0700 Subject: [Chimera-users] reset/savepos In-Reply-To: <25DA8834-F0CF-444D-93B3-59269FF5CF88@bcm.edu> References: <8BF26F03-EB20-4C44-AFEF-1071A1BCE40C@rosettadesigngroup.com> <39C5E804-B634-4207-9B7E-5D384690E97B@bcm.edu> <25DA8834-F0CF-444D-93B3-59269FF5CF88@bcm.edu> Message-ID: <8640F499-4B6E-40D5-990D-9883FF3EF744@cgl.ucsf.edu> Hi Matt, The command "reset list" will list the names of saved positions in the status line and Reply Log. Best, Elaine On Apr 2, 2009, at 1:37 PM, Matthew Dougherty wrote: > I have a chimera session file that is being passed around. > Different users are using savepos with no common nomenclature for the > view_name. > > How can I get a list of all view_names? > > thanks, Matt From matthewd at bcm.edu Thu Apr 2 14:06:13 2009 From: matthewd at bcm.edu (Matthew Dougherty) Date: Thu, 2 Apr 2009 16:06:13 -0500 Subject: [Chimera-users] reset/savepos In-Reply-To: <8640F499-4B6E-40D5-990D-9883FF3EF744@cgl.ucsf.edu> References: <8BF26F03-EB20-4C44-AFEF-1071A1BCE40C@rosettadesigngroup.com> <39C5E804-B634-4207-9B7E-5D384690E97B@bcm.edu> <25DA8834-F0CF-444D-93B3-59269FF5CF88@bcm.edu> <8640F499-4B6E-40D5-990D-9883FF3EF744@cgl.ucsf.edu> Message-ID: thanks, how would I get the same list in python? On Apr 2, 2009, at 4:01 PM, Elaine Meng wrote: > Hi Matt, > The command "reset list" will list the names of saved positions in > the status line and Reply Log. > Best, > Elaine > > On Apr 2, 2009, at 1:37 PM, Matthew Dougherty wrote: > >> I have a chimera session file that is being passed around. >> Different users are using savepos with no common nomenclature for the >> view_name. >> >> How can I get a list of all view_names? >> >> thanks, Matt > > > > From meng at cgl.ucsf.edu Thu Apr 2 14:10:28 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 2 Apr 2009 14:10:28 -0700 Subject: [Chimera-users] save/reset/new PDB In-Reply-To: References: <8BF26F03-EB20-4C44-AFEF-1071A1BCE40C@rosettadesigngroup.com> <39C5E804-B634-4207-9B7E-5D384690E97B@bcm.edu> Message-ID: Hi Matt, If the new structure is sufficiently well matched to the old one when they are in the default (untransformed) positions, then after you reset to the various positions, you can bring the new one in by applying the same transform as is used for the older similar structure. For example, if your older similar structure is model 3 and the newer one is model 10, and you have just reset to a position that leaves the new model stranded, try the command matrixcopy 3 10 to bring 10 into the proper position. How "reset" dealt with new models not in the original saved position was improved (after release 1.3) so that the new models will maintain their transformation relative to the lowest-numbered model that was included in the position. I guess your older similar model is not the lowest-numbered. Or, if it is, you could try using a recent daily build. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Apr 2, 2009, at 1:52 PM, Matthew Dougherty wrote: > I am trying to incorporate a new pdb structure into an existing > session file that has a number of savepos view_names. > > > The new pdb file that is pretty much the same as the old pdb file, > just a few side chains moved. > So in reset default, they are pretty much sync'd up. > > > when I try some of the other view_names, the new pdb structure does > not match. > Its as though the same transformations used in the old PDB structure > are not being applied to the new PDB structure. > > How can I sync the new PDB structure to the various view_names? > > thanks, Matt From pett at cgl.ucsf.edu Thu Apr 2 14:13:20 2009 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Thu, 2 Apr 2009 14:13:20 -0700 Subject: [Chimera-users] reset/savepos In-Reply-To: References: <8BF26F03-EB20-4C44-AFEF-1071A1BCE40C@rosettadesigngroup.com> <39C5E804-B634-4207-9B7E-5D384690E97B@bcm.edu> <25DA8834-F0CF-444D-93B3-59269FF5CF88@bcm.edu> <8640F499-4B6E-40D5-990D-9883FF3EF744@cgl.ucsf.edu> Message-ID: <833325B7-1AAC-4844-9BC9-4F042301E719@cgl.ucsf.edu> import Midas Midas.positions.keys() FYI, most command-line commands are implemented in the Midas module, usually in a function of the same name as the command. So the implementation of "reset" is in "def reset" in Midas/__init__.py. The implementation for commands that do the same things as tools (e.g. findhbonds, volume) are usually found in that tool's module though. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Apr 2, 2009, at 2:06 PM, Matthew Dougherty wrote: > thanks, > > > how would I get the same list in python? > > > On Apr 2, 2009, at 4:01 PM, Elaine Meng wrote: > >> Hi Matt, >> The command "reset list" will list the names of saved positions in >> the status line and Reply Log. >> Best, >> Elaine >> >> On Apr 2, 2009, at 1:37 PM, Matthew Dougherty wrote: >> >>> I have a chimera session file that is being passed around. >>> Different users are using savepos with no common nomenclature for >>> the >>> view_name. >>> >>> How can I get a list of all view_names? >>> >>> thanks, Matt >> >> >> >> > > _______________________________________________ > 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 Thu Apr 2 14:29:00 2009 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Thu, 2 Apr 2009 14:29:00 -0700 Subject: [Chimera-users] PDB data In-Reply-To: <63F18FF4-7697-4202-9064-E9C87B9BF488@bcm.edu> References: <8BF26F03-EB20-4C44-AFEF-1071A1BCE40C@rosettadesigngroup.com> <39C5E804-B634-4207-9B7E-5D384690E97B@bcm.edu> <63F18FF4-7697-4202-9064-E9C87B9BF488@bcm.edu> Message-ID: <78243766-6699-40AC-93A9-7BEF170BE826@cgl.ucsf.edu> Hi Matt, You can find out about the (C++) attributes/methods of a class by using help() in the IDLE interpreter, e.g.: help(chimera.Residue) There is also declaration of the Python-visible attributes of Atom/ Residue/etc. in the source distribution in libs/_chimera/pyinterface. The more convenient way nowadays to get pyinterface is by browsing our SVN repository, i.e. from: /trunk/libs/_chimera/pyinterface ? Chimera The other thing you might want to know that seems germane to your specific query is that the PDB headers are stored in the pdbHeaders dictionary in Molecule (key: header type [e.g. REMARK], value: list of strings). --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Apr 2, 2009, at 1:23 PM, Matthew Dougherty wrote: > I was writing some python code involving PDB data. > > looking at pre-existing code involving PDB: > > > m = om.open(pdb_path, 'PDB')[0] > rlist = m.residues > > for r in rlist: > > lc = 'monomer residue %d' % (r.id.position) > if r.isHelix: > lc += ' HELIX' > elif r.isSheet: > lc += ' SHEET' > > > > > > I was trying to track down the data structure for r/rlist, to see if > there are any other parameters I could use besides isHelix, isSheet, > and id.position. > where would that be located in the Chimera package? > > thanks, Matt > _______________________________________________ > 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 kandiahe at mail.nih.gov Fri Apr 3 08:30:10 2009 From: kandiahe at mail.nih.gov (Eaazhisai Kandiah) Date: Fri, 3 Apr 2009 11:30:10 -0400 Subject: [Chimera-users] delay in starting the program Message-ID: Hi Chimera-Developers, Recently, my work-computer was upgraded from MaC-OS 10.4 to 10.5. I installed the Chimera X-windows version for 10.5. Apparently, while starting the program, it takes almost 2min for the program to get activated. While checking the activity monitor, chimera tries to use 'OSASCRIPT' which together with Chimera, showed as 'not-responding'. I couldn't troubleshoot the reason for this huge delay in start and hence rectify it. Any help would be appreciated. Thank you, Eaazhisai Kandiah Laboratory of Structural Biology NIAMS, National Institutes of Health, Room 1511,Bldg 50 9000 Rockville Pike, Bethesda, MD-20892 kandiahe at mail.nih.gov Off: 301 451 2281 Fax: 301 480 7629 -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at cgl.ucsf.edu Fri Apr 3 11:21:26 2009 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Fri, 03 Apr 2009 11:21:26 -0700 Subject: [Chimera-users] delay in starting the program In-Reply-To: References: Message-ID: <49D653A6.4050402@cgl.ucsf.edu> Hi Eaazhisai, When Mac X11 Chimera starts it uses osascript to start the Apple X11 server if it is not already running. First it tries to determine if X11 is already running. That can take a bit of time since it simply tries to connect to X11 and has to wait until that connection fails. All of this start-up can take a bit of time -- on my 2 year old MacBook Pro laptop running Mac OS 10.5.6 it takes 15 seconds. The second time I start it takes only 2 seconds because X11 is already running and Chimera is already in the operating system in-memory disk cache. If you want a little faster start-up the first time you can use Mac Aqua Chimera -- took 8 seconds the first time, 2 seconds the second time on my machine. I recommend the Mac Aqua Chimera instead of the Mac X11 Chimera because Apple does not support X11 well. Tom Eaazhisai Kandiah wrote: > Hi Chimera-Developers, > > Recently, my work-computer was upgraded from MaC-OS 10.4 to 10.5. I > installed the Chimera X-windows version for 10.5. Apparently, while > starting the program, it takes almost 2min for the program to get > activated. While checking the activity monitor, chimera tries to use > 'OSASCRIPT' which together with Chimera, showed as 'not-responding'. I > couldn't troubleshoot the reason for this huge delay in start and > hence rectify it. Any help would be appreciated. > > Thank you, > > Eaazhisai Kandiah > Laboratory of Structural Biology > NIAMS, National Institutes of Health, > Room 1511,Bldg 50 > 9000 Rockville Pike, Bethesda, > MD-20892 > kandiahe at mail.nih.gov > Off: 301 451 2281 Fax: 301 480 7629 > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > From matthewd at bcm.tmc.edu Sat Apr 4 15:14:28 2009 From: matthewd at bcm.tmc.edu (Matthew Dougherty) Date: Sat, 4 Apr 2009 17:14:28 -0500 Subject: [Chimera-users] MPEG compression In-Reply-To: References: <8BF26F03-EB20-4C44-AFEF-1071A1BCE40C@rosettadesigngroup.com> <39C5E804-B634-4207-9B7E-5D384690E97B@bcm.edu> Message-ID: <4E1214C3-6646-409A-BC11-EF9422EAACE3@bcm.tmc.edu> One of the people in my lab has a series of images that they want to turn into MPEG's Because they are familiar with Chimera, I would like to solve their problem using Chimera rather than train them on FCP. Is there a way to do this either with chimera commands or developing a short python script? thanks, Matt From richard.marhoefer at sp.intervet.com Mon Apr 6 08:59:12 2009 From: richard.marhoefer at sp.intervet.com (Marhoefer, R (Richard)) Date: Mon, 6 Apr 2009 17:59:12 +0200 Subject: [Chimera-users] Enhancement request Povray Message-ID: <15BDC38CF17D784784B874C2634A3CA202B1A1C6@inbn223.d50.intra> Dear Development Team, I would like to generate raytraced images without any shadows. The shininess however should be retained. I experimented with modifying the povray output and added the "no_shadow" keyword to all objects included in the file. This did the job. Could you please add a "no_shadow" option to the povray options panel? It would be very helpful. Kind regards, Richard Dr. Richard Marhoefer Senior Scientist BioChemInformatics Intervet Innovation GmbH Zur Propstei 55270 Schwabenheim, Germany E-Mail: richard.marhoefer at sp.intervet.com Phone: +49 (6130) 948 204 Fax: +49 (6130) 948 517 Mobile: +49 175 723 081 4 Home http://www.intervet.com Sitz der Gesellschaft: Schwabenheim Amtsgericht Mainz, HRB 23 166 Gesch?ftsf?hrer: Dr. Peter Schmid -------------------------------------- This message and any attachments are solely for the intended recipient. If you are not the intended recipient, disclosure, copying, use or distribution of the information included in this message is prohibited -- please immediately and permanently delete. -------------------------------------- From goddard at cgl.ucsf.edu Mon Apr 6 10:42:06 2009 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Mon, 06 Apr 2009 10:42:06 -0700 Subject: [Chimera-users] MPEG compression In-Reply-To: <4E1214C3-6646-409A-BC11-EF9422EAACE3@bcm.tmc.edu> References: <8BF26F03-EB20-4C44-AFEF-1071A1BCE40C@rosettadesigngroup.com> <39C5E804-B634-4207-9B7E-5D384690E97B@bcm.edu> <4E1214C3-6646-409A-BC11-EF9422EAACE3@bcm.tmc.edu> Message-ID: <49DA3EEE.1040708@cgl.ucsf.edu> Hi Matt, Chimera uses ffmpeg to encode a series of images into a movie. ffmpeg is included with Chimera in the "bin" directory. If you record a movie in Chimera using the "movie" command or "Movie Recorder" dialog, the command used to encode the movie is reported in the reply log (Favorites menu). Here's an example: /Users/goddard/chimera/chimera-twain-AGL/install/Chimera.app/Contents/Resources/bin/ffmpeg -r 25 -i /var/folders/+g/+gO21g+SFqCxNgLVgIvElk+++TM/-Tmp-/chimovie_YZ1R-%05d.ppm -y -f mov -b 2000 -bufsize 200 /Users/goddard/chimera_movie.mov The "-r" option gives playback frame rate in frames per second. The -i gives the input image files. The "%05d" in that specification represents the 5 digit image number in the file name (e.g. image-%05d.jpg represents image-00000.jpg, image-00001.jpg, image-00002.jpg, ...) The "-f" is the output format (mov = quicktime). The "-b" gives bit rate it kilobits/second which determines quality versus file size. You can invoke ffmpeg directly from a terminal window on Mac or Linux without starting Chimera. For more options search for ffmpeg on the web. Tom Matthew Dougherty wrote: > One of the people in my lab has a series of images that they want to > turn into MPEG's > > Because they are familiar with Chimera, I would like to solve their > problem using Chimera rather than train them on FCP. > > Is there a way to do this either with chimera commands or developing a > short python script? > > thanks, Matt > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From goddard at cgl.ucsf.edu Mon Apr 6 15:16:39 2009 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Mon, 06 Apr 2009 15:16:39 -0700 Subject: [Chimera-users] Map Morphing questions In-Reply-To: <20090404120000.xix3sv0l0gcwsocs@webmail.biochem.mpg.de> References: <1097683522.e5b1fa099de6c@webmail.biochem.mpg.de> <200410131754.i9DHsjZu1931344@guanine.cgl.ucsf.edu> <1130527304.e6e1830efe186@webmail.biochem.mpg.de> <200510281935.j9SJZJk72027020@guanine.cgl.ucsf.edu> <1130543928.2c25ae47d086d@webmail.biochem.mpg.de> <200510290045.j9T0j9ZH1976407@guanine.cgl.ucsf.edu> <4948BC8B.80105@biochem.mpg.de> <4949D3E5.9060406@cgl.ucsf.edu> <20090404120000.xix3sv0l0gcwsocs@webmail.biochem.mpg.de> Message-ID: <49DA7F47.6030609@cgl.ucsf.edu> Hi Julio, While it is possible to rotate models and use Morph Map at the same time there isn't currently a command to do the morph part. This makes it difficult to record an animation since the morph has to be started by hand from the dialog. The turn command would look like "turn y 3 120" to turn around the y axis in 3 degree steps for 120 steps. Here's the Chimera 1.4 (daily build) "turn" documentation: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html I would like to make a morphmap command so it can be used in animation scripts. Can you explain a bit more your case involving more than 2 maps? Tom Dr .Julio Ortiz wrote: > Hi Tom, > I have been using recently the Morph Map function in Chimera. It is > really helpful! I would like to prepare several movies using this tool. > Three questions: > > 1)Is it possible to combine the morphing with some basic rotations, like > for example around Y axis?. > > 2)I am sure that is doable making some script, but actually..I am so > sorry..I haven't had time to sit down and read carefully how to make > your scripts. > Could you provide me with an initial script to do the rotation of the > morph map which I can start to modify in the future? > > 3) Would it be possible to add more than two maps for the morphing > automatically, and give a sequence of which pairs need to be morphed > instead of make sequential steps? > > Thanks for your help. I hope we can meet again in the near future I > would love to have an update of wht is possible with your wonderful > program. > > Greetings, > Julio > From ines.collings at esrf.fr Fri Apr 3 00:52:23 2009 From: ines.collings at esrf.fr (Ines COLLINGS) Date: Fri, 03 Apr 2009 09:52:23 +0200 Subject: [Chimera-users] chimera help Message-ID: <49D5C037.5060601@esrf.fr> Dear Madam/Sir, I would like to add the coordinates direction x,y,z in Chimera so that I may know the orientation of the unit cell. Could you let me know how to do this. Thank you very much in advance, Ines Collings From chris.d.lau at gmail.com Tue Apr 7 11:11:50 2009 From: chris.d.lau at gmail.com (christopher lau) Date: Tue, 7 Apr 2009 11:11:50 -0700 Subject: [Chimera-users] python scripts Message-ID: Dear Madam/Sir I am new to Chimera and this forum so I apologize in advance if I my question is inappropriate. I want to start writing python scripts such that I can run the script and the color code, orientation, etc of the molecule opened can be automated. Do you know of any good tutorials that teach what commands are available to use in python for chimera and how to run some basic python scripts in chimera? I have figured out enough to open the Python Shell in Chimera, but that is all. An example python script would be helpful. Thanks everyone, Chris Lau -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Tue Apr 7 11:51:48 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 7 Apr 2009 11:51:48 -0700 Subject: [Chimera-users] axes display in Chimera In-Reply-To: <49D5C037.5060601@esrf.fr> References: <49D5C037.5060601@esrf.fr> Message-ID: Dear Ines, I am not sure if this answers the question, but if you open the attached file named general-axes.bild in Chimera, it shows the axes (X red, Y yellow, Z blue). The BILD format is very simple. In fact, the file just contains the following text: .translate 0.0 0.0 0.0 .scale 5 .sphere 0 0 0 0.5 .color 1 0 0 .arrow 0 0 0 5 0 0 .color 1 1 0 .arrow 0 0 0 0 5 0 .color 0 0 1 .arrow 0 0 0 0 0 5 You can edit the file if you want to change the offset (the .translate line) or the size (the .scale line). BILD format is described here: I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html -------------- next part -------------- A non-text attachment was scrubbed... Name: general-axes.bild Type: application/octet-stream Size: 149 bytes Desc: not available URL: -------------- next part -------------- On Apr 3, 2009, at 12:52 AM, Ines COLLINGS wrote: > > Dear Madam/Sir, > I would like to add the coordinates direction x,y,z in Chimera so > that I > may know the orientation of the unit cell. > Could you let me know how to do this. > Thank you very much in advance, > > Ines Collings From meng at cgl.ucsf.edu Tue Apr 7 12:18:48 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 7 Apr 2009 12:18:48 -0700 Subject: [Chimera-users] python scripts In-Reply-To: References: Message-ID: Dear Chris, I can't answer about Python, but you may be able to do what you want using Chimera command scripts. There is a rich set of commands, and the same commands you would enter at the command line can be placed in a text file. Simply opening that command file in Chimera will execute all the commands. Chimera command documentation for the current daily build: Example command files: I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Apr 7, 2009, at 11:11 AM, christopher lau wrote: > Dear Madam/Sir > > I am new to Chimera and this forum so I apologize in advance if I > my question is inappropriate. > I want to start writing python scripts such that I can run the > script and the color code, orientation, etc of the molecule opened > can be automated. Do you know of any good tutorials that teach > what commands are available to use in python for chimera and how to > run some basic python scripts in chimera? I have figured out > enough to open the Python Shell in Chimera, but that is all. An > example python script would be helpful. > > Thanks everyone, > > Chris Lau > _ From pett at cgl.ucsf.edu Tue Apr 7 13:12:09 2009 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Tue, 7 Apr 2009 13:12:09 -0700 Subject: [Chimera-users] python scripts In-Reply-To: References: Message-ID: <5A0C3F3B-6610-41BF-A22E-891403A88A35@cgl.ucsf.edu> Hi Chris, And if you feel you still need to use Python (for looping perhaps) then you should look at the Chimera Programmer's Guide, particularly the examples and the FAQ. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Apr 7, 2009, at 12:18 PM, Elaine Meng wrote: > Dear Chris, > I can't answer about Python, but you may be able to do what you want > using Chimera command scripts. There is a rich set of commands, and > the same commands you would enter at the command line can be placed > in a text file. Simply opening that command file in Chimera will > execute all the commands. > > Chimera command documentation for the current daily build: > > > Example command files: > indexcommand.html#cmdfile> > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > http://www.cgl.ucsf.edu/home/meng/index.html > > > On Apr 7, 2009, at 11:11 AM, christopher lau wrote: > >> Dear Madam/Sir >> >> I am new to Chimera and this forum so I apologize in advance if I >> my question is inappropriate. >> I want to start writing python scripts such that I can run the >> script and the color code, orientation, etc of the molecule opened >> can be automated. Do you know of any good tutorials that teach >> what commands are available to use in python for chimera and how to >> run some basic python scripts in chimera? I have figured out >> enough to open the Python Shell in Chimera, but that is all. An >> example python script would be helpful. >> >> Thanks everyone, >> >> Chris Lau >> _ > _______________________________________________ > 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 bala.biophysics at gmail.com Wed Apr 8 03:49:41 2009 From: bala.biophysics at gmail.com (Bala subramanian) Date: Wed, 8 Apr 2009 12:49:41 +0200 Subject: [Chimera-users] 2drms Message-ID: <288df32a0904080349u1acae221wd8b1bd7b2a70f22b@mail.gmail.com> Friends, Kindly help me with the following queries. 