From huy.bui at mol.biol.ethz.ch Sun Feb 1 13:55:11 2009 From: huy.bui at mol.biol.ethz.ch (Bui Khanh Huy) Date: Sun, 1 Feb 2009 22:55:11 +0100 Subject: [Chimera-users] roll command: Message-ID: <7B0340B3488BF24DAEB8C70665C6B05806B90B@EX4.d.ethz.ch> Dear all, I tried the roll command with my model (EM map) open: roll z 30 1 center 50,50,50 Chimera showed msg "wait_frames argument not implemented". Just wonder how to implement that command without the error? Huy From meng at cgl.ucsf.edu Sun Feb 1 18:33:19 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Sun, 1 Feb 2009 18:33:19 -0800 Subject: [Chimera-users] roll command: In-Reply-To: <7B0340B3488BF24DAEB8C70665C6B05806B90B@EX4.d.ethz.ch> References: <7B0340B3488BF24DAEB8C70665C6B05806B90B@EX4.d.ethz.ch> Message-ID: <400E4CFF-8910-4300-8E64-D7DC6662CBD0@cgl.ucsf.edu> Dear Huy, When you report a problem, it is helpful to say what version of Chimera you are using. Probably you are looking at documentation that is newer than your version of Chimera. The roll command in your e-mail works fine in recent daily builds (Chimera version 1.4) but not the production release (1.3), because the syntax has changed. You can get a new daily build here: 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 Feb 1, 2009, at 1:55 PM, Bui Khanh Huy wrote: > Dear all, > > I tried the roll command with my model (EM map) open: > > roll z 30 1 center 50,50,50 > > Chimera showed msg "wait_frames argument not implemented". > > Just wonder how to implement that command without the error? > > Huy > From meng at cgl.ucsf.edu Mon Feb 2 10:28:32 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 2 Feb 2009 10:28:32 -0800 Subject: [Chimera-users] Question reagrding potential energy value In-Reply-To: References: <2F7FB66E9CAC6C46AF2A2C412D50DEB707880E11@NIHCESMLBX4.nih.gov> Message-ID: <9B1A3439-59D0-43FF-BE26-16688FBA7472@cgl.ucsf.edu> Dear Marie, I believe the units are kcal/mol and higher is less favorable. However, for several reasons, these values CANNOT be used to compare the stabilities of a wild-type and mutant protein: - each is only for a local minimum conformation, not the global minimum - they are not free energies, which would include entropic effects - they are only comparisons of the folded state and do not include the relative stabilities in the unfolded state - presumably the structures are not solvated To make statements about the relative stabilities of the proteins, you would need to do much more sophisticated calculations (not available in Chimera) such as free energy perturbation or thermodynamic integration to calculate values along the relevant legs of the free energy cycle. It is beyond the scope of this mailing list to explain further! There should be many descriptions of such approaches in the literature, textbooks, and software manuals (AMBER, GROMOS, ...). The "minimize structure" tool is intended only to clean up local strains and conflicts in the structures, not to provide relative stabilities. 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 Feb 2, 2009, at 10:08 AM, Pancera, Marie (NIH/VRC) [E] wrote: > Hello, > I am using the minimize structure tool under structure editing. > I am using this tool because I would like to compare energies for a > WT and a mutant structure (point mutant). > I am getting potential energy value in the reply log. > I wanted to check with you is there is a unit that I can use for > that potential energy. > I also would like to know if this means that the higher potential > energy value means that the protein is less stable. > Foe example, the potential energy for the WT is: 3132.577437 > The potential energy for the mutant is: 2858.355152 > So that means that the mutant protein has a lower energy and is more > stable, right? > Thanks you, > Marie > From mpancera at mail.nih.gov Mon Feb 2 10:08:47 2009 From: mpancera at mail.nih.gov (Pancera, Marie (NIH/VRC) [E]) Date: Mon, 2 Feb 2009 13:08:47 -0500 Subject: [Chimera-users] Question reagrding potential energy value In-Reply-To: References: <2F7FB66E9CAC6C46AF2A2C412D50DEB707880E11@NIHCESMLBX4.nih.gov> Message-ID: Hello, I am using the minimize structure tool under structure editing. I am using this tool because I would like to compare energies for a WT and a mutant structure (point mutant). I am getting potential energy value in the reply log. I wanted to check with you is there is a unit that I can use for that potential energy. I also would like to know if this means that the higher potential energy value means that the protein is less stable. Foe example, the potential energy for the WT is: 3132.577437 The potential energy for the mutant is: 2858.355152 So that means that the mutant protein has a lower energy and is more stable, right? Thanks you, Marie From a.pushpanath at mail.cryst.bbk.ac.uk Wed Feb 4 02:55:52 2009 From: a.pushpanath at mail.cryst.bbk.ac.uk (Ahir Utsav Pushpanath) Date: Wed, 04 Feb 2009 10:55:52 +0000 Subject: [Chimera-users] Is it possible? Message-ID: <49897438.70207@mail.cryst.bbk.ac.uk> Hello Dear Sir/Madam, I am very fond of chimera, and everytime I have looked at scripts for doign things, I find that chimera has them already inbuilt as features. There is one particular problem that I am sure chimera has the capability of doing but I am struggling to do it. 1) I want to use structural superposition servers such as Mammoth etc to produce a structural alignment of two proteins, 2nadA and 1ybaB. However, some of these servers do not produce a sequence alignment output in a format compatible with chimera (i.e such as .aln or aligned fasta). But they do produce a .pdb file showing the superposition. 