1) How to output the 2drms created for a md. trajectory using MD movie tool. 2) Is there any way to select a square box of a particular length around the molecule and save the image for publication with the desired resolution. I have seen in the chimera archieve that window size can be adjusted. I am not sure if this is the right way to get my job done. Thanks, Bala -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Wed Apr 8 08:01:34 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 8 Apr 2009 08:01:34 -0700 Subject: [Chimera-users] 2drms In-Reply-To: <288df32a0904080349u1acae221wd8b1bd7b2a70f22b@mail.gmail.com> References: <288df32a0904080349u1acae221wd8b1bd7b2a70f22b@mail.gmail.com> Message-ID: Hi Bala, For (2): there is no way to tell Chimera to save the image for only part of what is shown. Instead you need to adjust the view so that the window contains the same thing as you want in the image. Then, with File... Save Image you can specify as many or as few pixels as desired (the image can be at higher, lower, or same resolution as the Chimera window). If you want to specify certain pixel dimensions of the Chimera window, use the "windowsize" command (command "help windowsize" will show its manual page). I know it is common to have one figure that is zoomed out and another that is a closeup in the same rotational orientation. You can save positions with the "savepos" command and restore them with the "reset" command. If you prefer not to use the mouse to zoom (scale) or translate when creating these positions because it is easy to accidentally change the rotation, you can use the "scale" and "move" commands instead. Some of the image tutorials include saving and restoring positions. These are for version 1.4 (current daily build): 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 Apr 8, 2009, at 3:49 AM, Bala subramanian wrote: > Friends, > Kindly help me with the following queries. > > 1) How to output the 2drms created for a md. trajectory using MD > movie tool. > > 2) Is there any way to select a square box of a particular length > around the molecule and save the image for publication with the > desired resolution. I have seen in the chimera archieve that window > size can be adjusted. I am not sure if this is the right way to get > my job done. > Thanks, > Bala From goddard at cgl.ucsf.edu Wed Apr 8 09:54:05 2009 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Wed, 08 Apr 2009 09:54:05 -0700 Subject: [Chimera-users] Enhancement request Povray In-Reply-To: <15BDC38CF17D784784B874C2634A3CA202B1A1C6@inbn223.d50.intra> References: <15BDC38CF17D784784B874C2634A3CA202B1A1C6@inbn223.d50.intra> Message-ID: <49DCD6AD.2030805@cgl.ucsf.edu> Hi Richard, In our development version of Chimera (1.4) there is an option in the Lighting panel (menu Tools / Viewing Controls / Lighting) called "quality" with settings "normal" or "glossy". The glossy setting gives a shininess similar to raytracing by doing per-pixel light calculations. It also gives higher quality transparency. It can be used with normal (unraytraced) image saving to produce shadowless higher quality images. You would need a Chimera daily build. http://www.cgl.ucsf.edu/chimera/alpha-downloads.html This can be installed without uninstalling your production Chimera version. Greg Couch develops our raytracing code and would be the one to comment on the "no shadow" option. Tom Marhoefer, R (Richard) wrote: > Dear Development Team, > > I would like to generate raytraced images without any shadows. The shininess however should be retained. I experimented with modifying the povray output and added the "no_shadow" keyword to all objects included in the file. This did the job. Could you please add a "no_shadow" option to the povray options panel? It would be very helpful. > > Kind regards, > Richard > > > Dr. Richard Marhoefer > Senior Scientist BioChemInformatics > Intervet Innovation GmbH > Zur Propstei > 55270 Schwabenheim, Germany > > E-Mail: richard.marhoefer at sp.intervet.com > Phone: +49 (6130) 948 204 > Fax: +49 (6130) 948 517 > Mobile: +49 175 723 081 4 > Home http://www.intervet.com > > Sitz der Gesellschaft: Schwabenheim Amtsgericht Mainz, HRB 23 166 Gesch?ftsf?hrer: Dr. Peter Schmid > > -------------------------------------- > This message and any attachments are solely for the intended recipient. > > If you are not the intended recipient, disclosure, copying, use or distribution of the information included in this message is prohibited > > > > -- please immediately and permanently delete. > -------------------------------------- > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > From pett at cgl.ucsf.edu Wed Apr 8 10:39:14 2009 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 8 Apr 2009 10:39:14 -0700 Subject: [Chimera-users] 2drms In-Reply-To: References: <288df32a0904080349u1acae221wd8b1bd7b2a70f22b@mail.gmail.com> Message-ID: <8C8BE4F8-BF31-4985-86FA-D818E1139B60@cgl.ucsf.edu> For (1) there really isn't any output option, other than a screen grab. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Apr 8, 2009, at 8:01 AM, Elaine Meng wrote: > Hi Bala, > For (2): there is no way to tell Chimera to save the image for only > part of what is shown. Instead you need to adjust the view so that > the window contains the same thing as you want in the image. Then, > with File... Save Image you can specify as many or as few pixels as > desired (the image can be at higher, lower, or same resolution as the > Chimera window). > > If you want to specify certain pixel dimensions of the Chimera window, > use the "windowsize" command (command "help windowsize" will show its > manual page). > > I know it is common to have one figure that is zoomed out and another > that is a closeup in the same rotational orientation. You can save > positions with the "savepos" command and restore them with the "reset" > command. If you prefer not to use the mouse to zoom (scale) or > translate when creating these positions because it is easy to > accidentally change the rotation, you can use the "scale" and "move" > commands instead. > > Some of the image tutorials include saving and restoring positions. > These are for version 1.4 (current daily build): > > > > > > 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 Apr 8, 2009, at 3:49 AM, Bala subramanian wrote: > >> Friends, >> Kindly help me with the following queries. >> >> 1) How to output the 2drms created for a md. trajectory using MD >> movie tool. >> >> 2) Is there any way to select a square box of a particular length >> around the molecule and save the image for publication with the >> desired resolution. I have seen in the chimera archieve that window >> size can be adjusted. I am not sure if this is the right way to get >> my job done. >> Thanks, >> Bala > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at cgl.ucsf.edu Wed Apr 8 17:13:47 2009 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Wed, 08 Apr 2009 17:13:47 -0700 Subject: [Chimera-users] Modification of b-factor and occupancy In-Reply-To: <49DD30DA.7010009@scripps.edu> References: <49B6D29E.4000807@scripps.edu> <49B6D68B.2090203@cgl.ucsf.edu> <49DD30DA.7010009@scripps.edu> Message-ID: <49DD3DBB.7080008@cgl.ucsf.edu> Tsutomu Matsui wrote: > Hi Tom, > > Is it possible to change b-factor or occupancy of selected atoms, and > then output the coordinates including those changes? > > Tsutomu > Hi Tsutomu, Here are Chimera commands to set bfactor and occupancy of an atom (model #0, residue 13, chain B, atom CA) and write out the PDB: setattr a bfactor 12.3 #0:13.B at CA setattr a occupancy 0.123 #0:13.B at CA write 0 /tmp/test.pdb If you really mean you want change the "selected" atoms use a command like: setattr a bfactor 12.3 sel See the setattr and write documentation for more details. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/write.html Tom From meng at cgl.ucsf.edu Wed Apr 8 17:38:29 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 8 Apr 2009 17:38:29 -0700 Subject: [Chimera-users] Modification of b-factor and occupancy In-Reply-To: <49DD3DBB.7080008@cgl.ucsf.edu> References: <49B6D29E.4000807@scripps.edu> <49B6D68B.2090203@cgl.ucsf.edu> <49DD30DA.7010009@scripps.edu> <49DD3DBB.7080008@cgl.ucsf.edu> Message-ID: Hi Tsutomu, If there are lots of changes (if it would require an inconvenient number of setattr commands) you could create a "define attribute" file and read it in with the "defattr" command or the Define Attribute tool. Notice you can create your own new attributes named whatever you want, show them with colors, worms, etc., and save them to files in that same "define attribute" format. At least if you will be working with Chimera, there is no need to use bfactor and occupancy for things that aren't really bfactor and occupancy. However, if you really want them written out in a PDB file, it is necessary to put the values in bfactor or occupancy. It might cause you to lose digits on the values because those columns are not very wide. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Apr 8, 2009, at 5:13 PM, Tom Goddard wrote: > > Tsutomu Matsui wrote: >> Hi Tom, >> >> Is it possible to change b-factor or occupancy of selected atoms, and >> then output the coordinates including those changes? >> >> Tsutomu >> > > Hi Tsutomu, > > Here are Chimera commands to set bfactor and occupancy of an atom > (model #0, residue 13, chain B, atom CA) and write out the PDB: > > setattr a bfactor 12.3 #0:13.B at CA > setattr a occupancy 0.123 #0:13.B at CA > write 0 /tmp/test.pdb > > If you really mean you want change the "selected" atoms use a > command like: > > setattr a bfactor 12.3 sel > > See the setattr and write documentation for more details. > > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/write.html > > Tom > From pett at cgl.ucsf.edu Thu Apr 9 10:27:45 2009 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Thu, 9 Apr 2009 10:27:45 -0700 Subject: [Chimera-users] chimera difference map In-Reply-To: References: Message-ID: <1B20C5F1-1207-4049-AA76-875DBA15B6EC@cgl.ucsf.edu> On Apr 9, 2009, at 9:23 AM, Negi, Surendra S. wrote: > > Hi Eric, > > I have a quick question related to chimera. Can we use chimera to > calculate the difference map between two EM densities. Hi Surendra, I don't know the answer to this off the top of my head, so I'm cc'ing this to chimera-users, where someone who does know the answer can reply. --Eric From goddard at cgl.ucsf.edu Thu Apr 9 10:55:35 2009 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Thu, 09 Apr 2009 10:55:35 -0700 Subject: [Chimera-users] chimera difference map In-Reply-To: <1B20C5F1-1207-4049-AA76-875DBA15B6EC@cgl.ucsf.edu> References: <1B20C5F1-1207-4049-AA76-875DBA15B6EC@cgl.ucsf.edu> Message-ID: <49DE3697.4080909@cgl.ucsf.edu> Hi Surendra, The vop (volume operation) command can subtract two maps. For example vop #0 subtract map #1 creates a new map that is the difference between maps 0 and 1. The original maps must have identical grids. If they don't have identical grids then you can use the vop "resample" and "onGrid" options to interpolate one map the others grids. You may need to scale one of your maps before subtracting. There is no vop option to do a simple scaling yet. You can do it with a Chimera 1.4 daily build with the Tools / Volume Data / Volume Filter dialog using the Scale filter. To figure out a scale factor one approach is to equalize enclosed volume. You could use the Measure Volume and Area dialog (Tools / Volume Data) to achieve that. Tom Eric Pettersen wrote: > On Apr 9, 2009, at 9:23 AM, Negi, Surendra S. wrote: > >> Hi Eric, >> >> I have a quick question related to chimera. Can we use chimera to >> calculate the difference map between two EM densities. > > Hi Surendra, > I don't know the answer to this off the top of my head, so I'm cc'ing > this to chimera-users, where someone who does know the answer can reply. > > --Eric > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From FedotovT at upstate.edu Wed Apr 8 11:15:17 2009 From: FedotovT at upstate.edu (Tatyana Fedotova) Date: Wed, 08 Apr 2009 14:15:17 -0400 Subject: [Chimera-users] question Message-ID: <49DCB17502000009002955F8@gwmta2.upstate.edu> Dear Mrs/Sir, My name is Tatyana and I am new to Chimera. I hope that you can help me with my question. I have opened pdb file with DNA and protein coordinates. I would like to mutate some residues and base pairs. Do you know how I can introduce them? Thank you, Sincerely, Tanya Tatyana Fedotova, Dpt. of Biochemistry & Molecular Biology SUNY Upstate Medical University 750 East Adams Street Syracuse, NY 13210 Cell: 404-386-5950 Office: (315) 464-8734 Fax: (315) 464-8750 From meng at cgl.ucsf.edu Thu Apr 9 13:18:06 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 9 Apr 2009 13:18:06 -0700 Subject: [Chimera-users] mutating residues In-Reply-To: <49DCB17502000009002955F8@gwmta2.upstate.edu> References: <49DCB17502000009002955F8@gwmta2.upstate.edu> Message-ID: <43D451C8-3F9E-49C9-929E-91AF5E0FCBA2@cgl.ucsf.edu> Dear Tatyana, To mutate amino acids, you can use the command "swapaa" or the graphical interface Rotamers (under Tools... Structure Editing). To mutate nucleic acids from one base to another, you can use the command "swapna". Choose Favorites... Command Line to show the command line. Manual pages for the commands (you can also see these by using the commands "help swapaa" and "help swapna"): and for Rotamers (you can also see this by clicking Help on the Rotamers dialog): Example commands, could be used with PDB structure 10mh : swapaa leu :41.a [change residue 41 in chain A, which is a tryptophan, to leucine] swapna A :406.b [change residue 406 in chain B from DG to adenine nucleotide] swapna T :429.c [change residue 429 in chain C from DC to thymidine nucleotide] One easy way to figure out a residue number is to hover the mouse cursor over an atom in the structure -- that will pop up a "balloon" showing the residue name, number, and chain, as well as the atom name. Swapna only changes the base and swapaa only changes the side chain. Swapaa and Rotamers have lots of options, so you may want to look at their manual pages; for example, if you have a density map, you can choose the conformation that fits it best. There is some use of Rotamers in the "Structure Analysis and Comparison" tutorial: I hope this helps, ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Apr 8, 2009, at 11:15 AM, Tatyana Fedotova wrote: > > I have opened pdb file with DNA and protein coordinates. I would > like to > mutate some residues and base pairs. > Do you know how I can introduce them? From bzuber at mrc-lmb.cam.ac.uk Fri Apr 10 04:54:41 2009 From: bzuber at mrc-lmb.cam.ac.uk (Benoit Zuber) Date: Fri, 10 Apr 2009 12:54:41 +0100 Subject: [Chimera-users] reading complex-float mrc files Message-ID: <49DF3381.8090308@mrc-lmb.cam.ac.uk> Hi, I was wondering if it is possible to read mrc files where the data type is complex float. I get an error when I try to do that, but maybe there is a way around it (other than converting the data to a non complex type). Typically, this would be useful to read fourier transform volumes. Thanks, Ben -- Beno?t Zuber MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH United Kingdom +44 1223 402209 bzuber at mrc-lmb.cam.ac.uk From fajer at magnet.fsu.edu Fri Apr 10 06:58:56 2009 From: fajer at magnet.fsu.edu (Fajer) Date: Fri, 10 Apr 2009 09:58:56 -0400 Subject: [Chimera-users] Renaming chains in "combine" command Message-ID: <49DF50A0.6020405@magnet.fsu.edu> Hi, I am a complete newbie to chimera. I have added a loop sequences to using addaa but the new loop has a different chain designation from the rest of the molecule. "Combine" command preserved the differences in chain id. How can I make the new loop chain to be the same id as the host ? peter From bala.biophysics at gmail.com Fri Apr 10 08:57:44 2009 From: bala.biophysics at gmail.com (Bala subramanian) Date: Fri, 10 Apr 2009 17:57:44 +0200 Subject: [Chimera-users] deleting arrows Message-ID: <288df32a0904100857r3e4e4784od2b54e04a7fc324d@mail.gmail.com> Dear Chimerians, I created one .bild file and loaded it in chimera. When i use del command the object is not getting deleted. open eg.bild del #0 -> now the arrows that are displayed on the screen is not deleted. Why is it so ? Thanks, Bala -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Fri Apr 10 09:07:12 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 10 Apr 2009 09:07:12 -0700 Subject: [Chimera-users] Renaming chains in "combine" command In-Reply-To: <49DF50A0.6020405@magnet.fsu.edu> References: <49DF50A0.6020405@magnet.fsu.edu> Message-ID: Hi Peter, In my tests of "addaa", the new residue gets the same chain ID as the preceding residue. For example, open 1zik, choose menu "Presets... Interactive 2 (all atoms)" then use commands: rlabel :30 focus :30 addaa tyr,31,alpha :30.b rlabel :31 the new residue is 31 in chain B attached to 30 in chain B. The "combine" command either copies a model or combines multiple models into one. It does not change chain IDs within a single model. The only time it changes chain IDs is to avoid indistinguishable residues when combining multiple models into one model. I don't know how you got the loop to have a different chain ID. At this point, to change the chain ID of those residues, you would need to write out the PDB file (File... Save PDB) and text-edit it. Be careful not to make multiple residues with the same number and chain ID (i.e. there should not be two residues that are both number 30 in chain A). Editing could be done manually in a text editor, or it may be possible with one of these PDB-file-editing Web servers: The other way to build peptides in Chimera is with Build Structure (under Tools... Structure Editing), Add Atoms section, peptide sequence option. That builds peptides that are not connected to your existing structure, but you can enter whatever chain ID you want in the dialog. 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 Apr 10, 2009, at 6:58 AM, Fajer wrote: > Hi, > I am a complete newbie to chimera. I have added a loop sequences to > using addaa but the new loop has a different chain designation from > the > rest of the molecule. "Combine" command preserved the differences in > chain id. How can I make the new loop chain to be the same id as > the host ? > peter From meng at cgl.ucsf.edu Fri Apr 10 09:13:28 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 10 Apr 2009 09:13:28 -0700 Subject: [Chimera-users] deleting arrows In-Reply-To: <288df32a0904100857r3e4e4784od2b54e04a7fc324d@mail.gmail.com> References: <288df32a0904100857r3e4e4784od2b54e04a7fc324d@mail.gmail.com> Message-ID: Hi Bala, Deleting is applied to specified atoms, not other stuff like BILD objects or density maps. To get rid of those other types of models you would use the command "close", for example: close 0 [or] close #0 if the BILD model is #0. Normally delete is used to get rid of part of an atomic structure, (for example, "delete solvent") whereas "close" gets rid of whole models of all types. 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 Apr 10, 2009, at 8:57 AM, Bala subramanian wrote: > Dear Chimerians, > I created one .bild file and loaded it in chimera. When i use del > command the object is not getting deleted. > > open eg.bild > del #0 -> now the arrows that are displayed on the screen is not > deleted. Why is it so ? > > Thanks, > Bala From goddard at cgl.ucsf.edu Fri Apr 10 11:21:30 2009 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Fri, 10 Apr 2009 11:21:30 -0700 Subject: [Chimera-users] reading complex-float mrc files In-Reply-To: <49DF3381.8090308@mrc-lmb.cam.ac.uk> References: <49DF3381.8090308@mrc-lmb.cam.ac.uk> Message-ID: <49DF8E2A.3000209@cgl.ucsf.edu> Hi Benoit, Chimera cannot read volume data with complex values. It would be nice, but it would require special case handling in a lot of Chimera code: histogram display, contour levels, coloring by value, all could use the magnitude of the complex data values. But that could all be done by starting with a different volume data set that holds the magnitudes of the complex values. As you point out using the complex values could have use with Fourier analysis and there might even be specific visualization methods like looking at the complex phase. I'll put this on our feature request list but I think it is unlikely to ever be done given the many more widely useful enhancements already requested. Tom Benoit Zuber wrote: > Hi, > > I was wondering if it is possible to read mrc files where the data type > is complex float. I get an error when I try to do that, but maybe there > is a way around it (other than converting the data to a non complex type). > Typically, this would be useful to read fourier transform volumes. > > Thanks, > Ben > > From michaelz at iastate.edu Fri Apr 10 11:39:20 2009 From: michaelz at iastate.edu (Michael Zimmermann) Date: Fri, 10 Apr 2009 13:39:20 -0500 Subject: [Chimera-users] chimera error message Message-ID: <937091d80904101139o79c3cb35ye3af17113a1cab3a@mail.gmail.com> Dear Chimera Staff, I have been trying to learn to use your object model. My goal is to read in an electron density map in CCP4 format downloaded from emdatabank.org and parse out the 3D matrix of electron density values. However, to get started I was trying to just access atomic information in a sample PDB format file (like atomic coordinates). Running through a few of your examples though has proven confusing to me. The following are commands that I have entered into the IDLE. I am using alpha version 1.3 build 2577. >>> import chimera >>> opened = chimera.openModels.open('C:\DOCUME~1\Administrator\MYDOCU~1\MATLAB\\ribosome\\70s.pdb') >>> mol = opened[0] >>> from chimera.colorTable import getColorByName >>> red = getColorByName('red') >>> mol.color = red Traceback (most recent call last): File "", line 1, in mol.color = red ValueError: underlying C++ Molecule object is missing Why is there a module missing? How do I find out what module is missing and add it? >>> red.name >>> red.rgba What if I want the value displayed rather than the object's ID? Is there a get method that has to be invoked? What would the syntax be? >>> ATOMS = mol.atoms Traceback (most recent call last): File "", line 1, in ATOMS = mol.atoms ValueError: underlying C++ Molecule object is missing Again, why is a module missing, how do I find out what module is missing, and how do I add it? Thank you, Michael Z -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at cgl.ucsf.edu Fri Apr 10 12:03:19 2009 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Fri, 10 Apr 2009 12:03:19 -0700 Subject: [Chimera-users] chimera error message In-Reply-To: <937091d80904101139o79c3cb35ye3af17113a1cab3a@mail.gmail.com> References: <937091d80904101139o79c3cb35ye3af17113a1cab3a@mail.gmail.com> Message-ID: <49DF97F7.5010804@cgl.ucsf.edu> Hi Michael, The error message is that the "Molecule" is missing. That suggests that you closed the molecule (e.g using File / Close Session or the Model Panel dialog). You can't close the molecule and still access it from Python. To show the color name use: >>> red.name() 'red' If you type just red.name as you did it says that is a "built-in method", in other words a function, so you have to call the function by adding the parentheses (). Tom Michael Zimmermann wrote: > Dear Chimera Staff, > > I have been trying to learn to use your object model. My goal is to > read in an electron density map in CCP4 format downloaded from > emdatabank.org and parse out the 3D matrix of > electron density values. However, to get started I was trying to just > access atomic information in a sample PDB format file (like atomic > coordinates). Running through a few of your examples though has > proven confusing to me. The following are commands that I have > entered into the IDLE. I am using alpha version 1.3 build 2577. > > >>> import chimera > >>> opened = > chimera.openModels.open('C:\DOCUME~1\Administrator\MYDOCU~1\MATLAB\\ribosome\\70s.pdb') > >>> mol = opened[0] > >>> from chimera.colorTable import getColorByName > >>> red = getColorByName('red') > >>> mol.color = red > Traceback (most recent call last): > File "", line 1, in > mol.color = red > ValueError: underlying C++ Molecule object is missing > > Why is there a module missing? How do I find out what module is > missing and add it? > > >>> red.name > > >>> red.rgba > > > What if I want the value displayed rather than the object's ID? Is > there a get method that has to be invoked? What would the syntax be? > > >>> ATOMS = mol.atoms > Traceback (most recent call last): > File "", line 1, in > ATOMS = mol.atoms > ValueError: underlying C++ Molecule object is missing > > Again, why is a module missing, how do I find out what module is > missing, and how do I add it? > > Thank you, > > Michael Z > ------------------------------------------------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > From SHuo at clarku.edu Tue Apr 14 10:38:24 2009 From: SHuo at clarku.edu (Shuanghong Huo) Date: Tue, 14 Apr 2009 13:38:24 -0400 Subject: [Chimera-users] interhelical angle Message-ID: <73848327A96D9344B45109682FE31363263C0512DD@john.ad.clarku.edu> Dear Chimera Developers, My group needs to calculate the inter-helical angle for a large trajectory. We know Chimera can calculate the inter-helical angle for a conformation. We are wondering what the easiest way to use Chimera to process the whole trajectory. It is amber trajectory. Thanks, Sharon Huo, Ph.D. Associate Prof. of Chemistry & Biochemistry Clark University -------------- next part -------------- An HTML attachment was scrubbed... URL: From hsosa at aecom.yu.edu Tue Apr 14 13:22:01 2009 From: hsosa at aecom.yu.edu (hsosa at aecom.yu.edu) Date: Tue, 14 Apr 2009 16:22:01 -0400 Subject: [Chimera-users] Copy and Pasting sequences Message-ID: <49E4F069.8050509@aecom.yu.edu> Hi I noticed that in the latest version of Chimera (1.4) the sequence display tool (Model Panel > sequence) is different (nicer looking) than in previous versions. However, before I was able to copy the sequence as text and paste it into a text editor (using CTR-C & CTRL-V in Windows) but that is no longer the case. Is there an easy way to get this functionality back. Thanks Hernando -- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa at aecom.yu.edu ----------------------------------- From pett at cgl.ucsf.edu Tue Apr 14 14:22:12 2009 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Tue, 14 Apr 2009 14:22:12 -0700 Subject: [Chimera-users] interhelical angle In-Reply-To: <73848327A96D9344B45109682FE31363263C0512DD@john.ad.clarku.edu> References: <73848327A96D9344B45109682FE31363263C0512DD@john.ad.clarku.edu> Message-ID: <54B040FD-1186-4005-82B9-775310E368C0@cgl.ucsf.edu> Hi Sharon, It seems to me that there are some issues with this. In particular you need the helices you are measuring to maintain their helicity throughout the trajectory otherwise you will get meaningless angle values for frames with poor helicity (the computed axis direction will be fairly random). Also, to identify the helixes there have to be specific residues that always participate in the helix -- which I imagine would usually be the case but I can envision scenarios where a helix winds/unwinds up and down a sequence. Within those constraints, you can measure an inter-helical angle with the Python script I've attached. You would use it in MD Movie's Per- Frame->Define Script dialog (choose "Python" in "Interpret script as"). You would need to change the specific residue numbers in the script to correspond to the "core" (non-unraveling) resides of your helices. The angles will be printed to the Reply Log as the trajectory plays. Let me know if you have any questions/problems. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Apr 14, 2009, at 10:38 AM, Shuanghong Huo wrote: > Dear Chimera Developers, > > My group needs to calculate the inter-helical angle for a large > trajectory. We know Chimera can calculate the inter-helical angle > for a conformation. We are wondering what the easiest way to use > Chimera to process the whole trajectory. It is amber trajectory. > > Thanks, > Sharon Huo, Ph.D. > Associate Prof. of Chemistry & Biochemistry > Clark University -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: axesAngle.py Type: text/x-python-script Size: 376 bytes Desc: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From bala.biophysics at gmail.com Wed Apr 15 09:10:39 2009 From: bala.biophysics at gmail.com (Bala subramanian) Date: Wed, 15 Apr 2009 18:10:39 +0200 Subject: [Chimera-users] coloring with partial charges Message-ID: <288df32a0904150910j42b2624audccc950644a1d7e2@mail.gmail.com> Friends, How to do electrostatic coloring based on partial charges. I have a pdb generated from amber, i would like to assign amber charges and color the surface using assigned charges. Bala -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Wed Apr 15 09:26:26 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 15 Apr 2009 09:26:26 -0700 Subject: [Chimera-users] graphics problems, BIOMT, selecting by element, etc. In-Reply-To: <003801c9bdc6$05161f80$0f425e80$@ac.be> References: <004c01c85782$0cd8d100$268a7300$@ac.be> <37DD5D63-D1D7-4DA3-B011-D8DD0975019C@cgl.ucsf.edu> <004d01c9a894$6d06acf0$471406d0$@ac.be> <012101c9a8ae$9d862580$d8927080$@ac.be> <48742B16-788A-4849-8AB3-F01A3166CCA2@cgl.ucsf.edu> <001501c9abba$2fc4c060$8f4e4120$@ac.be> <28FBE257-EFF5-4B5C-90C9-B4758D43CE90@cgl.ucsf.edu> <06259A9E-894B-40D2-84E7-D2436F5B58F3@cgl.ucsf.edu> <49C7BA4C.7000401@ulb.ac.be> <49C7BBD7.8020004@ulb.ac.be> <003801c9bdc6$05161f80$0f425e80$@ac.be> Message-ID: On Apr 15, 2009, at 5:30 AM, C?dric Govaerts wrote: > Hi Elaine, Hi Cedric! I will put responses below, after your individual questions... > > I'm not posting my question to the mailing list because most of it > might be > due to my machine. > I've been encountering some problems running chimeras and I suspect a > graphic card issue(s). > Mostly it's the display that goes bananas, lows the machine ending > (sometimes) in a chimera crash. It's OK -- even if due to the machine, other people have these problems too and might want to see the discussion. > > Here are some of the issues : > > 1/ When I zoom in/out using my mouse wheel sometimes all the > displayed atoms > change from wire to CPK representation. I must explicitely change it > back to > wire to go back. > Normal ? > > 2/ When changing the display I have sometimes some very odd graphic > behavior, including part of the window turing colored or black. I > attach a > couple of screenshots. This started just after typing a display > command. For > a while everything became very slow until I tried to save the image > using > chimera itself which seemed to reset the graphics back to normal. > As you can see on the screenshots, some Photoshop tool windows (PS3 > was > running in the backgournd) appear on the image (although not visible > on > chimera itself) which leads me to think that it's a graphics card > issue or a > graphic card+Photoshop issue. These definitely sound like graphics driver issues. Definitely not normal behavior! Things to try are to update your graphics driver as possible, and/or use the Debug Graphics Driver dialog to selectively disable OpenGL features. One way to show this dialog is to go to Preferences (under Favorites), General category, set "debug OpenGL on startup" to true, quit, and restart Chimera. Documentation of the debug dialog and discussion of graphics driver problems: > > 1/ Can I easily build a biomolecule from the PDB file ? > I tried with > i) MultiScale Models but could only get low res surfaces > ii) Unit Cell but got the copies from the SMTRY records of the PDB > file, could not specify the BIOMT > I believe the "sym" command should work but I dunno how to make it > read the > BIOMT matrix in the PDB file. > For building using BIOMT: If you use Multiscale Models, you can force loading of the atomic coordinates for all copies by selecting All chains in the multiscale dialog and then changing the Style to anything other than surfaces. You can also use the "sym" command. If your structure with BIOMT records is model 0, for example, command "sym 0 0": > 2/ Is there a way I can select specifically all Mg atoms ? Or - > trickier- all > calcium (Ca) atoms ? commands: select Mg select Ca You can use all the end entries in the Select... Chemistry menu also in the command line. These symbols are in the element submenu. In cases where there is ambiguity, for example H appears both under element and under IDATM type, you can disambiguate like select element.H It will work to use element.Mg and element.Ca ... it's just more typing. > > 3/ When I select with the mouse, I only select one atom at a time. > What > would be the easiest/fastet way to display the residue that the > currently > atom belongs to ? > A/ Can I do it with the command line (does the command line > recognize the manually selected atoms?) ? > B/ I can use the menus and do Actions->Atoms->Backbone->Full and > then Actions->Atoms->Sidechain->Show, but that's a bit cumbersome to > do each > time I wanna see a residue it seems.. If you have some atom or bond in a residue selected, just hit the keyboard up arrow to broaden the selection to the whole residue. That is the same as using the command: select up You can specify the current selection regardless of how it was created (with mouse, Select menu, etc.) in commands with the word "sel" "selected" or "picked". For example, pick one atom, hit up arrow, use command "display sel" to display the whole residue. Actually if you use "rlabel sel" (show residue label for any selected atoms) you don't even need the up arrow part. > > That's it for now.. brr, thanks ! > > C > You're welcome! 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 meng at cgl.ucsf.edu Wed Apr 15 09:35:50 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 15 Apr 2009 09:35:50 -0700 Subject: [Chimera-users] coloring with partial charges In-Reply-To: <288df32a0904150910j42b2624audccc950644a1d7e2@mail.gmail.com> References: <288df32a0904150910j42b2624audccc950644a1d7e2@mail.gmail.com> Message-ID: <1CA5E6A7-7A2B-41B0-8F08-8C6449E02149@cgl.ucsf.edu> Hi Bala, In version 1.4 (you would need to get a recent daily build, not the production release) there is a Coulombic Surface Coloring tool under Tools... Surface/Binding Analysis. The documentation describes how it works: It will assign charges to your structure. It doesn't matter where the PDB file is from, except that it should be in correct PDB format and have standard atom names for standard residues so that they can be recognized correctly by the charge assignment step. Sometimes there are some format problems with PDB files created by Amber, however, so be sure to check in the Reply Log to see if there were problems with charge assignment. If there are, you may need to manually edit the file to correct any format problems. There is also an "Electrostatic Surface Coloring" tool, but it requires an electrostatic potential map previously calculated with some other program such as DelPhi, APBS, or UHBD. 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 Apr 15, 2009, at 9:10 AM, Bala subramanian wrote: > Friends, > How to do electrostatic coloring based on partial charges. I have a > pdb generated from amber, i would like to assign amber charges and > color the surface using assigned charges. > Bala From pett at cgl.ucsf.edu Wed Apr 15 12:13:14 2009 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 15 Apr 2009 12:13:14 -0700 Subject: [Chimera-users] Fwd: Copy and Pasting sequences References: Message-ID: Begin forwarded message: > From: Eric Pettersen > Date: April 14, 2009 2:36:02 PM PDT > To: hsosa at aecom.yu.edu > Subject: Re: [Chimera-users] Copy and Pasting sequences > > Oooh, you're right -- that's missing. There's a whole passel of > improvements I need to do for the sequence viewer and now that > you've pointed it out that's certainly one of them. There'll be > some kind of replacement functionality by the next release. In the > interim, a possible workaround is to save the sequence to a file > (using the viewer's File-Save As) and copy from that. Probably the > simplest format (and therefore the easiest to copy from) is FASTA. > > --Eric > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > > On Apr 14, 2009, at 1:22 PM, hsosa at aecom.yu.edu wrote: > >> Hi >> >> I noticed that in the latest version of Chimera (1.4) the sequence >> display tool (Model Panel > sequence) is different (nicer looking) >> than >> in previous versions. However, before I was able to copy the >> sequence as >> text and paste it into a text editor (using CTR-C & CTRL-V in >> Windows) >> but that is no longer the case. Is there an easy way to get this >> functionality back. >> >> Thanks >> >> Hernando >> >> >> -- >> ----------------------------------- >> Hernando Sosa >> Dept. of Physiology and Biophysics >> Albert Einstein College of Medicine >> 1300 Morris Park Av. >> Bronx NY 10461 >> phone (718) 430-3456 >> FAX (718) 430-8819 >> email hsosa at aecom.yu.edu >> ----------------------------------- >> >> >> >> _______________________________________________ >> 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 yokotakechang at hotmail.co.jp Wed Apr 15 14:23:03 2009 From: yokotakechang at hotmail.co.jp (=?iso-2022-jp?B?GyRCMiM7MxsoQiAbJEJJcDtKGyhC?=) Date: Thu, 16 Apr 2009 06:23:03 +0900 Subject: [Chimera-users] How to save fitted map as MRC file. Message-ID: Dear chimera developer I want to save fitted map after using "Tools/Volume Data/Fit in Map" as MRC file. How can I do this? Is there the same kind of function when we save fitted PDB file related to Map. Thank you in advance, Takeshi ------------------------------------------------------------------------------------------------------------------------- Takeshi yokoyama Ph.D. Postdoctoral scientist Wadsworth Center New York State Department of Health USA yokoyama at wadsworth.org -------------------------------------------------------------------------------------------------------------------------- _________________________________________________________________ ?????????????! ???????????????? http://career.jp.msn.com/article2/genba/default.htm -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Wed Apr 15 16:05:55 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 15 Apr 2009 16:05:55 -0700 Subject: [Chimera-users] How to save fitted map as MRC file. In-Reply-To: References: Message-ID: <6C683FBF-5F98-499D-8E15-B5FB1DEEA3DD@cgl.ucsf.edu> Dear Takeshi, For a PDB fitted to a map, just use "File... Save PDB" in the menu and make sure to choose the option to "save relative to" the map model. For saving a map fitted to another map, you could just save the Chimera session, which will preserve the orientations of the different models. However, if you want to save a map file to use in other programs, it is necessary to resample the map that you fit on the grid of the map you fit into. Resampling interpolates data values and can degrade map quality. You can create a resampled map with the "vop" command and then save that new map with the Volume Viewer dialog or "volume" command, as described in this previous post: More about "vop": I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Apr 15, 2009, at 2:23 PM, ?? ?? wrote: > Dear chimera developer > I want to save fitted map after using "Tools/Volume Data/Fit in > Map" as MRC file. > How can I do this? > Is there the same kind of function when we save fitted PDB > file related to Map. > Thank you in advance, > Takeshi From bala.biophysics at gmail.com Thu Apr 16 03:32:21 2009 From: bala.biophysics at gmail.com (Bala subramanian) Date: Thu, 16 Apr 2009 12:32:21 +0200 Subject: [Chimera-users] making slow movie Message-ID: <288df32a0904160332k50848a3o38bb28f3f188b709@mail.gmail.com> Friends, I am using MD movie with chimera to see the motion of a single pdb containing 25 models. I kept the play back speed at low value, then recorded the movie. But the movie comes very fast. I guess there is no related functionality between playback speed and the speed with which the movie is recorded. 1) How can i record a movie with low playback speed. 2) Is it possible to split the chimera screen in to two halfes or as quadrants (like in sybyl) and then load the molecules wherever we want. Now why i need it ?. I have two pdb files (each consisiting of 25 models). If i can split the chimera screen, i would like to load pdb1 left and pdb2 in rigth side using MD movie, then record the movie. Any better idea than this to achieve the same would be highly appreciated. 3) Kindly suggest me some better setting to record a movie with high clarity based on your experience. Thanks, Bala -------------- next part -------------- An HTML attachment was scrubbed... URL: From bala.biophysics at gmail.com Thu Apr 16 04:39:46 2009 From: bala.biophysics at gmail.com (Bala subramanian) Date: Thu, 16 Apr 2009 13:39:46 +0200 Subject: [Chimera-users] making slow movie In-Reply-To: <49E715F1.7010806@mrc-lmb.cam.ac.uk> References: <288df32a0904160332k50848a3o38bb28f3f188b709@mail.gmail.com> <49E715F1.7010806@mrc-lmb.cam.ac.uk> Message-ID: <288df32a0904160439m630d8cb4o791669463e2a2152@mail.gmail.com> Hi Benoit, Thank you. Actually i was recording the movie with the Record movie option in the MD movie tool where this setting is not there. I will try with movie recorded. Thanks, Bala On Thu, Apr 16, 2009 at 1:26 PM, Benoit Zuber wrote: > Hi Bala, > regarding your first point: you can set the number of frames per second in > the movie recorder window. Alternatively, if you encode your movie with a > command line, you can set the number of frames per second with the option > framerate > > Ben > > Bala subramanian wrote: > >> Friends, >> >> I am using MD movie with chimera to see the motion of a single pdb >> containing 25 models. I kept the play back speed at low value, then recorded >> the movie. But the movie comes very fast. I guess there is no related >> functionality between playback speed and the speed with which the movie is >> recorded. >> >> 1) How can i record a movie with low playback speed. >> 2) Is it possible to split the chimera screen in to two halfes or as >> quadrants (like in sybyl) and then load the molecules wherever we want. >> Now why i need it ?. >> I have two pdb files (each consisiting of 25 models). If i can split the >> chimera screen, i would like to load pdb1 left and pdb2 in rigth side using >> MD movie, then record the movie. Any better idea than this to achieve the >> same would be highly appreciated. >> >> 3) Kindly suggest me some better setting to record a movie with high >> clarity based on your experience. >> >> Thanks, >> Bala >> >> >> >> >> >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >> >> > > > -- > Beno?t Zuber > MRC Laboratory of Molecular Biology > Hills Road > Cambridge > CB2 0QH > United Kingdom > +44 1223 402209 > bzuber at mrc-lmb.cam.ac.uk > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Thu Apr 16 09:16:14 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 16 Apr 2009 09:16:14 -0700 Subject: [Chimera-users] making slow movie In-Reply-To: <288df32a0904160439m630d8cb4o791669463e2a2152@mail.gmail.com> References: <288df32a0904160332k50848a3o38bb28f3f188b709@mail.gmail.com> <49E715F1.7010806@mrc-lmb.cam.ac.uk> <288df32a0904160439m630d8cb4o791669463e2a2152@mail.gmail.com> Message-ID: Thanks Ben! Everything you said is right. I just wanted to add a few things about MD Movie: Bala, you can still use "File... Record movie" in the MD Movie tool and specify the frame rate. That dialog includes an entry field for "Additional encoding options". You could enter any of the same options used with the "movie encode" command in that box, including framerate 10 (or whatever number you wanted). If you put the MD Movie playback speed slider towards the left, that should also make the movie look slower because it will insert identical image frames. Click the Help button on your MD Movie recording dialog to see its documentation, including links to the command-line options that can be put in the "Additional recording options" and "Additional encoding options" boxes. Best, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Apr 16, 2009, at 4:39 AM, Bala subramanian wrote: > Hi Benoit, > Thank you. Actually i was recording the movie with the Record movie > option in the MD movie tool where this setting is not there. I will > try with movie recorded. > > Thanks, > Bala > > On Thu, Apr 16, 2009 at 1:26 PM, Benoit Zuber > wrote: > Hi Bala, > regarding your first point: you can set the number of frames per > second in the movie recorder window. Alternatively, if you encode > your movie with a command line, you can set the number of frames per > second with the option framerate > > Ben > > Bala subramanian wrote: > Friends, > > I am using MD movie with chimera to see the motion of a single pdb > containing 25 models. I kept the play back speed at low value, then > recorded the movie. But the movie comes very fast. I guess there is > no related functionality between playback speed and the speed with > which the movie is recorded. > > 1) How can i record a movie with low playback speed. > 2) Is it possible to split the chimera screen in to two halfes or as > quadrants (like in sybyl) and then load the molecules wherever we > want. > Now why i need it ?. > I have two pdb files (each consisiting of 25 models). If i can > split the chimera screen, i would like to load pdb1 left and pdb2 in > rigth side using MD movie, then record the movie. Any better idea > than this to achieve the same would be highly appreciated. > > 3) Kindly suggest me some better setting to record a movie with high > clarity based on your experience. > > Thanks, > Bala > > > > > > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > > -- > Beno?t Zuber > MRC Laboratory of Molecular Biology > Hills Road > Cambridge > CB2 0QH > United Kingdom > +44 1223 402209 > bzuber at mrc-lmb.cam.ac.uk > > > _______________________________________________ > 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 Apr 16 09:53:52 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 16 Apr 2009 09:53:52 -0700 Subject: [Chimera-users] correction: selecting by element References: <45302F00-2FFA-46E3-B9DB-C99575F11453@cgl.ucsf.edu> Message-ID: Begin forwarded message: >> >> You can use all the end entries in the Select... Chemistry menu also >> in the command line. These symbols are in the element submenu. In >> cases where there is ambiguity, for example H appears both under >> element and under IDATM type, you can disambiguate like >> >> select element.H >> >> It will work to use element.Mg and element.Ca ... it's just more >> typing. > > Hum that does not seem to work oddly. "Select element.Ca" gives me a > "mangled atom specifier" (that why I asked you in the first place). > Same thing for Mg btw (I originally though there was some ambiguity > between > Calcium and carbon-alpha naming). Whoops, my bad. Actually Mg and Ca are not at the top level of "Select... Chemistry... element" but in further submenus. You could use "Md-Ni.Mg" and "Be-Cl.Ca" but I don't think there is a need to use anything longer than Mg and Ca. Ca will not conflict with atom name because the command-line syntax requires @ to indicate atom name. "@ca" are atoms named CA, "@c" are atoms named C, "Ca" are calcium ions/atoms, "C" are carbon atoms. The capitalization is not important for atom names, but it IS important for the things that are also menu entries and should match what is shown in the menu. The potential for ambiguity with element symbols is with the entries under "Select... Chemistry... IDATM type" but in fact H is the only one I can think of that appears in both places. Best, Elaine From meng at cgl.ucsf.edu Thu Apr 16 10:47:32 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 16 Apr 2009 10:47:32 -0700 Subject: [Chimera-users] making slow movie In-Reply-To: <288df32a0904160332k50848a3o38bb28f3f188b709@mail.gmail.com> References: <288df32a0904160332k50848a3o38bb28f3f188b709@mail.gmail.com> Message-ID: <81668BE4-2266-418D-82D5-F1C61AAF3777@cgl.ucsf.edu> Hi Bala, Now to your question #2. The short answer is no. However, there are some possible approaches, requiring various levels of effort: (A) If it is OK if the two playbacks are not exactly synchronized (don't need frame 1 and frame 1 together, 2 and 2, etc.), you can just open the two files by starting MD Movie twice. Then you will have two playback controllers. For testing, I used NMR ensemble PDB entries 1g1p and 1g1z. These have 18 structures each. While just showing one frame of each (not playing through the frames), I used "mm #0 #1" to fit them into the same orientation. Then I resized the Chimera