2) If I load the .pdb onto chimera, sometimes in "model list" window, i see the two proteins, wheras in others I only see 1 model(yet there is clearly 2 models there) 3) I was wondering whether you can load the superposition onto chimera, and see the sequence alignment that gives rise to that structural superposition, so that I may save it as a .aln format using multialign viewer. How do I do this? Apologies if this is a very straightforward scenario. Thanks Ahir From meng at cgl.ucsf.edu Wed Feb 4 09:59:56 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 4 Feb 2009 09:59:56 -0800 Subject: [Chimera-users] Is it possible? In-Reply-To: <49897438.70207@mail.cryst.bbk.ac.uk> References: <49897438.70207@mail.cryst.bbk.ac.uk> Message-ID: Dear Ahir, We're glad you like Chimera! Your question is reasonable but there isn't a simple answer. First I'll explain how the superimposed structures are interpreted by Chimera, and then talk about the sequence alignment part. How the structures are handled in Chimera depends on the format of the PDB file created by the superposition server: (a) Some servers separate the structures with MODEL and ENDMDL lines, and this makes each one a separate model with separate listing in the Chimera Model Panel. This is more convenient than the other possibilities. (b) Some servers put the structures into one model but give them separate chain IDs, for example making one structure chain A and the other chain B. You can still separately control them in Chimera, but not as easily as separate models. (c) Some servers create incorrect PDB that have duplicate atom and residue numbers without using MODEL/ENDMDL or different chain IDs. These will display in Chimera, but it is very difficult to do anything else because you cannot uniquely specify the atoms or residues. I list several superposition servers and discuss their outputs in this page: If the server does not output a sequence alignment, it is not possible to back-calculate from the superposition that exact sequence alignment. Why? Because different sequence alignments (with different numbers of paired residues) can give essentially the same superposition, and we do not know the details of the fitting procedure used by the server: whether alpha-carbons or all backbone atoms were fitted, iteration cutoffs that could weight certain positions in the alignment more heavily than others, etc. That said, however, you can use the "Match->Align" tool in Chimera (under Tools... Structure Comparison) to create a sequence alignment consistent with your structural superposition. It uses CA-CA distances and a user-specified cutoff for how far apart the residues can be in space, yet end up in the same column of the output sequence alignment. If the server does give a sequence alignment but not in a standard format, you could manually edit it (not pleasant, but often required in bioinformatics!). Previously the Mammoth server allowed downloading the sequence alignment in a convenient format, but I see it has moved to a different URL and behaves differently now. You could try contacting the authors and see if they are willing to include the sequence alignment in the outputs. Finally, you may want to try Chimera's superposition tool: "MatchMaker" (under Tools... Structure Comparison) or command "matchmaker": These Chimera tools are also used in the "Superpositions and Alignments" tutorial: 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 Feb 4, 2009, at 2:55 AM, Ahir Utsav Pushpanath wrote: > Hello Dear Sir/Madam, > I am very fond of chimera, and everytime I have > looked at scripts for doign things, I find that chimera has them > already > inbuilt as features. There is one particular problem that I am sure > chimera has the capability of doing but I am struggling to do it. > > 1) I want to use structural superposition servers such as Mammoth > etc to > produce a structural alignment of two proteins, 2nadA and 1ybaB. > However, some of these servers do not produce a sequence alignment > output in a format compatible with chimera (i.e such as .aln or > aligned > fasta). But they do produce a .pdb file showing the superposition. > > 2) If I load the .pdb onto chimera, sometimes in "model list" > window, i > see the two proteins, wheras in others I only see 1 model(yet there is > clearly 2 models there) > > 3) I was wondering whether you can load the superposition onto > chimera, > and see the sequence alignment that gives rise to that structural > superposition, so that I may save it as a .aln format using multialign > viewer. How do I do this? > > Apologies if this is a very straightforward scenario. > > Thanks > Ahir > _______________________________________________ > 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 Feb 4 11:05:53 2009 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 4 Feb 2009 11:05:53 -0800 Subject: [Chimera-users] [chimera-dev] alias menu In-Reply-To: <874055BA140585479966DE1694AB0421F058B5@EX6.d.ethz.ch> References: <874055BA140585479966DE1694AB0421F058B5@EX6.d.ethz.ch> Message-ID: On Feb 4, 2009, at 5:09 AM, Richmond Timothy J. wrote: > Dear Chimera