window to make it longer horizontally and moved one model to the left and the other to the right. Something like these commands (using version 1.4, a daily build): move x -13 models #0 move x 13 models #1 Of course, you would also set colors, display styles, etc. as you want for the movie. Because these two structures are the same size, they play back at about the same speed if I put the two "Playback speed" sliders in the same place. I put both at the far left. If your two structures don't play back at nearly the same speed, move the sliders to try to make them update at the same rate. Now play back continuously for one ensemble. For the other one, stop the playback, choose File... Record movie and proceed as you have been doing. The movie will step through that ensemble, and the other one will just happen to be changing at the same time. Tada! I will send you the Quicktime movie from my test in a separate message. (B) If you need frame 1 with 1, 2 with 2, etc. it is much more effort. I can think of two different routes. (1) just open one ensemble and record with MD Movie, using recording options to control the name and location of the saved image files and the encoding option to keep those files rather than deleting them after encoding a movie. Do the same for the other ensemble. Then with some separate image-processing program combine the first image from each into a new first image with both side by side, etc. for the whole set of saved images. Then encode the new set of combined images into a movie. This would need to be done outside of Chimera, but I believe you could use the software embedded in Chimera to do it. I think the Reply Log shows what command is being used to encode the movie and you could use an analogous command in your system shell or terminal to do it. I haven't done this myself, however. (2) instead create a combined PDB file where each MODEL has both structures side by side. First you'd have to open the two files in Chimera, do any fitting and moving as described in (A), then save PDB for one ensemble "relative to" the other model. Then there would be a lot of painful editing to combine the coordinates into one multi-MODEL file. It would probably require renumbering so that there are not duplicate residues within a single MODEL. Then open that new file with MD Movie as a single trajectory, proceed with recording a movie. As for #3, I am not expert in this area. My general impression is that you could start with the default settings. If that does not look as nice as you want, you could try increasing the bitrate in the encoding options. It is always a trade-off of size and quality, however (nicer looking -> bigger file). I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Apr 16, 2009, at 3:32 AM, Bala subramanian wrote: > Friends, > I am using MD movie with chimera to see the motion of a single pdb > containing 25 models. I kept the play back speed at low value, then > recorded the movie. But the movie comes very fast. I guess there is > no related functionality between playback speed and the speed with > which the movie is recorded. > > 1) How can i record a movie with low playback speed. > > 2) Is it possible to split the chimera screen in to two halfes or as > quadrants (like in sybyl) and then load the molecules wherever we > want. > Now why i need it ?. > I have two pdb files (each consisiting of 25 models). If i can > split the chimera screen, i would like to load pdb1 left and pdb2 in > rigth side using MD movie, then record the movie. Any better idea > than this to achieve the same would be highly appreciated. > > 3) Kindly suggest me some better setting to record a movie with high > clarity based on your experience. > > Thanks, > Bala From pett at cgl.ucsf.edu Thu Apr 16 10:58:09 2009 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Thu, 16 Apr 2009 10:58:09 -0700 Subject: [Chimera-users] making slow movie In-Reply-To: <81668BE4-2266-418D-82D5-F1C61AAF3777@cgl.ucsf.edu> References: <288df32a0904160332k50848a3o38bb28f3f188b709@mail.gmail.com> <81668BE4-2266-418D-82D5-F1C61AAF3777@cgl.ucsf.edu> Message-ID: I think another approach is just to forget about MD Movie. Open the two ensembles using regular File..Open or the "open" command. Position one ensemble on the left side and one on the right. Then use a script like this: movie record ... ~disp; disp #0,25; wait 5 ~disp; disp #1,26; wait 5 ... ~disp; disp #24,49; wait 5 movie stop ... movie encode ... to record your movie. --Eric On Apr 16, 2009, at 10:47 AM, Elaine Meng wrote: > Hi Bala, > Now to your question #2. The short answer is no. However, there are > some possible approaches, requiring various levels of effort: > > (A) If it is OK if the two playbacks are not exactly synchronized > (don't need frame 1 and frame 1 together, 2 and 2, etc.), you can > just open the two files by starting MD Movie twice. Then you will > have two playback controllers. For testing, I used NMR ensemble PDB > entries 1g1p and 1g1z. These have 18 structures each. While just > showing one frame of each (not playing through the frames), I used "mm > #0 #1" to fit them into the same orientation. Then I resized the > Chimera window to make it longer horizontally and moved one model to > the left and the other to the right. Something like these commands > (using version 1.4, a daily build): > move x -13 models #0 > move x 13 models #1 > Of course, you would also set colors, display styles, etc. as you want > for the movie. Because these two structures are the same size, they > play back at about the same speed if I put the two "Playback speed" > sliders in the same place. I put both at the far left. If your two > structures don't play back at nearly the same speed, move the sliders > to try to make them update at the same rate. Now play back > continuously for one ensemble. For the other one, stop the playback, > choose File... Record movie and proceed as you have been doing. The > movie will step through that ensemble, and the other one will just > happen to be changing at the same time. Tada! I will send you the > Quicktime movie from my test in a separate message. > > (B) If you need frame 1 with 1, 2 with 2, etc. it is much more > effort. I can think of two different routes. > (1) just open one ensemble and record with MD Movie, using > recording options to control the name and location of the saved image > files and the encoding option to keep those files rather than deleting > them after encoding a movie. Do the same for the other ensemble. > Then with some separate image-processing program combine the first > image from each into a new first image with both side by side, etc. > for the whole set of saved images. Then encode the new set of > combined images into a movie. This would need to be done outside of > Chimera, but I believe you could use the software embedded in Chimera > to do it. I think the Reply Log shows what command is being used to > encode the movie and you could use an analogous command in your system > shell or terminal to do it. I haven't done this myself, however. > (2) instead create a combined PDB file where each MODEL has both > structures side by side. First you'd have to open the two files in > Chimera, do any fitting and moving as described in (A), then save PDB > for one ensemble "relative to" the other model. Then there would be a > lot of painful editing to combine the coordinates into one multi-MODEL > file. It would probably require renumbering so that there are not > duplicate residues within a single MODEL. Then open that new file > with MD Movie as a single trajectory, proceed with recording a movie. > > As for #3, I am not expert in this area. My general impression is > that you could start with the default settings. If that does not look > as nice as you want, you could try increasing the bitrate in the > encoding options. It is always a trade-off of size and quality, > however (nicer looking -> bigger file). > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > http://www.cgl.ucsf.edu/home/meng/index.html > > > > On Apr 16, 2009, at 3:32 AM, Bala subramanian wrote: > >> Friends, >> I am using MD movie with chimera to see the motion of a single pdb >> containing 25 models. I kept the play back speed at low value, then >> recorded the movie. But the movie comes very fast. I guess there is >> no related functionality between playback speed and the speed with >> which the movie is recorded. >> >> 1) How can i record a movie with low playback speed. >> >> 2) Is it possible to split the chimera screen in to two halfes or as >> quadrants (like in sybyl) and then load the molecules wherever we >> want. >> Now why i need it ?. >> I have two pdb files (each consisiting of 25 models). If i can >> split the chimera screen, i would like to load pdb1 left and pdb2 in >> rigth side using MD movie, then record the movie. Any better idea >> than this to achieve the same would be highly appreciated. >> >> 3) Kindly suggest me some better setting to record a movie with high >> clarity based on your experience. >> >> Thanks, >> Bala > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From goddard at cgl.ucsf.edu Thu Apr 16 11:11:17 2009 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Thu, 16 Apr 2009 11:11:17 -0700 Subject: [Chimera-users] making slow movie In-Reply-To: <81668BE4-2266-418D-82D5-F1C61AAF3777@cgl.ucsf.edu> References: <288df32a0904160332k50848a3o38bb28f3f188b709@mail.gmail.com> <81668BE4-2266-418D-82D5-F1C61AAF3777@cgl.ucsf.edu> Message-ID: <49E774C5.8080505@cgl.ucsf.edu> Hi Bala, As Elaine said increasing the bitrate is the most direct way to better movie quality. The value is in Kbits/sec and default is 2000, and 6000 is better but produces a movie file 3 times bigger. Also the supersample option can be set to 3x3 to produce smoother lines and edges with no increase in file size. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/movie.html Tom Elaine Meng wrote: > Hi Bala, > Now to your question #2. The short answer is no. However, there are > some possible approaches, requiring various levels of effort: > > (A) If it is OK if the two playbacks are not exactly synchronized > (don't need frame 1 and frame 1 together, 2 and 2, etc.), you can > just open the two files by starting MD Movie twice. Then you will > have two playback controllers. For testing, I used NMR ensemble PDB > entries 1g1p and 1g1z. These have 18 structures each. While just > showing one frame of each (not playing through the frames), I used "mm > #0 #1" to fit them into the same orientation. Then I resized the > Chimera window to make it longer horizontally and moved one model to > the left and the other to the right. Something like these commands > (using version 1.4, a daily build): > move x -13 models #0 > move x 13 models #1 > Of course, you would also set colors, display styles, etc. as you want > for the movie. Because these two structures are the same size, they > play back at about the same speed if I put the two "Playback speed" > sliders in the same place. I put both at the far left. If your two > structures don't play back at nearly the same speed, move the sliders > to try to make them update at the same rate. Now play back > continuously for one ensemble. For the other one, stop the playback, > choose File... Record movie and proceed as you have been doing. The > movie will step through that ensemble, and the other one will just > happen to be changing at the same time. Tada! I will send you the > Quicktime movie from my test in a separate message. > > (B) If you need frame 1 with 1, 2 with 2, etc. it is much more > effort. I can think of two different routes. > (1) just open one ensemble and record with MD Movie, using > recording options to control the name and location of the saved image > files and the encoding option to keep those files rather than deleting > them after encoding a movie. Do the same for the other ensemble. > Then with some separate image-processing program combine the first > image from each into a new first image with both side by side, etc. > for the whole set of saved images. Then encode the new set of > combined images into a movie. This would need to be done outside of > Chimera, but I believe you could use the software embedded in Chimera > to do it. I think the Reply Log shows what command is being used to > encode the movie and you could use an analogous command in your system > shell or terminal to do it. I haven't done this myself, however. > (2) instead create a combined PDB file where each MODEL has both > structures side by side. First you'd have to open the two files in > Chimera, do any fitting and moving as described in (A), then save PDB > for one ensemble "relative to" the other model. Then there would be a > lot of painful editing to combine the coordinates into one multi-MODEL > file. It would probably require renumbering so that there are not > duplicate residues within a single MODEL. Then open that new file > with MD Movie as a single trajectory, proceed with recording a movie. > > As for #3, I am not expert in this area. My general impression is > that you could start with the default settings. If that does not look > as nice as you want, you could try increasing the bitrate in the > encoding options. It is always a trade-off of size and quality, > however (nicer looking -> bigger file). > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > http://www.cgl.ucsf.edu/home/meng/index.html > > > > On Apr 16, 2009, at 3:32 AM, Bala subramanian wrote: > >> Friends, >> I am using MD movie with chimera to see the motion of a single pdb >> containing 25 models. I kept the play back speed at low value, then >> recorded the movie. But the movie comes very fast. I guess there is >> no related functionality between playback speed and the speed with >> which the movie is recorded. >> >> 1) How can i record a movie with low playback speed. >> >> 2) Is it possible to split the chimera screen in to two halfes or as >> quadrants (like in sybyl) and then load the molecules wherever we >> want. >> Now why i need it ?. >> I have two pdb files (each consisiting of 25 models). If i can >> split the chimera screen, i would like to load pdb1 left and pdb2 in >> rigth side using MD movie, then record the movie. Any better idea >> than this to achieve the same would be highly appreciated. >> >> 3) Kindly suggest me some better setting to record a movie with high >> clarity based on your experience. >> >> Thanks, >> Bala > > _______________________________________________ > 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 Apr 16 11:29:26 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 16 Apr 2009 11:29:26 -0700 Subject: [Chimera-users] making slow movie In-Reply-To: References: <288df32a0904160332k50848a3o38bb28f3f188b709@mail.gmail.com> <81668BE4-2266-418D-82D5-F1C61AAF3777@cgl.ucsf.edu> Message-ID: <38B495E7-AEB8-4815-ABCB-95B7880F1BE7@cgl.ucsf.edu> Eric's approach is MUCH better than what I suggested, especially for these relatively small ensembles and if you want them to be synchronized. I would probably modify his approach slightly by setting up all the display, styles, and colors beforehand and then just using modeldisplay to toggle which models are shown and hidden. Also, in Bala's case, each ensemble is one PDB file, so the individual structures would be submodels. The show/hide commands would look something like this: ~modeldisp; modeldisp #0.1,1.1; wait 5 ~modeldisp; modeldisp #0.2,1.2; wait 5 On Apr 16, 2009, at 10:58 AM, Eric Pettersen wrote: > I think another approach is just to forget about MD Movie. Open the > two ensembles using regular File..Open or the "open" command. > Position one ensemble on the left side and one on the right. Then use > a script like this: > > movie record ... > ~disp; disp #0,25; wait 5 > ~disp; disp #1,26; wait 5 > ... > ~disp; disp #24,49; wait 5 > movie stop ... > movie encode ... > > to record your movie. > > --Eric > > On Apr 16, 2009, at 10:47 AM, Elaine Meng wrote: > >> Hi Bala, >> Now to your question #2. The short answer is no. However, there are >> some possible approaches, requiring various levels of effort: >> >> (A) If it is OK if the two playbacks are not exactly synchronized >> (don't need frame 1 and frame 1 together, 2 and 2, etc.), you can >> just open the two files by starting MD Movie twice. Then you will >> have two playback controllers. For testing, I used NMR ensemble PDB >> entries 1g1p and 1g1z. These have 18 structures each. While just >> showing one frame of each (not playing through the frames), I used >> "mm >> #0 #1" to fit them into the same orientation. Then I resized the >> Chimera window to make it longer horizontally and moved one model to >> the left and the other to the right. Something like these commands >> (using version 1.4, a daily build): >> move x -13 models #0 >> move x 13 models #1 >> Of course, you would also set colors, display styles, etc. as you >> want >> for the movie. Because these two structures are the same size, they >> play back at about the same speed if I put the two "Playback speed" >> sliders in the same place. I put both at the far left. If your two >> structures don't play back at nearly the same speed, move the sliders >> to try to make them update at the same rate. Now play back >> continuously for one ensemble. For the other one, stop the playback, >> choose File... Record movie and proceed as you have been doing. The >> movie will step through that ensemble, and the other one will just >> happen to be changing at the same time. Tada! I will send you the >> Quicktime movie from my test in a separate message. >> >> (B) If you need frame 1 with 1, 2 with 2, etc. it is much more >> effort. I can think of two different routes. >> (1) just open one ensemble and record with MD Movie, using >> recording options to control the name and location of the saved image >> files and the encoding option to keep those files rather than >> deleting >> them after encoding a movie. Do the same for the other ensemble. >> Then with some separate image-processing program combine the first >> image from each into a new first image with both side by side, etc. >> for the whole set of saved images. Then encode the new set of >> combined images into a movie. This would need to be done outside of >> Chimera, but I believe you could use the software embedded in Chimera >> to do it. I think the Reply Log shows what command is being used to >> encode the movie and you could use an analogous command in your >> system >> shell or terminal to do it. I haven't done this myself, however. >> (2) instead create a combined PDB file where each MODEL has both >> structures side by side. First you'd have to open the two files in >> Chimera, do any fitting and moving as described in (A), then save PDB >> for one ensemble "relative to" the other model. Then there would >> be a >> lot of painful editing to combine the coordinates into one multi- >> MODEL >> file. It would probably require renumbering so that there are not >> duplicate residues within a single MODEL. Then open that new file >> with MD Movie as a single trajectory, proceed with recording a movie. >> >> As for #3, I am not expert in this area. My general impression is >> that you could start with the default settings. If that does not >> look >> as nice as you want, you could try increasing the bitrate in the >> encoding options. It is always a trade-off of size and quality, >> however (nicer looking -> bigger file). >> >> I hope this helps, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu >> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> http://www.cgl.ucsf.edu/home/meng/index.html >> >> >> >> On Apr 16, 2009, at 3:32 AM, Bala subramanian wrote: >> >>> Friends, >>> I am using MD movie with chimera to see the motion of a single pdb >>> containing 25 models. I kept the play back speed at low value, then >>> recorded the movie. But the movie comes very fast. I guess there is >>> no related functionality between playback speed and the speed with >>> which the movie is recorded. >>> >>> 1) How can i record a movie with low playback speed. >>> >>> 2) Is it possible to split the chimera screen in to two halfes or as >>> quadrants (like in sybyl) and then load the molecules wherever we >>> want. >>> Now why i need it ?. >>> I have two pdb files (each consisiting of 25 models). If i can >>> split the chimera screen, i would like to load pdb1 left and pdb2 in >>> rigth side using MD movie, then record the movie. Any better idea >>> than this to achieve the same would be highly appreciated. >>> >>> 3) Kindly suggest me some better setting to record a movie with high >>> clarity based on your experience. >>> >>> Thanks, >>> Bala >> >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From goddard at cgl.ucsf.edu Thu Apr 16 11:45:01 2009 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Thu, 16 Apr 2009 11:45:01 -0700 Subject: [Chimera-users] making slow movie In-Reply-To: <38B495E7-AEB8-4815-ABCB-95B7880F1BE7@cgl.ucsf.edu> References: <288df32a0904160332k50848a3o38bb28f3f188b709@mail.gmail.com> <81668BE4-2266-418D-82D5-F1C61AAF3777@cgl.ucsf.edu> <38B495E7-AEB8-4815-ABCB-95B7880F1BE7@cgl.ucsf.edu> Message-ID: <49E77CAD.70309@cgl.ucsf.edu> Hi Elaine, This movie recording would be simpler if there was a Chimera command to play an MD trajectory. I've long needed that for animation scripts. I've added that to the list of feature requests: http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/requests Tom Elaine Meng wrote: > Eric's approach is MUCH better than what I suggested, especially for > these relatively small ensembles and if you want them to be > synchronized. I would probably modify his approach slightly by > setting up all the display, styles, and colors beforehand and then > just using modeldisplay to toggle which models are shown and hidden. > Also, in Bala's case, each ensemble is one PDB file, so the individual > structures would be submodels. The show/hide commands would look > something like this: > > ~modeldisp; modeldisp #0.1,1.1; wait 5 > ~modeldisp; modeldisp #0.2,1.2; wait 5 > > On Apr 16, 2009, at 10:58 AM, Eric Pettersen wrote: > >> I think another approach is just to forget about MD Movie. Open the >> two ensembles using regular File..Open or the "open" command. >> Position one ensemble on the left side and one on the right. Then use >> a script like this: >> >> movie record ... >> ~disp; disp #0,25; wait 5 >> ~disp; disp #1,26; wait 5 >> ... >> ~disp; disp #24,49; wait 5 >> movie stop ... >> movie encode ... >> >> to record your movie. >> >> --Eric >> >> On Apr 16, 2009, at 10:47 AM, Elaine Meng wrote: >> >>> Hi Bala, >>> Now to your question #2. The short answer is no. However, there are >>> some possible approaches, requiring various levels of effort: >>> >>> (A) If it is OK if the two playbacks are not exactly synchronized >>> (don't need frame 1 and frame 1 together, 2 and 2, etc.), you can >>> just open the two files by starting MD Movie twice. Then you will >>> have two playback controllers. For testing, I used NMR ensemble PDB >>> entries 1g1p and 1g1z. These have 18 structures each. While just >>> showing one frame of each (not playing through the frames), I used >>> "mm >>> #0 #1" to fit them into the same orientation. Then I resized the >>> Chimera window to make it longer horizontally and moved one model to >>> the left and the other to the right. Something like these commands >>> (using version 1.4, a daily build): >>> move x -13 models #0 >>> move x 13 models #1 >>> Of course, you would also set colors, display styles, etc. as you >>> want >>> for the movie. Because these two structures are the