Developers, > > Perhaps I have missed it, but I would find a menu for selected > aliases very useful. Having returned to Chimera from PyMol recently, > it would be great to have an option for the alias command that > allowed the particular alias to be listed in a separate window and > ran the alias by clicking on the alias name listed there. > > Best regards, > > Tim Hi Tim, As Elaine pointed out in her reply, aliases are frequently used as shorthands for long atom specs rather than as replacements for complete commands. However, the form of the alias command that uses '^' (so that matching only occurs at the start of the line) typically is used to define full command aliases. So my thinking is this: aliases defined with the '^' character would be placed in an 'Aliases' top-level menu (created on the fly as needed). Such aliases would automatically be remembered across Chimera invocations (and populate an Aliases menu). The menu could be torn-off (except on Aqua) to make a stand-alone window. Those aliases could be deleted as normal with the ~alias command (which would remove them from the menu and no longer remember then in subsequent Chimeras). Would this be good enough? --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From richmond at mol.biol.ethz.ch Wed Feb 4 13:29:01 2009 From: richmond at mol.biol.ethz.ch (Richmond Timothy J.) Date: Wed, 4 Feb 2009 22:29:01 +0100 Subject: [Chimera-users] [chimera-dev] alias menu In-Reply-To: References: <874055BA140585479966DE1694AB0421F058B5@EX6.d.ethz.ch> Message-ID: <874055BA140585479966DE1694AB0421F058D5@EX6.d.ethz.ch> Hi Eric, This sounds great. I use aliases which are not commands also of course. That's why I suggested a setable flag as an option in the alias command to indicate that "this" alias is a command and should go to the menu. As I haven't needed '^' yet, using it as you suggest would work for me. Here is an example for highlighting a particular protein mutant (we have many mutants we use for mapping. Some give positive results, some don't). General for all positive mutants: alias pos_map_HSS color white $1; represent stick $1; setattr m stickScale 3 $1; color blue $1 at n=; color red $1 at o=; color green $1 at s=; ribcol c_HSS $1; Specific mutant: alias HSS_987N #0:987.B Highlight the mutant: pos_map_HSS HSS_987N New alias for new menu: alias ^pos_HSS_987N pos_map_HSS HSS_987N There can also be a paired alias to turn off the highlighting. Now I can do all on or all off by typing, but having the menu with all the individual mutants listed would be highly desirable. Tim From: Eric Pettersen [mailto:pett at cgl.ucsf.edu] Sent: Wednesday, 04 February 2009 20:06 To: Richmond Timothy J. Cc: chimera-dev at cgl.ucsf.edu; chimera-users at cgl.ucsf.edu BB Subject: Re: [chimera-dev] alias menu On Feb 4, 2009, at 5:09 AM, Richmond Timothy J. wrote: Dear Chimera Developers, Perhaps I have missed it, but I would find a menu for selected aliases very useful. Having returned to Chimera from PyMol recently, it would be great to have an option for the alias command that allowed the particular alias to be listed in a separate window and ran the alias by clicking on the alias name listed there. Best regards, Tim Hi Tim, As Elaine pointed out in her reply, aliases are frequently used as shorthands for long atom specs rather than as replacements for complete commands. However, the form of the alias command that uses '^' (so that matching only occurs at the start of the line) typically is used to define full command aliases. So my thinking is this: aliases defined with the '^' character would be placed in an 'Aliases' top-level menu (created on the fly as needed). Such aliases would automatically be remembered across Chimera invocations (and populate an Aliases menu). The menu could be torn-off (except on Aqua) to make a stand-alone window. Those aliases could be deleted as normal with the ~alias command (which would remove them from the menu and no longer remember then in subsequent Chimeras). Would this be good enough? --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From jsu at caltech.edu Thu Feb 5 07:52:40 2009 From: jsu at caltech.edu (Julius Su) Date: Thu, 05 Feb 2009 10:52:40 -0500 Subject: [Chimera-users] script command for writing out areaSAS attribute? Message-ID: <498B0B48.1010002@caltech.edu> Hello, Does anyone know what script command could be used to output an "attribute assignment file" in Chimera, specifically for the areaSAS attribute? I am trying to show how the solvent accessible surface area on various residues changes over the frames of a multitrajectory PDB file. To do this I am trying to write a small script in "MD movie" that computes the solvent accessible surface for each frame, then outputs the areaSAS values. I was previously able to do this by loading in all the PDB geometries at once, then using the "Render attributes by ..." dialog, but this method does not scale well to very large proteins (the program runs out of memory trying to compute all the surfaces at once). Thus I am trying to do this task sequentially with a script. Thanks much! Julius From pett at cgl.ucsf.edu Thu Feb 5 11:20:40 2009 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Thu, 5 Feb 2009 11:20:40 -0800 Subject: [Chimera-users] script command for writing out areaSAS attribute? In-Reply-To: <498B0B48.1010002@caltech.edu> References: <498B0B48.1010002@caltech.edu> Message-ID: Hi Julius, There is no command equivalent for that part of Render By Attribute unfortunately. I've put making a command equivalent on a to-do list. So you will have to resort to the Python part of the per-frame scripting dialog. I've attached a Python file that goes through currently open molecules and writes out the areaSAS attribute of residues into files named /var/tmp/sasNNN where NNN is 001 for frame 1, 002 for frame 2, etc. You will of course have to have added a surface. You can use the "Insert text file..." button of the per- frame dialog to directly enter the script from the file. If you know Python, the script is pretty straightforward. The only tricky part is right at the beginning where it calls checkForChanges(). This allows the surface-computation code to immediately notice that the structure coordinates have changed and recompute the surface. Otherwise, the surface-computation code wouldn't get that notification until after the per-frame script had run, so the surface areas we print out would always be off by one frame. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Feb 5, 2009, at 7:52 AM, Julius Su wrote: > Hello, > > Does anyone know what script command could be used to output an > "attribute assignment file" in Chimera, specifically for the areaSAS > attribute? > > I am trying to show how the solvent accessible surface area on > various > residues changes over the frames of a multitrajectory PDB file. To do > this I am trying to write a small script in "MD movie" that computes > the > solvent accessible surface for each frame, then outputs the areaSAS > values. > > I was previously able to do this by loading in all the PDB geometries > at once, then using the "Render attributes by ..." dialog, but this > method does not scale well to very large proteins (the program runs > out > of memory trying to compute all the surfaces at once). Thus I am > trying > to do this task sequentially with a script. > > Thanks much! > > Julius > _______________________________________________ > 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: -------------- next part -------------- A non-text attachment was scrubbed... Name: writeAttr.py Type: text/x-python-script Size: 323 bytes Desc: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From pett at cgl.ucsf.edu Thu Feb 5 17:06:49 2009 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Thu, 5 Feb 2009 17:06:49 -0800 Subject: [Chimera-users] [chimera-dev] alias menu In-Reply-To: <874055BA140585479966DE1694AB0421F058D5@EX6.d.ethz.ch> References: <874055BA140585479966DE1694AB0421F058B5@EX6.d.ethz.ch> <874055BA140585479966DE1694AB0421F058D5@EX6.d.ethz.ch> Message-ID: <46819635-A291-4487-ABE0-19D27BFE36AF@cgl.ucsf.edu> Hi Tim, Though this is an excellent idea, it is competing with a lot of other projects I'm already working on. It might make it into our next release (middle of this year) but the following release is more likely. I'm going to open a feature-request for this in our Trac database, with you on the recipient list so that you will get mail when it gets done. --Eric On Feb 4, 2009, at 1:29 PM, Richmond Timothy J. wrote: > Hi Eric, > > This sounds great. I use aliases which are not commands also of > course. That?s why I suggested a setable flag as an option in the > alias command to indicate that ?this? alias is a command and should > go to the menu. As I haven?t needed ?^? yet, using it as you suggest > would work for me. > > Here is an example for highlighting a particular protein mutant (we > have many mutants we use for mapping. Some give positive results, > some don?t). > > General for all positive mutants: > alias pos_map_HSS color white $1; represent stick $1; setattr m > stickScale 3 $1; color blue $1 at n=; color red $1 at o=; color green > $1 at s=; ribcol c_HSS $1; > > Specific mutant: > alias HSS_987N #0:987.B > > Highlight the mutant: > pos_map_HSS HSS_987N > > New alias for new menu: > alias ^pos_HSS_987N pos_map_HSS HSS_987N > > There can also be a paired alias to turn off the highlighting. Now I > can do all on or all off by typing, but having the menu with all the > individual mutants listed would be highly desirable. > > Tim > > > > From: Eric Pettersen [mailto:pett at cgl.ucsf.edu] > Sent: Wednesday, 04 February 2009 20:06 > To: Richmond Timothy J. > Cc: chimera-dev at cgl.ucsf.edu; chimera-users at cgl.ucsf.edu BB > Subject: Re: [chimera-dev] alias menu > > On Feb 4, 2009, at 5:09 AM, Richmond Timothy J. wrote: > > > Dear Chimera Developers, > > Perhaps I have missed it, but I would find a menu for selected > aliases very useful. Having returned to Chimera from PyMol recently, > it would be great to have an option for the alias command that > allowed the particular alias to be listed in a separate window and > ran the alias by clicking on the alias name listed there. > > Best regards, > > Tim > > Hi Tim, > As Elaine pointed out in her reply, aliases are > frequently used as shorthands for long atom specs rather than as > replacements for complete commands. However, the form of the alias > command that uses '^' (so that matching only occurs at the start of > the line) typically is used to define full command aliases. > > So my thinking is this: aliases defined with the '^' > character would be placed in an 'Aliases' top-level menu (created on > the fly as needed). Such aliases would automatically be remembered > across Chimera invocations (and populate an Aliases menu). The menu > could be torn-off (except on Aqua) to make a stand-alone window. > Those aliases could be deleted as normal with the ~alias command > (which would remove them from the menu and no longer remember then > in subsequent Chimeras). > > Would this be good enough? > > --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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From kerenl at salilab.org Fri Feb 6 01:32:17 2009 From: kerenl at salilab.org (Keren Lasker) Date: Fri, 6 Feb 2009 01:32:17 -0800 Subject: [Chimera-users] making movies with CMM files Message-ID: <861842E9-4F9A-470E-B6EB-EA9033B46E80@salilab.org> hello, Is there a way to generate a movie out of a set of CMM files ( similar to MD Movie with PDB files)? thank you very much, Keren. From goddard at cgl.ucsf.edu Fri Feb 6 05:11:24 2009 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Fri, 06 Feb 2009 05:11:24 -0800 Subject: [Chimera-users] making movies with CMM files In-Reply-To: <861842E9-4F9A-470E-B6EB-EA9033B46E80@salilab.org> References: <861842E9-4F9A-470E-B6EB-EA9033B46E80@salilab.org> Message-ID: <498C36FC.4000106@cgl.ucsf.edu> Hi Keren, Only the MD Movie tool knows how to play through a series of models for an animation. I tried writing several Chimera marker models to a single PDB file (File / Save PDB...) and playing it with MD Movie but it flopped. Markers did not get connected properly and sizes and colors were lost. That leaves me with ~disp ; disp #1 ~disp ; disp #2 .... ~disp ; disp #25 as a means to flip through the Chimera marker models. Could save this in a *.cmd file and open it in Chimera. Could use some Python code instead for more flexibility: from chimera import runCommand as r for i in range(1,26): r('~disp ; disp #%d' % i) that would go in a *.py file that you would open (possibly with the open command). The movie making capabilities of Chimera are very limited. Tom Keren Lasker wrote: > hello, > > Is there a way to generate a movie out of a set of CMM files ( similar > to MD Movie with PDB files)? > > thank you very much, > Keren. > _______________________________________________ > 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 Fri Feb 6 11:00:06 2009 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Fri, 6 Feb 2009 11:00:06 -0800 Subject: [Chimera-users] making movies with CMM files In-Reply-To: <498C36FC.4000106@cgl.ucsf.edu> References: <861842E9-4F9A-470E-B6EB-EA9033B46E80@salilab.org> <498C36FC.4000106@cgl.ucsf.edu> Message-ID: <113B2380-3F1C-4A77-8ED2-7EDFD7824785@cgl.ucsf.edu> On Feb 6, 2009, at 5:11 AM, Tom Goddard wrote: > Hi Keren, > > Only the MD Movie tool knows how to play through a series of models > for an animation. I tried writing several Chimera marker models to a > single PDB file (File / Save PDB...) and playing it with MD Movie > but it > flopped. Markers did not get connected properly and sizes and colors > were lost. MD Movie plays trajectories, which results in the implicit assumption that the atoms and bonds don't change between frames (which also allows for much less memory use). So it is naturally not going to work for a series of marker sets where presumably the atoms (markers) and bonds (connections) vary each frame. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From bala.biophysics at gmail.com Wed Feb 11 08:25:39 2009 From: bala.biophysics at gmail.com (Bala subramanian) Date: Wed, 11 Feb 2009 17:25:39 +0100 Subject: [Chimera-users] examples of python scripts Message-ID: <288df32a0902110825v3562ebf6q9dcc703a53e7770@mail.gmail.com> Dear Chimerians, Can someone help me by providing examples of python scripts written for analyzing structures inside chimera. I have seen the chimera programmers guide but i need some more scripts written for different tasks to understand the way of accessing certain residues or atoms in a structure and extracting its attributes etc. Cheers, Bala -------------- next part -------------- An HTML attachment was scrubbed... URL: From bzuber at mrc-lmb.cam.ac.uk Wed Feb 11 08:53:08 2009 From: bzuber at mrc-lmb.cam.ac.uk (Benoit Zuber) Date: Wed, 11 Feb 2009 16:53:08 +0000 Subject: [Chimera-users] maps handling Message-ID: <49930274.5010403@mrc-lmb.cam.ac.uk> Hi, I want to handle a large number of small density maps (around 1000 maps of approx 50x50x50 pixels). I need to group them (in around 5 groups). Then I need to treat all the maps of each group in a certain way. For example, I would like to change the level threshold for display, or the display style for every maps in a group at once. Also I would like to show or hide all maps of a group at once. The maps are not opened in an order related to their group. I remember someone recently suggested model 'folders' as a new functionality. Has this been incorporated in the latest versions of chimera? Even if it is the case, It would be too tedious to have to click on each individual model to assign it to a group. Similarly a simple command passed at the command line wouldn't be very elegant: I would have to write each volume number since they are unsorted. I suppose a python script would be much more appropriate. The script would have some functions to do tasks like those described above on each members of a group and a function to read group composition from a text file. I looked in chimera's programmer guide for a section on volume handling but I couldn't find much material on that. Did I miss it? What approach would you recommend? I guess I could use runCommand() but there are maybe better ways. Also the script would have to run in interactive mode. I suppose that IDLE would work for that purpose. How should I do that? Open IDLE and import my module? Where can you define the paths that chimera uses to look for packages? Thanks in advance! 