same size, they >>> play back at about the same speed if I put the two "Playback speed" >>> sliders in the same place. I put both at the far left. If your two >>> structures don't play back at nearly the same speed, move the sliders >>> to try to make them update at the same rate. Now play back >>> continuously for one ensemble. For the other one, stop the playback, >>> choose File... Record movie and proceed as you have been doing. The >>> movie will step through that ensemble, and the other one will just >>> happen to be changing at the same time. Tada! I will send you the >>> Quicktime movie from my test in a separate message. >>> >>> (B) If you need frame 1 with 1, 2 with 2, etc. it is much more >>> effort. I can think of two different routes. >>> (1) just open one ensemble and record with MD Movie, using >>> recording options to control the name and location of the saved image >>> files and the encoding option to keep those files rather than >>> deleting >>> them after encoding a movie. Do the same for the other ensemble. >>> Then with some separate image-processing program combine the first >>> image from each into a new first image with both side by side, etc. >>> for the whole set of saved images. Then encode the new set of >>> combined images into a movie. This would need to be done outside of >>> Chimera, but I believe you could use the software embedded in Chimera >>> to do it. I think the Reply Log shows what command is being used to >>> encode the movie and you could use an analogous command in your >>> system >>> shell or terminal to do it. I haven't done this myself, however. >>> (2) instead create a combined PDB file where each MODEL has both >>> structures side by side. First you'd have to open the two files in >>> Chimera, do any fitting and moving as described in (A), then save PDB >>> for one ensemble "relative to" the other model. Then there would >>> be a >>> lot of painful editing to combine the coordinates into one multi- >>> MODEL >>> file. It would probably require renumbering so that there are not >>> duplicate residues within a single MODEL. Then open that new file >>> with MD Movie as a single trajectory, proceed with recording a movie. >>> >>> As for #3, I am not expert in this area. My general impression is >>> that you could start with the default settings. If that does not >>> look >>> as nice as you want, you could try increasing the bitrate in the >>> encoding options. It is always a trade-off of size and quality, >>> however (nicer looking -> bigger file). >>> >>> I hope this helps, >>> Elaine >>> ----- >>> Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu >>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >>> Department of Pharmaceutical Chemistry >>> University of California, San Francisco >>> http://www.cgl.ucsf.edu/home/meng/index.html >>> >>> >>> >>> On Apr 16, 2009, at 3:32 AM, Bala subramanian wrote: >>> >>>> Friends, >>>> I am using MD movie with chimera to see the motion of a single pdb >>>> containing 25 models. I kept the play back speed at low value, then >>>> recorded the movie. But the movie comes very fast. I guess there is >>>> no related functionality between playback speed and the speed with >>>> which the movie is recorded. >>>> >>>> 1) How can i record a movie with low playback speed. >>>> >>>> 2) Is it possible to split the chimera screen in to two halfes or as >>>> quadrants (like in sybyl) and then load the molecules wherever we >>>> want. >>>> Now why i need it ?. >>>> I have two pdb files (each consisiting of 25 models). If i can >>>> split the chimera screen, i would like to load pdb1 left and pdb2 in >>>> rigth side using MD movie, then record the movie. Any better idea >>>> than this to achieve the same would be highly appreciated. >>>> >>>> 3) Kindly suggest me some better setting to record a movie with high >>>> clarity based on your experience. >>>> >>>> Thanks, >>>> Bala >>> _______________________________________________ >>> 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 > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From meng at cgl.ucsf.edu Fri Apr 17 08:50:22 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 17 Apr 2009 08:50:22 -0700 Subject: [Chimera-users] Superimpose In-Reply-To: <00be01c9bf70$de4cd770$9ae68650$@ac.be> References: <288df32a0904160332k50848a3o38bb28f3f188b709@mail.gmail.com> <81668BE4-2266-418D-82D5-F1C61AAF3777@cgl.ucsf.edu> <38B495E7-AEB8-4815-ABCB-95B7880F1BE7@cgl.ucsf.edu> <00be01c9bf70$de4cd770$9ae68650$@ac.be> Message-ID: <4D88D9C8-0EBD-4CCA-A371-E5532E4EDF39@cgl.ucsf.edu> Hi Cedric, The "match" command fits whatever atoms you specify: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html> I should mention that MatchMaker (or "matchmaker" command) generally does pretty well even with low sequence identity because it also uses secondary structure assignments: the score favors aligning helix with helix, strand with strand. However, if you need it, "match" can be used in any situation, including molecules other than proteins and nucleic acids. The tradeoff is that it is more work for the user, since you have to tell it which atoms to use. Discussion of the different ways to superimpose structures in Chimera: I hope this helps, Elaine On Apr 17, 2009, at 8:26 AM, C?dric Govaerts wrote: > Hi Elaine, > > So of course I have a new question: > > Matchmaker will take to proteins, align the sequences and then > align the > structures. > > But what I need to do is to align the structure according to the > pairs of > atoms I have selected. > > For example this could be particularly useful for : > > 1/ Superimpose two structures that are different but have a few common > catalytic residues. They would be two different for Match maker to > find the > correct alignment, however, the user (that's me) would know which > residues > should be used. > > 2/ I tried to superimpose two isoforms of the same proteins using > ions or > ligand as superimposing element. I wanted to see what was the > conformational > change *relative* to the bound metals. > > I believe that creating an alignment for MultiAlign would not work for > either. > > Is there a way I can superimpose two structures after explicitely > choosing > the pairs (minimum) and the Chimera would make a lest-square > regression > based on those ? > > Thanks again > > Cedric > From meng at cgl.ucsf.edu Sat Apr 18 12:36:38 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Sat, 18 Apr 2009 12:36:38 -0700 Subject: [Chimera-users] reflection of docking poses with chimera In-Reply-To: <003b01c9c044$ccdc2b60$6501a8c0@dioskouridis.pharm.uoa.gr> References: <003b01c9c044$ccdc2b60$6501a8c0@dioskouridis.pharm.uoa.gr> Message-ID: On Apr 18, 2009, at 9:43 AM, Antonios Kolocouris wrote: > Hi Elaine, > I have obtained the results of the docking claculations of some > compounds > with a symmetric - by 180 degrees - receptor. To obtain a > consistent set of > structures for further 3D QSAR I need to know how I can reflect a > docking pose by 180 degrees > vertically and horizontally with Chimera. > My kind regards, > Antonios > ---------------------------------------------------------------------- > --------------------- > Antonios Kolocouris, Assistant Professor of Medicinal Chemsitry > Department of Pharmacy, Univ. of Athens, Greece > Hi Antonios, The main issue is figuring out the proper transformation to superimpose one binding site on the other. It will not exactly be a reflection (you will still have the same enantiomers) but a rotation. You would need a recent daily build for what I describe. If you are certain only rotations about the exact horizontal and vertical axis are needed, and you know what the center of rotation should be, use the "turn" command with specified axis and center of rotation to move the ligand model(s). The horizontal axis is x, the vertical axis is y. The rest of this message addresses the more general case where the axis of symmetry and thus the proper transformation is not known: -- To find out the transformation, (A) put the two parts containing the two binding sites in different models. This could be done by manually text-editing your PDB file to create two files that can then be read into Chimera. Or, if they are already two different chains, you can use the "split" command to divide the already open model into separate models. (B) superimpose the two binding sites. It could be done with matchmaker, or match, or manually. Which is best depends on the situation. These methods are discussed and there are links to their manual pages here: (C) find out the relative transformation of the two models using the "measure" command, for example to report the transformation of model #0.2 relative to #0.1: measure rotation #0.1 #0.2 the transformation is sent to the Reply Log (under Favorites menu), both as a matrix and as an axis of rotation and point on the axis, as described in the manual page: -- To apply the transformation to the ligands, I would first use the command "reset" (without arguments) to put everything back into their untransformed positions and then either (A) use the "turn" command with specified axis and center of rotation to move the ligand model(s) - or - (B) save the matrix from the Reply Log to a file and then apply it with the "matrixset" command I'm not sure if the "reset" is necessary (some of these transformation issues confuse me), but that's what I would try first. I recommend sending questions to chimera-users at cgl.ucsf.edu rather than to me directly, to be certain they will not fall through the cracks. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html From chiendarret at gmail.com Sun Apr 19 09:56:37 2009 From: chiendarret at gmail.com (Francesco Pietra) Date: Sun, 19 Apr 2009 18:56:37 +0200 Subject: [Chimera-users] Straighten a helix Message-ID: I would like to straighten a helix in a complex composition of helices, i.e., at least some of them may vdw interact with each other if moved. Therefore, I plan to let molecular dynamics (MD) changing dihedral angles at the pivot amino acid. I wonder whether chimera might aid through "adjust torsion" or other tool. If not else to provide alternative conformations for input to MD and see if the adjustments converge. Bending of the helix occurs along 5 amino acids, the central one probably the pivot. Thanks francesco pietra From meng at cgl.ucsf.edu Sun Apr 19 12:46:23 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Sun, 19 Apr 2009 12:46:23 -0700 Subject: [Chimera-users] Straighten a helix In-Reply-To: References: Message-ID: <60A2B72E-0C5F-408A-919F-9435DF92F070@cgl.ucsf.edu> Hi Francesco, Yes, you can use Adjust Torsions to rotate several different bonds along the backbone. It might be a lot of work, and it would not prevent you from creating structures with bad contacts, but you could certainly try it if MD alone is not successful in generating the desired conformations. 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 Apr 19, 2009, at 9:56 AM, Francesco Pietra wrote: > I would like to straighten a helix in a complex composition of > helices, i.e., at least some of them may vdw interact with each other > if moved. Therefore, I plan to let molecular dynamics (MD) changing > dihedral angles at the pivot amino acid. I wonder whether chimera > might aid through "adjust torsion" or other tool. If not else to > provide alternative conformations for input to MD and see if the > adjustments converge. Bending of the helix occurs along 5 amino acids, > the central one probably the pivot. > Thanks > francesco pietra > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From cdlau at ucsd.edu Sun Apr 19 17:57:34 2009 From: cdlau at ucsd.edu (cdlau at ucsd.edu) Date: Sun, 19 Apr 2009 17:57:34 -0700 (PDT) Subject: [Chimera-users] [Chimera-Users] help with IDLE Message-ID: <49548.66.75.245.116.1240189054.squirrel@acs-webmail.ucsd.edu> Dear Sir/Miss, I am using the IDLE extensively and I have noticed I cannot paste text or to run previous commands. I was wondering if anyone knew how to change these features or if it is possible. I explored the options>configure IDLE, but haven't found any preference changes that change these problems I am having. Thanks for your help in advance. Best Regards, Christopher From booth at wadsworth.org Mon Apr 20 08:57:23 2009 From: booth at wadsworth.org (booth at wadsworth.org) Date: Mon, 20 Apr 2009 11:57:23 -0400 (EDT) Subject: [Chimera-users] spider volumes look incomplete or sliced. Version Linux SUSE 10.2 Message-ID: <59748.172.16.1.163.1240243043.squirrel@info.wadsworth.org> Im having a problem with the latest Chimera version, as well as previous ones for linux2 platform. When loading spider volumes they are imcomplete and sliced. Anyone have any suggestions? A much older version build 2470 from 2007/11/15 runs just fine. Thanks. Tim Booth IMPORTANT NOTICE: This e-mail and any attachments may contain confidential or sensitive information which is, or may be, legally privileged or otherwise protected by law from further disclosure. It is intended only for the addressee. If you received this in error or from someone who was not authorized to send it to you, please do not distribute, copy or use it or any attachments. Please notify the sender immediately by reply e-mail and delete this from your system. Thank you for your cooperation. From pett at cgl.ucsf.edu Mon Apr 20 10:36:58 2009 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 20 Apr 2009 10:36:58 -0700 Subject: [Chimera-users] [Chimera-Users] help with IDLE In-Reply-To: <49548.66.75.245.116.1240189054.squirrel@acs-webmail.ucsd.edu> References: <49548.66.75.245.116.1240189054.squirrel@acs-webmail.ucsd.edu> Message-ID: <82CAAAE8-705D-4D39-8582-BFDF0BA830F7@cgl.ucsf.edu> On Apr 19, 2009, at 5:57 PM, cdlau at ucsd.edu wrote: > Dear Sir/Miss, > > I am using the IDLE extensively and I have noticed I cannot paste > text or > to run previous commands. I was wondering if anyone knew > how > to change these features or if it is possible. I explored the > options>configure IDLE, but haven't found any preference changes that > change these problems I am having. Thanks for your help in advance. Hi Christopher, To reuse/edit a command, either up-arrow to or mouse-click into the command you want and hit return. A copy of the command will appear at the current Python prompt. You can then edit it with the arrow keys or the mouse and then hit Return to execute the modified command. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at cgl.ucsf.edu Mon Apr 20 10:52:48 2009 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Mon, 20 Apr 2009 10:52:48 -0700 Subject: [Chimera-users] spider volumes look incomplete or sliced. Version Linux SUSE 10.2 In-Reply-To: <59748.172.16.1.163.1240243043.squirrel@info.wadsworth.org> References: <59748.172.16.1.163.1240243043.squirrel@info.wadsworth.org> Message-ID: <49ECB670.6070907@cgl.ucsf.edu> Hi Tim, We have seen this before. It is a bug in the old Mesa OpenGL library that comes with your Linux distribution. The bug is specifically in the use of a high performance OpenGL feature called vertex buffer objects. The solution is to install a graphics driver from the video card manufacturer (nvidia or ati/amd). This will also give 10x to 100x faster rendering because the manufacturer driver will use hardware acceleration where Mesa does all graphics calculation in software. See our graphics driver bug web page for more details. http://www.cgl.ucsf.edu/chimera/graphics/graphicsbugs.html This bug is not specific to SPIDER maps and will effect all Chimera surfaces. It did not occur in old Chimera versions which used older lower performance rendering methods. Tom booth at wadsworth.org wrote: > Im having a problem with the latest Chimera version, as well as previous > ones for linux2 platform. > > When loading spider volumes they are imcomplete and sliced. Anyone have > any suggestions? A much older version build 2470 from 2007/11/15 runs just > fine. > > Thanks. > > Tim Booth > > From blgrech at ozonline.com.au Mon Apr 20 13:23:49 2009 From: blgrech at ozonline.com.au (Brian and Lanie Grech) Date: Tue, 21 Apr 2009 06:23:49 +1000 Subject: [Chimera-users] Selecting subassemblies Message-ID: <000601c9c1f5$ead389d0$c8c9adca@2935d57> Hi everyone In reference to the publication in the March 2005 edition of Structure, titled "Software extension to UCSF Chimera for interactive visualization of large molecular assemblies". Under the subheading "Selecting subassemblies", page 480, it talks about two methods to select part of the outer capsid layer of the model of bluetongue virus and not the inner capsid layers. I am unable to find the documentation explaining how to do this, could someone please direct me to the documentation or explain how to do this. Regards Brian Grech -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at cgl.ucsf.edu Mon Apr 20 16:14:04 2009 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Mon, 20 Apr 2009 16:14:04 -0700 Subject: [Chimera-users] Selecting subassemblies In-Reply-To: <000601c9c1f5$ead389d0$c8c9adca@2935d57> References: <000601c9c1f5$ead389d0$c8c9adca@2935d57> Message-ID: <49ED01BC.1010603@cgl.ucsf.edu> Hi Brian, Documentation for the Chimera Multiscale Models tool that is described in that paper is in the Chimera User's Guide: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemulti.html The subsection on selecting components would be relevant. Here's a little tutorial on display of viruses using this tool. http://www.cgl.ucsf.edu/chimera/tutorials/virus-howto/showvirus.html In practice I would select the outer capsid of bluetongue virus (2btv) by selecting one chain with the mouse (ctrl-click on it) then use the keyboard shortcut that extends the selection to all chains with the same sequence (shortcut "xc" - extend to equiv chains). When the paper was written that didn't exist. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/accelerators/alist.html If I forgot about shortcut xc my next quickest route would be to select the two inner chains using ctrl-click, then shift-ctrl-click through holes in the outer capsid, then press the Copies button on the multiscale dialog then menu Select / Invert on the main window. If I really didn't know much about the capsid I'd probably select one chain of each different color in the outer layer (ctrl-click, then shift-ctrl-click to add more) then press the Copies button. All of this presumes you don't have any hierarchy info. The paper describes how with a script it is possible to define a hierarchy of structures (trimers, outer capsid, inner capsid, whole capsid). Unfortunately a script is still needed to do that. The script for that is in the above Chimera User Guide documentation under Structural Hierarchy. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/bluetongue.py You open the script file in Chimera (File / Open) to show the capsid with the hierarchy, then select one chain (ctrl-click), then press the Up button on the multiscale dialog to promote to the trimer, all trimers, .... That script had to work around an error in the 2btv PDB file which has since been fixed by the PDB. So the original script doesn't work unless the script is edited to remove "given = True". I've made that change in the online development documentation. Tom Brian and Lanie Grech wrote: > Hi everyone > > > > In reference to the publication in the March 2005 edition of Structure, > titled ?Software extension to UCSF Chimera for interactive visualization > of large molecular assemblies?. Under the subheading ?Selecting > subassemblies?, page 480, it talks about two methods to select part of > the outer capsid layer of the model of bluetongue virus and not the > inner capsid layers. I am unable to find the documentation explaining > how to do this, could someone please direct me to the documentation or > explain how to do this. > > > > Regards > > Brian Grech > > > ------------------------------------------------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From damien.lariviere at fourmentinguilbert.org Mon Apr 20 23:58:20 2009 From: damien.lariviere at fourmentinguilbert.org (=?ISO-8859-1?Q?Damien_Larivi=E8re?=) Date: Tue, 21 Apr 2009 08:58:20 +0200 Subject: [Chimera-users] delete model Message-ID: <49ED6E8C.2040808@fourmentinguilbert.org> Dear Chimera team, I have used the multiscale model for generating a surfacic model of (pdb) file 1YAU.mmol (from pdb sum). Two models are displayed (see attached image): one is an all-atom model and the other is the surfacic model. I would like to know : - how to delete the all-atom model in order to export in the vrml format only the surfacic model (the two-model scene is fast for exporting but very long for opening in software like 3DSmax) ? - why, sometimes, are displayed in the same view the surfacic model as well as the original structure ? My best regards Damien -------------- next part -------------- A non-text attachment was scrubbed... Name: 1YAU.JPG Type: image/jpeg Size: 38767 bytes Desc: not available URL: From cgovaert at ulb.ac.be Tue Apr 21 06:23:09 2009 From: cgovaert at ulb.ac.be (=?iso-8859-1?Q?C=E9dric_Govaerts?=) Date: Tue, 21 Apr 2009 15:23:09 +0200 Subject: [Chimera-users] (no subject) Message-ID: <014901c9c284$4ffe5770$effb0650$@ac.be> Hi there, I want to compute accessible surface area for the backbone, as I want to compare the predicted amide deuteration between two conformations of a protein (I have PDBs for both). I tried with VADAR but the results are puzzling, I suspect they are not correct (the more open structure gets a lower score). Is there a way I can do something like that in Chimera ? In other word I need to compute how exposed to the solvent are the backbone atoms (in fact just the NH) and get a table for every position. Cannot seem to find a simple way to do that with Chimera... Thanks again for your help Cedric Cedric Govaerts, Ph.D. Structure et Fonction des Membranes Biologiques (SFMB) Universite Libre de Bruxelles Boulevard du Triomphe - CP 206/2 B-1050 Bruxelles (Belgium) Tel: +32-2-650.53.77 Fax: +32-2-650.53.82 From meng at cgl.ucsf.edu Tue Apr 21 08:45:35 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 21 Apr 2009 08:45:35 -0700 Subject: [Chimera-users] (no subject) In-Reply-To: <014901c9c284$4ffe5770$effb0650$@ac.be> References: <014901c9c284$4ffe5770$effb0650$@ac.be> Message-ID: <375BECE9-964E-4B6E-B396-148ACDADEBD7@cgl.ucsf.edu> Hi Cedric, When a molecular surface is calculated (the first time it is shown), the solvent-excluded and solvent-accessible areas are also calculated. The overall totals and total per disconnected part ("component") are reported in the Reply Log. At the same time, it creates atom and residue attributes named areaSES and areaSAS. Chimera only shows the solvent-excluded surface, but areas for both types of surfaces are computed: So after you show a surface, you can use these atomic or residue attributes in various ways. To see a histogram of the values, start Render/Select by Attribute (under Tools... Structure Analysis, among other places). With this tool, you could color by the values, or select only atoms (or residues) with values in a certain range, or write out the values for all atoms or just the selected atoms to a text file with "File... Save Attributes". The values can also be used in command-line specifications, and you can show them as labels. Example commands: open 1zik surf color green @/areaSAS>40 ~surf labelopt info areaSAS la @n You can get totals over selected atoms using Attribute Calculator (under Tools... Structure Analysis). I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Apr 21, 2009, at 6:23 AM, C?dric Govaerts wrote: > Hi there, > I want to compute accessible surface area for the backbone, as I > want to > compare the predicted amide deuteration between two conformations of a > protein (I have PDBs for both). I tried with VADAR but the results are > puzzling, I suspect they are not correct (the more open structure > gets a > lower score). > > Is there a way I can do something like that in Chimera ? > > In other word I need to compute how exposed to the solvent are the > backbone > atoms (in fact just the NH) and get a table for every position. > Cannot seem to find a simple way to do that with Chimera... > > Thanks again for your help > Cedric From meng at cgl.ucsf.edu Tue Apr 21 09:05:51 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 21 Apr 2009 09:05:51 -0700 Subject: [Chimera-users] delete model In-Reply-To: <49ED6E8C.2040808@fourmentinguilbert.org> References: <49ED6E8C.2040808@fourmentinguilbert.org> Message-ID: <6FF9724B-80B8-48F0-B9F7-BE03738A648A@cgl.ucsf.edu> Dear Damien, When you click "Make models" in Multiscale Models, it leaves the original input structure as atoms, but shows any additional copies as surfaces. That is the initial appearance, but you can display each chain in whatever style you want by using the dialog (select chain, act on selected chains). You could show them all as surfaces or all as atoms, for example. If you already have all the surfaces you want, you could just use "Actions... Atoms/Bonds... hide" or command "~display" to hide the atoms. In your case, I am guessing it would also work to use the Multiscale dialog to select chains "with loaded atoms" and then act on selected chains to "hide all styles." I believe only what is displayed will be exported. I tried 1yau from the PDB, which is slightly different from what you get from pdbsum. From your picture, it looks like the file from pdbsum includes one whole ellipsoid-shaped complex, and Multiscale Models created an additional copy of that complex. The file from the PDB includes one half-ellipsoid and Multiscale Models adds the other half. But either way, you can control the display as described above. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Apr 20, 2009, at 11:58 PM, Damien Larivi?re wrote: > Dear Chimera team, > I have used the multiscale model for generating a surfacic model of > (pdb) file 1YAU.mmol (from pdb sum). > > Two models are displayed (see attached image): one is an all-atom > model and the other is the surfacic model. > > I would like to know : > > - how to delete the all-atom model in order to export in the vrml > format only the surfacic model (the two-model scene is fast for > exporting but very long for opening in software like 3DSmax) ? > > - why, sometimes, are displayed in the same view the surfacic model > as well as the original structure ? > > My best regards > Damien From cdlau at ucsd.edu Tue Apr 21 20:59:50 2009 From: cdlau at ucsd.edu (cdlau at ucsd.edu) Date: Tue, 21 Apr 2009 20:59:50 -0700 (PDT) Subject: [Chimera-users] [Chimera Help] Multiple Instances Message-ID: <49703.128.54.60.121.1240372790.squirrel@acs-webmail.ucsd.edu> Dear Madam/Sir, I found this from a response 5 years ago in 2004 > As it works now, if you wish to send commands to an already running > Chimera, you cannot specify which instance of Chimera. So it is not > possible to communicate with multiple instances of Chimera as you might > want to support multiple web sessions. Dan Greenblatt may have ideas > for addressing this. > > Tom I was wondering if this is still the case. I am interested in running multiple instances of Chimera on a Tiled Wall Display and have global control over all the instances. Does anyone have any suggestions or resources for me to look into? Thanks in advance, Christoper From meng at cgl.ucsf.edu Wed Apr 22 09:36:55 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 22 Apr 2009 09:36:55 -0700 Subject: [Chimera-users] surface failures In-Reply-To: <002801c9c323$ff91b2a0$feb517e0$@ac.be> References: <014901c9c284$4ffe5770$effb0650$@ac.be> <375BECE9-964E-4B6E-B396-148ACDADEBD7@cgl.ucsf.edu> <002801c9c323$ff91b2a0$feb517e0$@ac.be> Message-ID: On Apr 22, 2009, at 1:26 AM, C?dric Govaerts wrote: > Hi Elaine, > Here is my problem, seems like I cannot compute these surfaces on > some PDBs > and receive the following message in the Reply Log: > > C:\Program Files\Chimera\bin\mscalc.exe 1.400000 2.000000 1 > Calculation of some surface components failed (code 5). > Falling back to single-component calculation. > C:\Program Files\Chimera\bin\mscalc.exe 1.400000 2.000000 0 > Surface calculation failed, mscalc returned code 5 > > I attach the PDB so you can try it for yourself. Hi Cedric, This is an uber-common problem in Chimera due to the numerical failure of the embedded MSMS code on some structures. There are many workarounds that are slight changes to the surfacing parameters or VDW radii, but it is an art rather than science to find them -- just requires trial and error and typically is different on different machines. For example, on both my mac 10.4 laptop and mac 10.5 desktop machines, I just opened your structure and showed the surface without any problems or doing anything special. Because of the MSMS problems, we have been working for many months on code to replace it. We are hoping to have our own surfacing code ready for the next production release. In the meanwhile, I will briefly summarize some things to try (but be aware they can affect your surface area results): - if your structure has multiple chains and you don't mind having a separate surface for each chain, use the "split" command to split it into separate models before surfacing - before creating the surface, adjust related parameters in the New Surfaces category of Preferences (under Favorites). For example, you can adjust vertex density and/or probe radius. if you only care about the main outer surface and not interior bubbles you can turn off "show disjoint". Actually you might prefer not to have interior bubbles included in your results. Sometimes the components that fail are just those interior bubbles, and "single-component calculation" as mentioned in your message of the main outer surface still works. However, in your case both failed. - slightly change VDW radii, e.g. with command "vdwdefine +.05" (you can put them back to default with command "~vdwdefine") Here are several previous posts on this issue: > >> ("component") are reported in the Reply Log. At the same time, it >> creates atom and residue attributes named areaSES and areaSAS. > > Hum, anyway I can retrieve such per residue information ? > Maybe in a text file or something ? > Just to make sure, I can compute the SAS for each atoms based on the > complete structure (including sidechains) and then obtain the > individual > values for each atoms (say backbone nitrogens in this case.) You can save the attribute values (atom or residue attribute named areaSAS or areaSES) to text files using the Render by Attribute dialog's File menu. I will mail you the text file for atom attribute areaSAS for your structure in a separate message. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html From meng at cgl.ucsf.edu Wed Apr 22 10:05:58 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 22 Apr 2009 10:05:58 -0700 Subject: [Chimera-users] Rainbow-coloring In-Reply-To: <200904221608.n3MG8WKL031676@mstest.dicp.ac.cn> References: <200904221608.n3MG8WKL031676@mstest.dicp.ac.cn> Message-ID: <6A738024-2ADF-4513-9BCF-10C20B2A0977@cgl.ucsf.edu> On Apr 22, 2009, at 9:13 AM, YangMingjun wrote: > Dear Professor, > I am going to use Chimera to plot 20 molecular frames (saved in > 10 files with the file name frame_$n.pdb) in one figure and have a > question about the color scheme. I'd like to check the > conformational changes from frame 1 to frame 20. Can you please tell > me how to color the frames, e.g. with gradual change of each frame > in color from red to blue ? > Does Chimera adopt a default method to color an ensemble of > structures when loaded? > Thanks so much. > Mingjun > Dear Mingjun, There isn't really a default just for ensembles. The default behavior is to use a different color for each "model" (generally each structure file makes one model). It is in the preferences, New Molecules category: You can use "rainbow" for coloring different models or chains or residues, gradually changing from one color to another. You can use either the "rainbow" command or the "Rainbow" graphical interface. For graphical interface, choose Tools... Depiction... Rainbow. In your case you would want to use the "model" option. You can change the colors by clicking the squares and using the Color Editor. Similarly, you could just use the command "rainbow models" to use the default coloring, but there are additional keywords to use different colors. For example, if you really only want red->blue and not all the rainbow colors in between, the command would be rainbow models red,blue Here are the built-in color names: For asking Chimera questions, please send mail to chimera-user at cgl.ucsf.edu and not to me directly, unless you are sending private data. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html From mjyang at dicp.ac.cn Wed Apr 22 09:27:14 2009 From: mjyang at dicp.ac.cn (YangMingjun) Date: Thu, 23 Apr 2009 00:27:14 +0800 Subject: [Chimera-users] Question about Chimera Message-ID: <200904221622.n3MGMC3n031709@mstest.dicp.ac.cn> Dear Professor, I am going to use Chimera to plot 20 molecular frames (saved in 10 files with the file name frame_$n.pdb) in one figure and have a question about the color scheme. I'd like to check the conformational changes from frame 1 to frame 20. Can you please tell me how to color the frames, e.g. with gradual change of each frame in color from red to blue ? Does Chimera adopt a default method to color an ensemble of structures when loaded? Thanks so much. Mingjun From meng at cgl.ucsf.edu Wed Apr 22 10:39:59 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 22 Apr 2009 10:39:59 -0700 Subject: [Chimera-users] atomic fluctuations In-Reply-To: <288df32a0904221026q52339394n1538354f394c4f72@mail.gmail.com> References: <288df32a0904221026q52339394n1538354f394c4f72@mail.gmail.com> Message-ID: <59C64A37-BD64-492D-B44B-664510C1BAA1@cgl.ucsf.edu> On Apr 22, 2009, at 10:26 AM, Bala subramanian wrote: > Dear Elaine and Pett, > > Greetings. I have a matrix of atomic fluctuations, is it possible to > map it on to the structure using chimera. Say i would prefer to color > differently all atoms having a fluctuation of more than a threshold. > Similarly if i give a matrix of correlations, i should color > differently those atoms which are highly correlated. > > Thanks, > Bala Dear Bala, To do this you would create an "attribute assignment file" (a simple text format) with the values and read it in with Define Attribute (or command "defattr"). That will assign the values to your structure as an "attribute." Then you can show the values of your new attribute with colors, etc., and select atoms based on those values, and use them in command-line specifications, just like any other attributes (bfactor, kdHydrophobicity, etc.). This is exactly what you need for the fluctuation values. Showing the correlation would be more complicated, because attributes are properties of atoms and not atom pairs. You could assign each "row" of your correlation matrix as a different attribute with a different name. Define Attribute and the concept of "attributes": Attribute assignment file format: Render/Select by Attribute: Please send questions about Chimera to chimera-users at cgl.ucsf.edu and not to our personal addresses, unless you are sending private data or information. Best, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html From meng at cgl.ucsf.edu Wed Apr 22 10:42:33 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 22 Apr 2009 10:42:33 -0700 Subject: [Chimera-users] Question about Chimera In-Reply-To: <200904221622.n3MGMC3n031709@mstest.dicp.ac.cn> References: <200904221622.n3MGMC3n031709@mstest.dicp.ac.cn> Message-ID: <178F209D-7F0F-4095-868A-CF0CF2B2E5BE@cgl.ucsf.edu> Please see answer already sent. 8-) On Apr 22, 2009, at 9:27 AM, YangMingjun wrote: > Dear Professor, > > I am going to use Chimera to plot 20 molecular frames (saved in > 10 files with the file name frame_$n.pdb) in one figure and have a > question about the color scheme. I'd like to check the > conformational changes from frame 1 to frame 20. Can you please tell > me how to color the frames, e.g. with gradual change of each frame > in color from red to blue ? > Does Chimera adopt a default method to color an ensemble of > structures when loaded? > > Thanks so much. > > Mingjun From meng at cgl.ucsf.edu Wed Apr 22 10:51:45 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 22 Apr 2009 10:51:45 -0700 Subject: [Chimera-users] Straighten a helix In-Reply-To: References: <60A2B72E-0C5F-408A-919F-9435DF92F070@cgl.ucsf.edu> Message-ID: <47557CAC-BC14-4A9D-A6D7-63B714402D88@cgl.ucsf.edu> Hi Francesco, You don't have to give the atom names for each residue, e.g. how about match #0:24-30 #1:24-30 (assuming these residues have equal numbers of atoms with the same names in the two structures) or match #0:24-30 at n,ca,c,o #1:24-30 at n,ca,c,o or match #0:24-30 at ca #1:24-30 at ca You may want to try the "iterate" option of the match command. You could use matchmaker instead of match, but that would use the whole chain rather than specific residues, so I doubt it fits your situation. Here is a discussion of the different ways to match things in Chimera: Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Apr 22, 2009, at 10:32 AM, Francesco Pietra wrote: > Elaine: > I have found a way to get a nearly perfect alpha helix from what was a > bent alpha helix by imposing the phi and psi angles where they were > out of the norm. However, both the barycenter and the orientation of > the rectified helix have changed, so that it does no more fit its > partners. > > What I would like to do is using the Chimera "match" command to > superimpose the rectified helix to the bent helix, then remove the > bent helix and save pdb. Surely clashes will be there but perhaps not > so many to hinder MD. Is there a short command to tell to Chimera to > do the job without having to list atom per atom. The helix is long and > trial and errors will be many...it is not laziness alone. > > Or is anything better in Chimera than the match command? > thanks > francesco From pett at cgl.ucsf.edu Wed Apr 22 11:48:51 2009 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 22 Apr 2009 11:48:51 -0700 Subject: [Chimera-users] [Chimera Help] Multiple Instances In-Reply-To: <49703.128.54.60.121.1240372790.squirrel@acs-webmail.ucsd.edu> References: <49703.128.54.60.121.1240372790.squirrel@acs-webmail.ucsd.edu> Message-ID: <9D0E48C6-5CA9-4C4B-A82A-2B733D1573E5@cgl.ucsf.edu> On Apr 21, 2009, at 8:59 PM, cdlau at ucsd.edu wrote: > Dear Madam/Sir, > I found this from a response 5 years ago in 2004 > >> As it works now, if you wish to send commands to an already running >> Chimera, you cannot specify which instance of Chimera. So it is not >> possible to communicate with multiple instances of Chimera as you >> might >> want to support multiple web sessions. Dan Greenblatt may have ideas >> for addressing this. >> >> Tom > > I was wondering if this is still the case. I am interested in running > multiple instances of Chimera on a Tiled Wall Display and have global > control over all the instances. Does anyone have any suggestions or > resources for me to look into? Hi Chris, The quote refers to the situation where a user has started multiple Chimera sessions and then executes a Chimera script from a web page. The script might run in any of the Chimera instances. If _you_ start multiple Chimeras you can absolutely control which one does what as long as the commands aren't coming from a web page. There is a ReadStdin extension that you can use to have each Chimera read commands from standard input (documentation: http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/readstdin/readstdin.html) . It reads Chimera commands but you can use the "open" command to run Python scripts. Let me know if this isn't sufficient for your needs. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at cgl.ucsf.edu Wed Apr 22 11:59:56 2009 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Wed, 22 Apr 2009 11:59:56 -0700 Subject: [Chimera-users] [Chimera Help] Multiple Instances In-Reply-To: <9D0E48C6-5CA9-4C4B-A82A-2B733D1573E5@cgl.ucsf.edu> References: <49703.128.54.60.121.1240372790.squirrel@acs-webmail.ucsd.edu> <9D0E48C6-5CA9-4C4B-A82A-2B733D1573E5@cgl.ucsf.edu> Message-ID: <49EF692C.8010300@cgl.ucsf.edu> Hi Chris, Eric's suggestion sounds good if you start all the Chimera instances from one process (maybe with popen) that can then hold on to the sockets used to feed commands to each Chimera. The alternative approach used for a web browser to send a file to an already running Chimera works by executing a command "chimera --send myfile" which sends the file to the instance of Chimera on the local machine (and owned by the same user) that most recently had the focus, as described in the documentation: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/options.html That would probably be troublesome to use in your situation. While you could probably give the focus to the specific Chimera instance before sending the file (using an operating system specific call), it would only work after that Chimera actually processes the focus event. It would be hard to know how long to wait before sending the file. Tom Eric Pettersen wrote: > On Apr 21, 2009, at 8:59 PM, cdlau at ucsd.edu wrote: > >> Dear Madam/Sir, >> I found this from a response 5 years ago in 2004 >> >>> As it works now, if you wish to send commands to an already running >>> Chimera, you cannot specify which instance of Chimera. So it is not >>> possible to communicate with multiple instances of Chimera as you might >>> want to support multiple web sessions. Dan Greenblatt may have ideas >>> for addressing this. >>> >>> Tom >> >> I was wondering if this is still the case. I am interested in running >> multiple instances of Chimera on a Tiled Wall Display and have global >> control over all the instances. Does anyone have any suggestions or >> resources for me to look into? > > Hi Chris, > The quote refers to the situation where a user has started multiple > Chimera sessions and then executes a Chimera script from a web page. > The script might run in any of the Chimera instances. > If _you_ start multiple Chimeras you can absolutely control which one > does what as long as the commands aren't coming from a web page. > There is a ReadStdin extension that you can use to have each Chimera > read commands from standard input > (documentation: http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/readstdin/readstdin.html) > . > It reads Chimera commands but you can use the "open" command to run > Python scripts. > Let me know if this isn't sufficient for your needs. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > ------------------------------------------------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > From mjyang at dicp.ac.cn Wed Apr 22 18:54:29 2009 From: mjyang at dicp.ac.cn (YangMingjun) Date: Thu, 23 Apr 2009 09:54:29 +0800 Subject: [Chimera-users] (no subject) Message-ID: <200904230149.n3N1nDgV003269@mstest.dicp.ac.cn> Dear Professor, Thanks very much for your detailed instruction. If I use rainbow models red,blue then can Chimera produce a color panel to denote the colors used? Thanks Mingjun > Dear Professor, > I am going to use Chimera to plot 20 molecular frames (saved in > 10 files with the file name frame_$n.pdb) in one figure and have a > question about the color scheme. I'd like to check the > conformational changes from frame 1 to frame 20. Can you please tell > me how to color the frames, e.g. with gradual change of each frame > in color from red to blue ? > Does Chimera adopt a default method to color an ensemble of > structures when loaded? > Thanks so much. > Mingjun > Dear Mingjun, There isn't really a default just for ensembles. The default behavior is to use a different color for each "model" (generally each structure file makes one model). It is in the preferences, New Molecules category: You can use "rainbow" for coloring different models or chains or residues, gradually changing from one color to another. You can use either the "rainbow" command or the "Rainbow" graphical interface. For graphical interface, choose Tools... Depiction... Rainbow. In your case you would want to use the "model" option. You can change the colors by clicking the squares and using the Color Editor. Similarly, you could just use the command "rainbow models" to use the default coloring, but there are additional keywords to use different colors. For example, if you really only want red->blue and not all the rainbow colors in between, the command would be rainbow models red,blue Here are the built-in color names: For asking Chimera questions, please send mail to chimera-user at cgl.ucsf.edu and not to me directly, unless you are sending private data. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html From meng at cgl.ucsf.edu Wed Apr 22 20:58:50 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 22 Apr 2009 20:58:50 -0700 Subject: [Chimera-users] (no subject) In-Reply-To: <200904230149.n3N1nDgV003269@mstest.dicp.ac.cn> References: <200904230149.n3N1nDgV003269@mstest.dicp.ac.cn> Message-ID: Dear Mingjun, After the rainbow-coloring, open the Model Panel (under Favorites in the menu). There it will show the color for each model in a square. If you click any of those squares, called "color wells," it will bring up the color panel (Color Editor) set to that color. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Apr 22, 2009, at 6:54 PM, YangMingjun wrote: > Dear Professor, > Thanks very much for your detailed instruction. > If I use rainbow models red,blue > then can Chimera produce a color panel to denote the colors used? > Thanks > Mingjun > From mjyang at dicp.ac.cn Thu Apr 23 00:18:26 2009 From: mjyang at dicp.ac.cn (YangMingjun) Date: Thu, 23 Apr 2009 15:18:26 +0800 Subject: [Chimera-users] (no subject) Message-ID: <200904230713.n3N7D3HB007900@mstest.dicp.ac.cn> Dear Professor, Thanks so much. I am the first time to use Chimera so I am sorry that if my questions seem to be too simple... Sorry that I didn't describe my question clearly in last post. I had got the figure of 20 frames which are colored by using the command "rainbow models red, blue". Then I saved the figure with the file name a.png. Now I'd like to use the color range to denote each frame in the paper, e.g. color range from red to blue gradual changes corresponds to colors used by model 1 to 20 in the saved figure. Since I don't know what is the name it is should be called in English language, I send you an example in the attachment. Many thanks. Mingjun >Dear Mingjun, >After the rainbow-coloring, open the Model Panel (under Favorites in >the menu). There it will show the color for each model in a square. >If you click any of those squares, called "color wells," it will >bring up the color panel (Color Editor) set to that color. >I hope this helps, >Elaine >----- >Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu >UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >Department of Pharmaceutical Chemistry >University of California, San Francisco > http://www.cgl.ucsf.edu/home/meng/index.html > >On Apr 22, 2009, at 6:54 PM, YangMingjun wrote: > >> Dear Professor, >> Thanks very much for your detailed instruction. >> If I use rainbow models red,blue >> then can Chimera produce a color panel to denote the colors used? >> Thanks >> Mingjun >> >. -------------- next part -------------- A non-text attachment was scrubbed... Name: color.PNG Type: application/octet-stream Size: 33998 bytes Desc: not available URL: From meng at cgl.ucsf.edu Thu Apr 23 09:32:05 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 23 Apr 2009 09:32:05 -0700 Subject: [Chimera-users] Color Key In-Reply-To: <200904230713.n3N7D3HB007900@mstest.dicp.ac.cn> References: <200904230713.n3N7D3HB007900@mstest.dicp.ac.cn> Message-ID: <68DDED9E-E816-42B3-AEF3-6138C60F2BDA@cgl.ucsf.edu> Dear Mingjun, Oh, now I see -- you want a color key! Yes, you can do that in Chimera: choose Tools... Utilities... Color Key. In that dialog you can set the colors and the value labels. You can click and drag with the mouse to draw the key in the Chimera window. If you need more text, you can add it with 2D Labels, which is another tab on the same dialog as Color Key. Here is the full description: and here is an example image with both Color Key and 2D Labels: You would add that stuff while you are still in Chimera, and then when you save the image, it will be included. You might also be interested in this page on "tips" for making images: I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Apr 23, 2009, at 12:18 AM, YangMingjun wrote: > Dear Professor, > Thanks so much. I am the first time to use Chimera so I am sorry > that if my questions seem to be too simple... Sorry that I didn't > describe my question clearly in last post. > I had got the figure of 20 frames which are colored by using the > command "rainbow models red, blue". Then I saved the figure with > the file name a.png. Now I'd like to use the color range to denote > each frame in the paper, e.g. color range from red to blue gradual > changes corresponds to colors used by model 1 to 20 in the saved > figure. Since I don't know what is the name it is should be called > in English language, I send you an example in the attachment. > Many thanks. > Mingjun From meng at cgl.ucsf.edu Thu Apr 23 10:34:06 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 23 Apr 2009 10:34:06 -0700 Subject: [Chimera-users] Color Key In-Reply-To: <68DDED9E-E816-42B3-AEF3-6138C60F2BDA@cgl.ucsf.edu> References: <200904230713.n3N7D3HB007900@mstest.dicp.ac.cn> <68DDED9E-E816-42B3-AEF3-6138C60F2BDA@cgl.ucsf.edu> Message-ID: <02C7876C-10D1-4B2D-B6C4-0619D6EC2065@cgl.ucsf.edu> I forgot to mention that you can drag colors from the squares in the Model Panel to the squares in the Color Key dialog. That is probably the easiest way to make the intermediate colors match. Best, Elaine On Apr 23, 2009, at 9:32 AM, Elaine Meng wrote: > Dear Mingjun, > Oh, now I see -- you want a color key! Yes, you can do that in > Chimera: choose Tools... Utilities... Color Key. In that dialog you > can set the colors and the value labels. You can click and drag with > the mouse to draw the key in the Chimera window. If you need more > text, you can add it with 2D Labels, which is another tab on the same > dialog as Color Key. > > Here is the full description: > 2dlabels.html#colorkey> > > and here is an example image with both Color Key and 2D Labels: > > > You would add that stuff while you are still in Chimera, and then > when you save the image, it will be included. You might also be > interested in this page on "tips" for making images: > > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > http://www.cgl.ucsf.edu/home/meng/index.html > > On Apr 23, 2009, at 12:18 AM, YangMingjun wrote: > >> Dear Professor, >> Thanks so much. I am the first time to use Chimera so I am sorry >> that if my questions seem to be too simple... Sorry that I didn't >> describe my question clearly in last post. >> I had got the figure of 20 frames which are colored by using the >> command "rainbow models red, blue". Then I saved the figure with >> the file name a.png. Now I'd like to use the color range to denote >> each frame in the paper, e.g. color range from red to blue gradual >> changes corresponds to colors used by model 1 to 20 in the saved >> figure. Since I don't know what is the name it is should be called >> in English language, I send you an example in the attachment. >> Many thanks. >> Mingjun > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From Priyaranjan.Bhakat at csiro.au Wed Apr 22 19:07:33 2009 From: Priyaranjan.Bhakat at csiro.au (Priyaranjan.Bhakat at csiro.au) Date: Thu, 23 Apr 2009 12:07:33 +1000 Subject: [Chimera-users] Re. Volume squeeze Message-ID: Hi, I was trying to overlay two volumes one from PDB and other from single particle reconstruction software EMAN (*.mrc). When I open EMAN generated 3D volume and then PDB file, EMAN 3D volume got reduce. However, when EMAN generated 3D volume is only in the 'volume viewer' screen, there is no change. Furthermore, if I press 'center' tab of 'volume viewer' volume became squeeze again. Alternatively, what the best way to overlay and compare two volumes. Thanks in advance for any clue, Priya -------------- next part -------------- An HTML attachment was scrubbed... URL: From kandiahe at mail.nih.gov Thu Apr 23 14:27:10 2009 From: kandiahe at mail.nih.gov (Eaazhisai Kandiah) Date: Thu, 23 Apr 2009 17:27:10 -0400 Subject: [Chimera-users] transition command Message-ID: <3D464119-9B5D-4153-843E-C9BC27F13BE5@mail.nih.gov> Hello Developers, I would like to use the transition command to travel through the radius of an icosahedron surface. The builds and release I have, do not recognize the command 'transition'. Could you please tell me which version/build of chimera I should be using for this command? Thanks a lot, Eaazhisai Kandiah Laboratory of Structural Biology NIAMS, National Institutes of Health, Room 1511,Bldg 50 9000 Rockville Pike, Bethesda, MD-20892 kandiahe at mail.nih.gov Off: 301 451 2281 Fax: 301 480 7629 -------------- next part -------------- An HTML attachment was scrubbed... URL: From kandiahe at mail.nih.gov Thu Apr 23 14:36:58 2009 From: kandiahe at mail.nih.gov (Eaazhisai Kandiah) Date: Thu, 23 Apr 2009 17:36:58 -0400 Subject: [Chimera-users] transition command Message-ID: <85E6046C-3350-403C-9652-1F0FF5DA54A3@mail.nih.gov> Hi, I found the answer for the transition command. Actually It has been discussed in the forum before. It is in the Experimental features site and under Animation commands. Will try that. Sorry about repeating the question. Eaazhisai Kandiah Laboratory of Structural Biology NIAMS, National Institutes of Health, Room 1511,Bldg 50 9000 Rockville Pike, Bethesda, MD-20892 kandiahe at mail.nih.gov Off: 301 451 2281 Fax: 301 480 7629 -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at cgl.ucsf.edu Thu Apr 23 16:52:28 2009 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Thu, 23 Apr 2009 16:52:28 -0700 Subject: [Chimera-users] Re. Volume squeeze In-Reply-To: References: Message-ID: <49F0FF3C.3040803@cgl.ucsf.edu> Hi Priya, Sounds like the voxel size (grid plane spacing) in your map (MRC file) is not set. Use the Coordinates panel in the volume dialog (menu Features / Coordinates) and set the voxel size value to the correct size in Angstroms for your map. Then the scale of the map and PDB should match. Look at the Fit in Map tool for aligning the two. http://www.cgl.ucsf.edu/chimera/tutorials/volumetour/volumetour.html#fitmodel Tom Priyaranjan.Bhakat at csiro.au wrote: > Hi, > I was trying to overlay two volumes one from PDB and other from single > particle reconstruction software EMAN (*.mrc). When I open EMAN > generated 3D volume and then PDB file, EMAN 3D volume got reduce. > However, when EMAN generated 3D volume is only in the 'volume viewer' > screen, there is no change. Furthermore, if I press 'center' tab of > 'volume viewer' volume became squeeze again. > Alternatively, what the best way to overlay and compare two volumes. > Thanks in advance for any clue, > Priya > > > ------------------------------------------------------------------------ > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From mjyang at dicp.ac.cn Thu Apr 23 18:45:22 2009 From: mjyang at dicp.ac.cn (YangMingjun) Date: Fri, 24 Apr 2009 09:45:22 +0800 Subject: [Chimera-users] Color Key Message-ID: <200904240139.n3O1dUZu018033@mstest.dicp.ac.cn> Dear Professor, Thanks very much. I can't find the Color Key icon in my installed Chimera following the step in the link. Is it due to the version I am using? I am using Windows os and chimera-1[1].2422-win32.exe Mingjun >I forgot to mention that you can drag colors from the squares in the >Model Panel to the squares in the Color Key dialog. That is probably >the easiest way to make the intermediate colors match. >Best, >Elaine > >On Apr 23, 2009, at 9:32 AM, Elaine Meng wrote: > >> Dear Mingjun, >> Oh, now I see -- you want a color key! Yes, you can do that in >> Chimera: choose Tools... Utilities... Color Key. In that dialog you >> can set the colors and the value labels. You can click and drag with >> the mouse to draw the key in the Chimera window. If you need more >> text, you can add it with 2D Labels, which is another tab on the same >> dialog as Color Key. >> >> Here is the full description: >> > 2dlabels.html#colorkey> >> >> and here is an example image with both Color Key and 2D Labels: >> >> >> You would add that stuff while you are still in Chimera, and then >> when you save the image, it will be included. You might also be >> interested in this page on "tips" for making images: >> >> >> I hope this helps, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu >> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> http://www.cgl.ucsf.edu/home/meng/index.html >> >> On Apr 23, 2009, at 12:18 AM, YangMingjun wrote: >> >>> Dear Professor, >>> Thanks so much. I am the first time to use Chimera so I am sorry >>> that if my questions seem to be too simple... Sorry that I didn't >>> describe my question clearly in last post. >>> I had got the figure of 20 frames which are colored by using the >>> command "rainbow models red, blue". Then I saved the figure with >>> the file name a.png. Now I'd like to use the color range to denote >>> each frame in the paper, e.g. color range from red to blue gradual >>> changes corresponds to colors used by model 1 to 20 in the saved >>> figure. Since I don't know what is the name it is should be called >>> in English language, I send you an example in the attachment. >>> Many thanks. >>> Mingjun >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > >. -------------- next part -------------- A non-text attachment was scrubbed... Name: tools.PNG Type: application/octet-stream Size: 36290 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: renderbyattri.PNG Type: application/octet-stream Size: 58121 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: surfacecolor.PNG Type: application/octet-stream Size: 95820 bytes Desc: not available URL: From mjyang at dicp.ac.cn Thu Apr 23 18:47:10 2009 From: mjyang at dicp.ac.cn (YangMingjun) Date: Fri, 24 Apr 2009 09:47:10 +0800 Subject: [Chimera-users] Chimera-users Digest, Vol 72, Issue 26 Message-ID: <200904240141.n3O1fIwj018077@mstest.dicp.ac.cn> Sorry that I send my question to you directly by replying your last response in the mailing list. I have sent one to the chimera-users at cgl.ucsf.edu Mingjun >Send Chimera-users mailing list submissions to > chimera-users at cgl.ucsf.edu > >To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >or, via email, send a message with subject or body 'help' to > chimera-users-request at cgl.ucsf.edu > >You can reach the person managing the list at > chimera-users-owner at cgl.ucsf.edu > >When replying, please edit your Subject line so it is more specific >than "Re: Contents of Chimera-users digest..." > > >Today's Topics: > > 1. Color Key (Elaine Meng) > 2. Re: Color Key (Elaine Meng) > 3. Re. Volume squeeze (Priyaranjan.Bhakat at csiro.au) > > >---------------------------------------------------------------------- > >Message: 1 >Date: Thu, 23 Apr 2009 09:32:05 -0700 >From: Elaine Meng >Subject: [Chimera-users] Color Key >To: YangMingjun >Cc: Chimera-users >Message-ID: <68DDED9E-E816-42B3-AEF3-6138C60F2BDA at cgl.ucsf.edu> >Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > >Dear Mingjun, >Oh, now I see -- you want a color key! Yes, you can do that in >Chimera: choose Tools... Utilities... Color Key. In that dialog you >can set the colors and the value labels. You can click and drag with >the mouse to draw the key in the Chimera window. If you need more >text, you can add it with 2D Labels, which is another tab on the same >dialog as Color Key. > >Here is the full description: >2dlabels.html#colorkey> > >and here is an example image with both Color Key and 2D Labels: > > >You would add that stuff while you are still in Chimera, and then >when you save the image, it will be included. You might also be >interested in this page on "tips" for making images: > > >I hope this helps, >Elaine >----- >Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu >UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >Department of Pharmaceutical Chemistry >University of California, San Francisco > http://www.cgl.ucsf.edu/home/meng/index.html > >On Apr 23, 2009, at 12:18 AM, YangMingjun wrote: > >> Dear Professor, >> Thanks so much. I am the first time to use Chimera so I am sorry >> that if my questions seem to be too simple... Sorry that I didn't >> describe my question clearly in last post. >> I had got the figure of 20 frames which are colored by using the >> command "rainbow models red, blue". Then I saved the figure with >> the file name a.png. Now I'd like to use the color range to denote >> each frame in the paper, e.g. color range from red to blue gradual >> changes corresponds to colors used by model 1 to 20 in the saved >> figure. Since I don't know what is the name it is should be called >> in English language, I send you an example in the attachment. >> Many thanks. >> Mingjun > > >------------------------------ > >Message: 2 >Date: Thu, 23 Apr 2009 10:34:06 -0700 >From: Elaine Meng >Subject: Re: [Chimera-users] Color Key >To: YangMingjun >Cc: Chimera-users BB >Message-ID: <02C7876C-10D1-4B2D-B6C4-0619D6EC2065 at cgl.ucsf.edu> >Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > >I forgot to mention that you can drag colors from the squares in the >Model Panel to the squares in the Color Key dialog. That is probably >the easiest way to make the intermediate colors match. >Best, >Elaine > >On Apr 23, 2009, at 9:32 AM, Elaine Meng wrote: > >> Dear Mingjun, >> Oh, now I see -- you want a color key! Yes, you can do that in >> Chimera: choose Tools... Utilities... Color Key. In that dialog you >> can set the colors and the value labels. You can click and drag with >> the mouse to draw the key in the Chimera window. If you need more >> text, you can add it with 2D Labels, which is another tab on the same >> dialog as Color Key. >> >> Here is the full description: >> > 2dlabels.html#colorkey> >> >> and here is an example image with both Color Key and 2D Labels: >> >> >> You would add that stuff while you are still in Chimera, and then >> when you save the image, it will be included. You might also be >> interested in this page on "tips" for making images: >> >> >> I hope this helps, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu >> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> http://www.cgl.ucsf.edu/home/meng/index.html >> >> On Apr 23, 2009, at 12:18 AM, YangMingjun wrote: >> >>> Dear Professor, >>> Thanks so much. I am the first time to use Chimera so I am sorry >>> that if my questions seem to be too simple... Sorry that I didn't >>> describe my question clearly in last post. >>> I had got the figure of 20 frames which are colored by using the >>> command "rainbow models red, blue". Then I saved the figure with >>> the file name a.png. Now I'd like to use the color range to denote >>> each frame in the paper, e.g. color range from red to blue gradual >>> changes corresponds to colors used by model 1 to 20 in the saved >>> figure. Since I don't know what is the name it is should be called >>> in English language, I send you an example in the attachment. >>> Many thanks. >>> Mingjun >> _______________________________________________ >> Chimera-users mailing list >> Chimera-users at cgl.ucsf.edu >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > > >------------------------------ > >Message: 3 >Date: Thu, 23 Apr 2009 12:07:33 +1000 >From: >Subject: [Chimera-users] Re. Volume squeeze >To: >Message-ID: > >Content-Type: text/plain; charset="us-ascii" > >Hi, >I was trying to overlay two volumes one from PDB and other from single particle reconstruction software EMAN (*.mrc). When I open EMAN generated 3D volume and then PDB file, EMAN 3D volume got reduce. However, when EMAN generated 3D volume is only in the 'volume viewer' screen, there is no change. Furthermore, if I press 'center' tab of 'volume viewer' volume became squeeze again. >Alternatively, what the best way to overlay and compare two volumes. >Thanks in advance for any clue, >Priya >-------------- next part -------------- >An HTML attachment was scrubbed... >URL: http://www.cgl.ucsf.edu/pipermail/chimera-users/attachments/20090423/40e230f9/attachment-0001.html > >------------------------------ > >_______________________________________________ >Chimera-users mailing list >Chimera-users at cgl.ucsf.edu >http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > >End of Chimera-users Digest, Vol 72, Issue 26 >********************************************* From meng at cgl.ucsf.edu Thu Apr 23 18:57:19 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 23 Apr 2009 18:57:19 -0700 Subject: [Chimera-users] Color Key In-Reply-To: <200904240139.n3O1dUZu018033@mstest.dicp.ac.cn> References: <200904240139.n3O1dUZu018033@mstest.dicp.ac.cn> Message-ID: Hi Mingjun, your version is very, very old. For Color Key you need at least the last production release, version 1.3 from 2008. If you go to the Chimera home page, http://www.cgl.ucsf.edu/chimera/index.html there are download links on the left, "production release" for the most recent production release, and "daily builds" for even newer ones if you want the things that are described in the "what's new" link right next to "daily builds." There are release notes for each version that say what is new in that version. Color Key was a new feature in the 1.3 release. Your version is so old it might not even have those color squares in the Model Panel that I mentioned before! Best, Elaine On Apr 23, 2009, at 6:45 PM, YangMingjun wrote: > Dear Professor, > > Thanks very much. > I can't find the Color Key icon in my installed Chimera > following the step in the link. Is it due to the version I am using? > I am using Windows os and chimera-1[1].2422-win32.exe From mjyang at dicp.ac.cn Fri Apr 24 08:26:25 2009 From: mjyang at dicp.ac.cn (YangMingjun) Date: Fri, 24 Apr 2009 23:26:25 +0800 Subject: [Chimera-users] Color Key Message-ID: <200904241520.n3OFKGQE027045@mstest.dicp.ac.cn> Dear Professor, Thanks so much. It works well now. Mingjun >Hi Mingjun, >your version is very, very old. For Color Key you need at least the >last production release, version 1.3 from 2008. If you go to the >Chimera home page, > >http://www.cgl.ucsf.edu/chimera/index.html > >there are download links on the left, "production release" for the >most recent production release, and "daily builds" for even newer >ones if you want the things that are described in the "what's new" >link right next to "daily builds." There are release notes for each >version that say what is new in that version. Color Key was a new >feature in the 1.3 release. > >Your version is so old it might not even have those color squares in >the Model Panel that I mentioned before! >Best, >Elaine > > >On Apr 23, 2009, at 6:45 PM, YangMingjun wrote: > >> Dear Professor, >> >> Thanks very much. >> I can't find the Color Key icon in my installed Chimera >> following the step in the link. Is it due to the version I am using? >> I am using Windows os and chimera-1[1].2422-win32.exe >. From antranda at unina.it Fri Apr 24 08:52:36 2009 From: antranda at unina.it (Randazzo Antonio) Date: Fri, 24 Apr 2009 17:52:36 +0200 Subject: [Chimera-users] noeshow Message-ID: <831FE062-56AF-4A82-929A-1BBD7102960B@unina.it> Hi all, I am new of chimera and I am trying to display the NOEs that I have used in my calculations along with the structured I have obtained. With my big surprise I have discovered that in a previous version of the program (MIDAS) this was possible (by the command NOESHOW), but it seems that this features is not supported in this version of the program. Do you have any clue in how to resolve this? Is there a workaround or I have to use another program? If this is the case, which program (sometimes I need to display an Amber restraint file or a Discover restraint file). Thanks in advance for your help From hsosa at aecom.yu.edu Fri Apr 24 10:39:56 2009 From: hsosa at aecom.yu.edu (hsosa at aecom.yu.edu) Date: Fri, 24 Apr 2009 13:39:56 -0400 Subject: [Chimera-users] Stereo Monitors Message-ID: <49F1F96C.5030102@aecom.yu.edu> Hi, I was wondering if chimera work with one of these stereo monitors that split the image into two opposite circularly polarized images (e.g. MIRACUBE G170S) so that you can use cheap passive glasses, similar to the disposable ones used in some movies. Also I'll be interested If anybody has experience using these monitors. I think they are under $1000 now for a 17' monitor Best Hernando -- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa at aecom.yu.edu ----------------------------------- From gregc at cgl.ucsf.edu Fri Apr 24 10:53:17 2009 From: gregc at cgl.ucsf.edu (Greg Couch) Date: Fri, 24 Apr 2009 10:53:17 -0700 (PDT) Subject: [Chimera-users] Stereo Monitors In-Reply-To: <49F1F96C.5030102@aecom.yu.edu> References: <49F1F96C.5030102@aecom.yu.edu> Message-ID: On Fri, 24 Apr 2009, hsosa at aecom.yu.edu wrote: > I was wondering if chimera work with one of these stereo monitors that > split the image into two opposite circularly polarized images (e.g. > MIRACUBE G170S) so that you can use cheap passive glasses, similar to > the disposable ones used in some movies. Also I'll be interested If > anybody has experience using these monitors. I think they are under > $1000 now for a 17' monitor > > Best > > Hernando The answer is yes! You have to use the chimera daily build (this will be standard in 1.4) and switch the camera to "row interleaved" stereo. Row interleaved stereo works on the Miracube and the Zalman stereo monitors on all platforms (Windows, Linux, Mac). See our tech note on the Miracube at . Greg Couch UCSF Computer Graphics Lab From meng at cgl.ucsf.edu Fri Apr 24 11:22:46 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 24 Apr 2009 11:22:46 -0700 Subject: [Chimera-users] Stereo Monitors In-Reply-To: References: <49F1F96C.5030102@aecom.yu.edu> Message-ID: Just a little more detail: you can switch the camera using the Camera tool (under Tools... Viewing Controls) or the "stereo" command, see Best, Elaine On Apr 24, 2009, at 10:53 AM, Greg Couch wrote: > On Fri, 24 Apr 2009, hsosa at aecom.yu.edu wrote: > >> I was wondering if chimera work with one of these stereo monitors >> that >> split the image into two opposite circularly polarized images (e.g. >> MIRACUBE G170S) so that you can use cheap passive glasses, similar >> to >> the disposable ones used in some movies. Also I'll be interested If >> anybody has experience using these monitors. I think they are under >> $1000 now for a 17' monitor >> >> Best >> >> Hernando > > The answer is yes! You have to use the chimera daily build (this > will be > standard in 1.4) and switch the camera to "row interleaved" stereo. > Row > interleaved stereo works on the Miracube and the Zalman stereo > monitors on > all platforms (Windows, Linux, Mac). See our tech note on the > Miracube at > . > > Greg Couch > UCSF Computer Graphics Lab From meng at cgl.ucsf.edu Mon Apr 27 09:39:17 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 27 Apr 2009 09:39:17 -0700 Subject: [Chimera-users] noeshow In-Reply-To: <831FE062-56AF-4A82-929A-1BBD7102960B@unina.it> References: <831FE062-56AF-4A82-929A-1BBD7102960B@unina.it> Message-ID: <5907177E-C9D0-4554-8543-5A488372A485@cgl.ucsf.edu> Hi Randazzo, Sorry about the slow reply, I had to dig up my old Midas manual and read about NOESHOW. Currently there is nothing in Chimera that (like NOESHOW) reads constraints/restraints from files and displays them on structures. We have discussed adding similar capabilities, but it has not been done. Related things you can do now in Chimera are: - measure and display distances - measure angles - rotate torsions, with automatic update of any distance measurements - draw lines between any pair of atoms, with control over color and optional label of each line. You would do that by creating a simple text file describing the lines and reading it in with Pseudobond Reader. However, you would still have to calculate the violations yourself and assign colors accordingly -- not nearly as automatic and convenient as using NOESHOW. Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Apr 24, 2009, at 8:52 AM, Randazzo Antonio wrote: > Hi all, > > I am new of chimera and I am trying to display the NOEs that I have > used in my calculations along with the structured I have obtained. > With my big surprise I have discovered that in a previous version of > the program (MIDAS) this was possible (by the command NOESHOW), but it > seems that this features is not supported in this version of the > program. Do you have any clue in how to resolve this? Is there a > workaround or I have to use another program? If this is the case, > which program (sometimes I need to display an Amber restraint file or > a Discover restraint file). > > Thanks in advance for your help > From pett at cgl.ucsf.edu Mon Apr 27 11:25:44 2009 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Mon, 27 Apr 2009 11:25:44 -0700 Subject: [Chimera-users] noeshow In-Reply-To: <5907177E-C9D0-4554-8543-5A488372A485@cgl.ucsf.edu> References: <831FE062-56AF-4A82-929A-1BBD7102960B@unina.it> <5907177E-C9D0-4554-8543-5A488372A485@cgl.ucsf.edu> Message-ID: On Apr 27, 2009, at 9:39 AM, Elaine Meng wrote: > - draw lines between any pair of atoms, with control over color and > optional label of each line. You would do that by creating a simple > text file describing the lines and reading it in with Pseudobond > Reader. > > > However, you would still have to calculate the violations yourself and > assign colors accordingly -- not nearly as automatic and convenient as > using NOESHOW. Also, if the violation criteria were uniform, or only depended on heavy-atom element types or atom types, then it wouldn't be too hard to write a Python script to color the pseudobonds after they were read in. More sophisticated analysis that noeshow was capable of, such as exponential averaging across an ensemble of structures, would be some work though. --Eric -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at cgl.ucsf.edu Mon Apr 27 11:43:00 2009 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Mon, 27 Apr 2009 11:43:00 -0700 Subject: [Chimera-users] Problem recording raytraced movie In-Reply-To: <006701c9c710$10722510$31566f30$@com> References: <001d01c9bc12$554c8080$ffe58180$@com> <49E38375.6070303@cgl.ucsf.edu> <006701c9c710$10722510$31566f30$@com> Message-ID: <49F5FCB4.4060000@cgl.ucsf.edu> maya shcushan wrote: > Dear Tom, > Thanks, this was very helpful... > I have a new question: I want to make a simple movie in which the molecule > rotates. Using the commands script I found on the internet, the movie is of > very low quality (attached). Moreover, running it with windows media player > shows the opening in the script, embedded in the movie. This were the > commands: > > "movie record > turn y 3 150 > wait 150 > movie encode mformat avi output spin.avi bitrate 4000" > > I want to record the same movie in good quality, like the pictures I get > with pov-raying. I tried running: > "movie record raytrace true > turn y 3 150 > wait 150 > movie encode mformat avi output spin.avi bitrate 4000" > But it falls all the time. > > I looked in the internet for scripts but didn't find an answer. Can you > please help me to create a simple script in which the molecule rotates and > presented in ray-tracing and high quality? > > Thanksm > Maya > > Hi Maya, In Chimera 1.3 before the movie encode command you need the command "movie stop". movie record raytrace true turn y 3 150 wait 150 movie stop movie encode mformat avi output spin.avi bitrate 4000 Otherwise it keeps on recording frames forever. In Chimera 1.4 (daily builds) this is unnecessary and your original script works correctly because in 1.4 movie encode does a movie stop implicitly. Tom From meng at cgl.ucsf.edu Mon Apr 27 12:24:53 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 27 Apr 2009 12:24:53 -0700 Subject: [Chimera-users] Problem recording raytraced movie In-Reply-To: <49F5FCB4.4060000@cgl.ucsf.edu> References: <001d01c9bc12$554c8080$ffe58180$@com> <49E38375.6070303@cgl.ucsf.edu> <006701c9c710$10722510$31566f30$@com> <49F5FCB4.4060000@cgl.ucsf.edu> Message-ID: Hi Maya, The "making movies" page in the User's Guide includes links to a few example scripts. Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html From jort at nmr.mpibpc.mpg.de Tue Apr 28 06:31:56 2009 From: jort at nmr.mpibpc.mpg.de (julien(GWDG)) Date: Tue, 28 Apr 2009 15:31:56 +0200 Subject: [Chimera-users] measure Message-ID: <49F7054C.50202@nmr.mpibpc.mpg.de> Dear all, I have the last vesion of chimera 1.4 (27371) under a linux machine. I want to use the measure function. I have two models. The difference between this 2 models is a 5 degree rotation around the x axis. >> matrix rotation #1 #0 >>reply in the log Position of test.pdb (#0) relative to test1.pdb (#1) coordinates: Matrix rotation and translation 1.00000000 0.00000000 0.00000000 0.00000000 0.00000000 1.00000000 0.00000000 0.00000000 0.00000000 0.00000000 1.00000000 0.00000000 Axis 0.00000000 0.00000000 1.00000000 Axis point 0.00000000 0.00000000 0.00000000 Rotation angle (degrees) 0.00000000 Shift along axis 0.00000000 I think the command does not work in this version (if I misunderstood the command please tell me as well). It always give me the same answer for any different models I did try. Since I have to ask my admin each time I want to install something, could you just tell me in which version of chimera this command will work. Many many thanks. best Julien -- European Molecular Biology Laboratory Structural and Computational Biology Unit Meyerhofstra?e 1 D-69117 Heidelberg Max-Planck-Institute for Biophysical Chemistry NMR based Structural Biology Am Fassberg 11 D-37077 G?ttingen From meng at cgl.ucsf.edu Tue Apr 28 09:27:49 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 28 Apr 2009 09:27:49 -0700 Subject: [Chimera-users] measure In-Reply-To: <49F7054C.50202@nmr.mpibpc.mpg.de> References: <49F7054C.50202@nmr.mpibpc.mpg.de> Message-ID: <2601C1EE-E725-4EA0-B67F-B2A1BFD91AA7@cgl.ucsf.edu> Dear Julien, I believe the command is working in your version. It does not compare the two structures, it only reports how one file has been transformed relative to the other in Chimera. If the coordinates in the two file are already rotated relative to each other, Chimera would not detect that. It would report a rotation only if you had moved one model relative to the other in Chimera. If the untransformed coordinates of the two structures are already rotated relative to each other, to find out the rotation in Chimera you could superimpose them, and THEN use measure to report what relative transformation had been employed in the superposition. I hope this makes sense, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Apr 28, 2009, at 6:31 AM, julien(GWDG) wrote: > Dear all, > > I have the last vesion of chimera 1.4 (27371) under a linux machine. > > I want to use the measure function. > I have two models. The difference between this 2 models is a 5 degree > rotation around the x axis. >>> matrix rotation #1 #0 > >>> reply in the log > Position of test.pdb (#0) relative to test1.pdb (#1) coordinates: > Matrix rotation and translation > 1.00000000 0.00000000 0.00000000 0.00000000 > 0.00000000 1.00000000 0.00000000 0.00000000 > 0.00000000 0.00000000 1.00000000 0.00000000 > Axis 0.00000000 0.00000000 1.00000000 > Axis point 0.00000000 0.00000000 0.00000000 > Rotation angle (degrees) 0.00000000 > Shift along axis 0.00000000 > > I think the command does not work in this version (if I misunderstood > the command please tell me as well). It always give me the same answer > for any different models I did try. > Since I have to ask my admin each time I want to install something, > could you just tell me in which version of chimera this command will > work. Many many thanks. > > best > > Julien > > -- > European Molecular Biology Laboratory > Structural and Computational Biology Unit > Meyerhofstra?e 1 > D-69117 Heidelberg > > Max-Planck-Institute for Biophysical Chemistry > NMR based Structural Biology > Am Fassberg 11 > D-37077 G?ttingen > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From goddard at cgl.ucsf.edu Tue Apr 28 13:06:31 2009 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Tue, 28 Apr 2009 13:06:31 -0700 Subject: [Chimera-users] Problem recording raytraced movie In-Reply-To: <49F5FCB4.4060000@cgl.ucsf.edu> References: <001d01c9bc12$554c8080$ffe58180$@com> <49E38375.6070303@cgl.ucsf.edu> <006701c9c710$10722510$31566f30$@com> <49F5FCB4.4060000@cgl.ucsf.edu> Message-ID: <49F761C7.4070803@cgl.ucsf.edu> Hi Maya, Please send the error message. You can press the Report a Bug button if an error dialog appears with that option to send us the error message. Here are several factors that would improve the quality of the movie you sent me. First use a higher bitrate. Using 4000 Kbits/sec for a 1280x667 movie frame is too little. The maximum will depend on the codec but you can try 10000. Most movies are not at that high resolution (1280x667) and your machine may not be able to play it at full speed in for example powerpoint. Almost all of your window waas white space. Use a smaller window, or zoom in to make the molecule fill more of the frame. Instead of using raytracing you can use several other options (that have no effect if you raytrace). Use supersampling when recording the movie to reduce jagged edges on the spheres (movie record supersample 3). Use glossy lighting in Chimera 1.4 (Tools / Viewing Controls / Lighting). Use silhouette edges (Tools / Viewing Controls / Effects) for better edge definition. Tom maya shcushan wrote: > Dear Tom, > I added the "stop" but still get a runtime error. The examples do not > include using the ray-pov option, but the movie without it is of very low > quality. > > I am sure you could see that from the attached movie in the last email. > > Do you have an advice on how to produce a movie with good quality, or should > I just resort to PyMol, even though I am a better fan of Chimera... :) ? > Thanks, > Maya > > > > -----Original Message----- > From: Tom Goddard [mailto:goddard at cgl.ucsf.edu] > Sent: Monday, April 27, 2009 9:43 PM > To: maya shcushan > Cc: 'Chimera BB' > Subject: Problem recording raytraced movie > > maya shcushan wrote: >> Dear Tom, >> Thanks, this was very helpful... >> I have a new question: I want to make a simple movie in which the molecule >> rotates. Using the commands script I found on the internet, the movie is > of >> very low quality (attached). Moreover, running it with windows media > player >> shows the opening in the script, embedded in the movie. This were the >> commands: >> >> "movie record >> turn y 3 150 >> wait 150 >> movie encode mformat avi output spin.avi bitrate 4000" >> >> I want to record the same movie in good quality, like the pictures I get >> with pov-raying. I tried running: >> "movie record raytrace true >> turn y 3 150 >> wait 150 >> movie encode mformat avi output spin.avi bitrate 4000" >> But it falls all the time. >> >> I looked in the internet for scripts but didn't find an answer. Can you >> please help me to create a simple script in which the molecule rotates and >> presented in ray-tracing and high quality? >> >> Thanksm >> Maya >> >> > > Hi Maya, > > In Chimera 1.3 before the movie encode command you need the command > "movie stop". > > movie record raytrace true > turn y 3 150 > wait 150 > movie stop > movie encode mformat avi output spin.avi bitrate 4000 > > Otherwise it keeps on recording frames forever. In Chimera 1.4 (daily > builds) this is unnecessary and your original script works correctly > because in 1.4 movie encode does a movie stop implicitly. > > Tom > From pett at cgl.ucsf.edu Tue Apr 28 16:08:30 2009 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Tue, 28 Apr 2009 16:08:30 -0700 Subject: [Chimera-users] color by element In-Reply-To: <298627.2460.qm@web53903.mail.re2.yahoo.com> References: <298627.2460.qm@web53903.mail.re2.yahoo.com> Message-ID: <3D160C33-9234-456B-B124-1579B52F5D53@cgl.ucsf.edu> On Apr 28, 2009, at 3:31 PM, Thiruvarangan Ramaraj wrote: > Hi Eric, > > I have a question regarding the colouring by element option. > > If I select a surface and I go to colour and choose by element, does > it colour in any order, if so what is the order, how do i find out > what element is given what colour. > > Thanks for your time > > Thiru Hi Thiru, I'm not sure what you mean by "does it colour in any order", but the colors assigned to each element are described here: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/colortables.html#byelement and how you can change them is described here: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/colordef.html --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From nils.becker at ens-lyon.fr Wed Apr 29 04:40:11 2009 From: nils.becker at ens-lyon.fr (Nils Becker) Date: Wed, 29 Apr 2009 13:40:11 +0200 Subject: [Chimera-users] creating volume maps Message-ID: <49F83C9B.4070204@ens-lyon.fr> Hi, I would like to use chimera for measuring the steric accessibility of particular atoms in a structure to reactive species in solution. To do that I had the following idea: 1. create a volume map which represents a solid sphere centered on the atom in question (alternatively, a Gaussian blob), with some chosen radius. 2. mask this sphere using the solvent accessible surface of the protein (for example, if the atom is at the surface and the surface is flat, half of the sphere would be cut away) 3. measure the volume of the remaining piece of the sphere. So now my question is: can this work, and how can I generate the sphere in step 1. ? thanks for any advice! Nils From meng at cgl.ucsf.edu Wed Apr 29 08:06:44 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 29 Apr 2009 08:06:44 -0700 Subject: [Chimera-users] creating volume maps In-Reply-To: <49F83C9B.4070204@ens-lyon.fr> References: <49F83C9B.4070204@ens-lyon.fr> Message-ID: Hi Nils, You could do that, but there are several caveats, which I will describe below. First, some alternative suggestions: (a) why not just use the solvent-accessible surface area of each atom? Perhaps the reactive species is bigger than water, but you can just increase the probe radius as needed to to approximate this species. As soon as you calculate a molecular surface, the per-atom and per-residue solvent-accessible and solvent-excluded areas are assigned and can be saved or used in various ways. Details: (b) however, it sounds like your proposed measure involves not only the accessible surface area of an atom, but the convexity of the molecular surface at that atom. If that is true, you could use this measure of convexity: solvent-accessible surface area divided by solvent-excluded surface area (solvent-accessible is where the probe center goes, solvent-excluded is where the probe surface goes). Exactly this quantity is calculated in the Attributes tutorial, part 2, and shown in the figure with color: As to what you described, here is an example of how to do it (commands): open 1zik molmap :17.a at oh 5 modelId 1 surf mask #1 #0 measure volume #1 measure volume #2 which reports in the Reply Log 114 A*3 for the original volume, 53 A* for the masked volume. See the manual pages for molmap, mask, and measure (requires Chimera 1.4): The caveats: - Chimera does not show the solvent-accessible surface but the solvent- excluded, so you would be masking using the latter - not sure what you would use for the Gaussian resolution in the molmap command - you might want to make the surface of the Gaussian sphere blob more finely triangulated for these measurements, which could be done with the Volume Viewer GUI or the volume command (see surface and mesh options) 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 Apr 29, 2009, at 4:40 AM, Nils Becker wrote: > Hi, > I would like to use chimera for measuring the steric accessibility of > particular atoms in a structure to reactive species in solution. To do > that I had the following idea: > > 1. create a volume map which represents a solid sphere centered on the > atom in question (alternatively, a Gaussian blob), with some chosen > radius. > > 2. mask this sphere using the solvent accessible surface of the > protein > (for example, if the atom is at the surface and the surface is flat, > half of the sphere would be cut away) > > 3. measure the volume of the remaining piece of the sphere. > > So now my question is: can this work, and how can I generate the > sphere > in step 1. ? > > thanks for any advice! > Nils From meng at cgl.ucsf.edu Thu Apr 30 12:25:21 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 30 Apr 2009 12:25:21 -0700 Subject: [Chimera-users] pivot point In-Reply-To: <49F9ACFA0200000900296547@gwmta2.upstate.edu> References: <49F9ACFA0200000900296547@gwmta2.upstate.edu> Message-ID: <6ED559C7-DEA5-4908-B72F-CB0EEF3633CC@cgl.ucsf.edu> On Apr 30, 2009, at 10:51 AM, Tatyana Fedotova wrote: > Dear Mrs. Meng, > I have a question about pivot point. > Could you explain howfor example I can rotate part of a helix from a > chosen pivot point. > I fount how I can selet and move atoms. But that's not what I need. > Thanks, > Tanya Dear Tanya, I can think of two ways to move only part of a structure rather than a whole model: (a) by rotating bonds, see Adjust Torsions, where the bonds define the pivots (b) with Movement Mouse Mode, which is probably what you were talking about Although method (b) does not include control over the center of rotation (pivot point), you can set the center of rotation before using that tool. You can set the center of rotation to an atom or centroid of a set of atoms by selecting the atom(s) and using "Actions... Set Pivot" in the menu. Or, you can use the "cofr" command to do the same thing, or if you have a fairly recent version of Chimera (1.4, so a daily build), specify particular X,Y,Z coordinates as the center. The center of rotation set as described above also applies when you are rotating whole models. In newer versions of Chimera (1.4), the rotation commands "roll" and "turn" also allow specifying the center to use when executing that command. Please send Chimera questions to chimera-users at cgl.ucsf.edu rather than my personal address, unless you are describing private data. Even though I answer a lot of those messages, I might be sick, or on vacation, or not know the answer! Best, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html From meng at cgl.ucsf.edu Thu Apr 30 14:49:16 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 30 Apr 2009 14:49:16 -0700 Subject: [Chimera-users] Merging models In-Reply-To: <08EE7A4D7809E2419AB6AFEC92F84DE004A09A44@MAIL21.student.main.ntu.edu.sg> References: <08EE7A4D7809E2419AB6AFEC92F84DE004A09A44@MAIL21.student.main.ntu.edu.sg> Message-ID: On Apr 30, 2009, at 1:45 PM, #MAZIAR SOLEYMANI ARDEJANI# wrote: > Hi everybody, > > I'm working with a pdb file (http://www.rcsb.org/pdb/files/2vxi.pdb1.gz > ) made of two models. I need to merge this two models into one. How > can I do that? > > Thanks in advance, > > Maziar S. Ardejani > Lab 9, The Orner Lab > Division of Chemistry and Biological Chemistry > School of Physical and Mathematical Sciences > 21 Nanyang Link > Nanyang Technological University > Singapore 637371 > Hi Maziar, In general, you can merge models with the "copy/combine" button on the right side of the Model Panel (Favorites... Model Panel) or with the "combine" command. However, I opened 2vxi from the PDB and it is only one model, not two. Maybe you opened it two times by mistake? There are a few cases where structures have so many atoms or chains that the PDB has split them into multiple files (e.g. 3bz1 and 3bz2). If those parts collectively have more than 63 chains it won't work to merge them with Chimera because there are only 63 possible different chain ID symbols. Please send Chimera questions to chimera-users at cgl.ucsf.edu and not to me directly, and if possible use an informative "subject" line - thanks! I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html From meng at cgl.ucsf.edu Thu Apr 30 14:55:05 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 30 Apr 2009 14:55:05 -0700 Subject: [Chimera-users] Merging models In-Reply-To: References: <08EE7A4D7809E2419AB6AFEC92F84DE004A09A44@MAIL21.student.main.ntu.edu.sg> Message-ID: <61906BE0-1334-4B7E-B3E2-2B04020A81D9@cgl.ucsf.edu> Hi Maziar, Oh, now I see that your file is different than just getting entry 2vxi from the PDB, sorry I misunderstood. To merge the models, it should work to use one of the methods described in my previous message. Best, Elaine ----- Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Apr 30, 2009, at 2:49 PM, Elaine Meng wrote: > > On Apr 30, 2009, at 1:45 PM, #MAZIAR SOLEYMANI ARDEJANI# wrote: > >> Hi everybody, >> >> I'm working with a pdb file (http://www.rcsb.org/pdb/files/2vxi.pdb1.gz >> ) made of two models. I need to merge this two models into one. How >> can I do that? >> >> Thanks in advance, >> >> Maziar S. Ardejani >> Lab 9, The Orner Lab >> Division of Chemistry and Biological Chemistry >> School of Physical and Mathematical Sciences >> 21 Nanyang Link >> Nanyang Technological University >> Singapore 637371 >> > > Hi Maziar, > In general, you can merge models with the "copy/combine" button on the > right side of the Model Panel (Favorites... Model Panel) or with the > "combine" command. > > > > However, I opened 2vxi from the PDB and it is only one model, not > two. Maybe you opened it two times by mistake? > > > There are a few cases where structures have so many atoms or chains > that the PDB has split them into multiple files (e.g. 3bz1 and 3bz2). > If those parts collectively have more than 63 chains it won't work to > merge them with Chimera because there are only 63 possible different > chain ID symbols. > > Please send Chimera questions to chimera-users at cgl.ucsf.edu and not to > me directly, and if possible use an informative "subject" line - > thanks! > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > http://www.cgl.ucsf.edu/home/meng/index.html > > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users