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 goddard at cgl.ucsf.edu Wed Feb 11 09:09:31 2009 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Wed, 11 Feb 2009 09:09:31 -0800 Subject: [Chimera-users] maps handling In-Reply-To: <49930274.5010403@mrc-lmb.cam.ac.uk> References: <49930274.5010403@mrc-lmb.cam.ac.uk> Message-ID: <4993064B.1090406@cgl.ucsf.edu> Hi Ben, You can make these groupings with the alias command and operate on all maps in a group with the volume command. Here's an example setting the contour level of 5 maps and mesh display style. alias g1 #1,2,17,25,33 volume g1 level 0.5 style mesh You will probably want to ut the alias commands giving the model id numbers of the 5 groups in a command file (.cmd suffix) and then just open that file in Chimera (e.g. "open galiases.cmd"). Here's documentation for the commands. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html Model "folders" have not been implemented. The programmer's guide has little useful information except for the examples section. The rest is auto-generated from scant code comments. There is not a volume example, though there have been many volume scripts posted to the mailing list. Can't think of any easy way to find those though -- maybe search the archives for the word python. I intend to make a web page of Chimera scripts some day. The usual method of running Python scripts in Chimera is to write them in a text editor to a file and open that file in Chimera with File / Open or the open command. Tom Benoit Zuber wrote: > Hi, > > I want to handle a large number of small density maps (around 1000 maps > of approx 50x50x50 pixels). > I need to group them (in around 5 groups). Then I need to treat all the > maps of each group in a certain way. For example, I would like to change > the level threshold for display, or the display style for every maps in > a group at once. Also I would like to show or hide all maps of a group > at once. > > The maps are not opened in an order related to their group. > > I remember someone recently suggested model 'folders' as a new > functionality. Has this been incorporated in the latest versions of chimera? > Even if it is the case, It would be too tedious to have to click on each > individual model to assign it to a group. Similarly a simple command > passed at the command line wouldn't be very elegant: I would have to > write each volume number since they are unsorted. > > I suppose a python script would be much more appropriate. The script > would have some functions to do tasks like those described above on each > members of a group and a function to read group composition from a text > file. > > I looked in chimera's programmer guide for a section on volume handling > but I couldn't find much material on that. Did I miss it? What approach > would you recommend? I guess I could use runCommand() but there are > maybe better ways. > Also the script would have to run in interactive mode. I suppose that > IDLE would work for that purpose. How should I do that? Open IDLE and > import my module? Where can you define the paths that chimera uses to > look for packages? > > Thanks in advance! > Ben > > From pett at cgl.ucsf.edu Wed Feb 11 11:00:00 2009 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Wed, 11 Feb 2009 11:00:00 -0800 Subject: [Chimera-users] examples of python scripts In-Reply-To: <288df32a0902110825v3562ebf6q9dcc703a53e7770@mail.gmail.com> References: <288df32a0902110825v3562ebf6q9dcc703a53e7770@mail.gmail.com> Message-ID: Hi Bala, I've attached 5 scripts I've written over the last few months. Their functions are: 1) show anisotropic ellipsoids on selected atoms 2) print cis peptides to reply log 3) measure atom distance or atom-atom angle to a plane 4) drive the chi angles of a selected residue in 10 degree increments and write the clashes to files 5) measure the minimum distance of single-character chain residues (i.e. no het, water) to a selection (typically a ligand) Which ones are which should be obvious from the file names I think. --Eric On Feb 11, 2009, at 8:25 AM, Bala subramanian wrote: > Dear Chimerians, > > Can someone help me by providing examples of python scripts written > for analyzing structures inside chimera. I have seen the chimera > programmers guide but i need some more scripts written for different > tasks to understand the way of accessing certain residues or atoms > in a structure and extracting its attributes etc. > > Cheers, > Bala -------------- next part -------------- A non-text attachment was scrubbed... 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Name: minResDist.py Type: text/x-python-script Size: 434 bytes Desc: not available URL: From bzuber at mrc-lmb.cam.ac.uk Wed Feb 11 11:55:40 2009 From: bzuber at mrc-lmb.cam.ac.uk (=?iso-8859-1?Q?Beno=EEt_Zuber?=) Date: Wed, 11 Feb 2009 19:55:40 -0000 (UTC) Subject: [Chimera-users] maps handling In-Reply-To: <4993064B.1090406@cgl.ucsf.edu> References: <49930274.5010403@mrc-lmb.cam.ac.uk> <4993064B.1090406@cgl.ucsf.edu> Message-ID: <35824.84.69.214.254.1234382140.squirrel@mail.mrc-lmb.cam.ac.uk> Hi Tom, Thank you very much for all the tips! It sounds very straightforward. I'll try it tomorrow. Ben > Hi Ben, > > You can make these groupings with the alias command and operate on all > maps in a group with the volume command. Here's an example setting the > contour level of 5 maps and mesh display style. > > alias g1 #1,2,17,25,33 > volume g1 level 0.5 style mesh > > You will probably want to ut the alias commands giving the model id > numbers of the 5 groups in a command file (.cmd suffix) and then just > open that file in Chimera (e.g. "open galiases.cmd"). > > Here's documentation for the commands. > > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html > > http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html > > Model "folders" have not been implemented. > > The programmer's guide has little useful information except for the > examples section. The rest is auto-generated from scant code comments. > There is not a volume example, though there have been many volume > scripts posted to the mailing list. Can't think of any easy way to find > those though -- maybe search the archives for the word python. I intend > to make a web page of Chimera scripts some day. The usual method of > running Python scripts in Chimera is to write them in a text editor to a > file and open that file in Chimera with File / Open or the open command. > > Tom > > > Benoit Zuber wrote: >> Hi, >> >> I want to handle a large number of small density maps (around 1000 maps >> of approx 50x50x50 pixels). >> I need to group them (in around 5 groups). Then I need to treat all the >> maps of each group in a certain way. For example, I would like to change >> the level threshold for display, or the display style for every maps in >> a group at once. Also I would like to show or hide all maps of a group >> at once. >> >> The maps are not opened in an order related to their group. >> >> I remember someone recently suggested model 'folders' as a new >> functionality. Has this been incorporated in the latest versions of >> chimera? >> Even if it is the case, It would be too tedious to have to click on each >> individual model to assign it to a group. Similarly a simple command >> passed at the command line wouldn't be very elegant: I would have to >> write each volume number since they are unsorted. >> >> I suppose a python script would be much more appropriate. The script >> would have some functions to do tasks like those described above on each >> members of a group and a function to read group composition from a text >> file. >> >> I looked in chimera's programmer guide for a section on volume handling >> but I couldn't find much material on that. Did I miss it? What approach >> would you recommend? I guess I could use runCommand() but there are >> maybe better ways. >> Also the script would have to run in interactive mode. I suppose that >> IDLE would work for that purpose. How should I do that? Open IDLE and >> import my module? Where can you define the paths that chimera uses to >> look for packages? >> >> Thanks in advance! >> Ben >> >> > From meng at cgl.ucsf.edu Wed Feb 11 15:35:51 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 11 Feb 2009 15:35:51 -0800 Subject: [Chimera-users] Command Line - Slecting Zone Parameters In-Reply-To: <781131.22586.qm@web53909.mail.re2.yahoo.com> References: <781131.22586.qm@web53909.mail.re2.yahoo.com> Message-ID: On Feb 11, 2009, at 2:54 PM, Thiruvarangan Ramaraj wrote: > Hi all, > I am trying to find all the atoms that lie within a certain > distance from a selected chains. I am able to do this by going to > select -> zone and giving the distance I want and selecting all the > atoms that met my criteria. I would like to do this on command > line. I am unable to figure it out. > Any help would be greatly appreciated. > Thank You > Thiru Ramaraj Hi Thiru, The following command would select all residues with any atom within 4.5 angstroms of your current selection: select sel z<4.5 You could use "za" instead of "z" if you want an atom-based cutoff instead of whole residues, > instead of < to get the atoms farther away, and of course, a different distance. Also, you don't have to use selections. For example, this would color all atoms within 5 angstroms of chain A red: color red :.a za<5 Description of command-line zone specification: More examples appear in various tutorials: 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 goddard at cgl.ucsf.edu Fri Feb 13 12:53:28 2009 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Fri, 13 Feb 2009 12:53:28 -0800 Subject: [Chimera-users] Animating a C-alpha chain trace In-Reply-To: References: Message-ID: <4995DDC8.4000208@cgl.ucsf.edu> Hi Matt, A Python script can make a chain trace movie with density display that adds one residue at a time. I've attached an example script and movie. I used the today's Chimera daily build that has a nice 1-layer transparency option. That won't work in earlier Chimera versions. Tom Matthew Dougherty wrote: > Hi Tom, > > Over the last couple years I have moved my animation off the > SGI/IrisExplorer to Chimera/Amira. > > I have one piece of code on Explorer that I have not moved; attached > is a typical animation. > > what is being accomplished is a demonstration of the folding of a > protein based on c-alpha backbone and related density. > starting at the first residue, it proceeds by adding one residue at a > time. > > How would you suggest to move this to chimera? > > Matt > > > > > > > > > > > > > > > -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: catrace.py URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 1fav-catrace.mov Type: video/quicktime Size: 541503 bytes Desc: not available URL: From kerenl at salilab.org Sat Feb 14 20:12:13 2009 From: kerenl at salilab.org (Keren Lasker) Date: Sat, 14 Feb 2009 20:12:13 -0800 Subject: [Chimera-users] Volume->Fit in Map question Message-ID: <78E31D46-D8C1-4D7B-A70A-212E8E445624@salilab.org> hello, Is there a way to fit a density map to a pdb rather than a pdb to a density map ? Or in other words, that in the end of the fitting procedure the map would move to best fit the model rather than the other way around. thank you, Keren Lasker. From bshaanan at bgu.ac.il Mon Feb 16 06:20:38 2009 From: bshaanan at bgu.ac.il (Boaz Shaanan) Date: Mon, 16 Feb 2009 14:20:38 GMT Subject: [Chimera-users] Consurf .chimerax file under linux Message-ID: An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: error.log Type: application/octet-stream Size: 488 bytes Desc: not available URL: From meng at cgl.ucsf.edu Mon Feb 16 10:40:21 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 16 Feb 2009 10:40:21 -0800 Subject: [Chimera-users] Chimera 3D labels In-Reply-To: References: Message-ID: On Feb 16, 2009, at 6:53 AM, nettles wrote: > > Dear Elaine, > I'm thinking this should be possible, but don't know how to do it. > Can the labeling function in Chimera could be made more spacially > flexible? > > An example is below. The residue label coordinates are anchored to > a fixed 3D point that may, or may not be desirable for a given > view. Can this be adjusted? > > It looks like these references may be set at centroids. Maybe one > could have a toggle switch that sets the anchor projected a certain > distance from a C-alpha along the viewing vector. That might give > quick access unified text float-over > > Thanks again for such a great tool. > Jim [attachment removed by Elaine] Dear Jim, I am frequently irked by the same issue. Currently residue labels are anchored at the centroid of the displayed atoms, whereas sometimes it would look better if they were anchored at the alpha- carbon. I've previously created a bug report about this. Longer term we would also like them to be movable with the mouse, but that also can't be done currently. Here is the bug/request tracking info: http://socrates2.cgl.ucsf.edu/trac/chimera/ticket/6866 http://socrates2.cgl.ucsf.edu/trac/chimera/ticket/167 One current workaround is that you can label some particular atom in the residue with residue information. However, currently that atom must be explicitly displayed (won't work to label some backbone atom if ribbon is shown and suppresses that atom... which I've also complained about!). Commands to do that: labelopt info residue la @ca [or if ribbon is shown, "la @cb" instead if you can live without the glycine residue labels] 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 Mon Feb 16 10:51:07 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 16 Feb 2009 10:51:07 -0800 Subject: [Chimera-users] Consurf .chimerax file under linux In-Reply-To: References: Message-ID: <9DFED232-1107-4C0C-B8EE-3A5066E314A8@cgl.ucsf.edu> Dear Boaz, We're glad you like the ConSurf/Chimera setup! The error log you sent says this: trying to import std_webdata Error reading /home/boaz/data/esrf_nov04/esrf_gcl3/consurf/ pdb2pan_isd.chimerax: Couldn't find url 'http://consurf.tau.ac.il/results/1234779578/ isd_pdb2pan_view_ConSurf.pdb': Received HTTP error 404 ('Not Found') trying to import std_webdata Error reading /home/boaz/data/esrf_nov04/esrf_gcl3/consurf/ consurf_1234779578.chimerax: Couldn't find url 'http://consurf.tau.ac.il/results/1234779578/ pdb2pan_view_ConSurf.pdb': Received HTTP error 404 ('Not Found') which I can only interpret as some problem finding the file at the ConSurf site - maybe there was some error in creating the pdb file, or for some other reason the URL given in the chimerax file (Chimera Web data) from ConSurf is incorrect. You could also try entering those URLs directly into a Web browser on your machine, to make sure it is not related to Chimera. Did you have that chimerax file around for a long time? The ConSurf people must remove the results files periodically from their site. If you want to keep the results yourself long term, I think you have to also download all the files from the URLs given in the chimerax file, and then edit the chimerax file to point to them locally. It sounds like you have successfully viewed ConSurf results in Chimera before, so that is my best guess of what is happening. Regards, 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 Mon Feb 16 11:10:37 2009 From: chiendarret at gmail.com (Francesco Pietra) Date: Mon, 16 Feb 2009 20:10:37 +0100 Subject: [Chimera-users] stereo view Message-ID: Hi: I would greatly appreciate advice about the following requests (between "".."") by the referees (interaction between two proteins; graphics by chimera): 1) "there is way too much wasted black space in figures". As the complex of proteins is elongated along one axis, I found it unavoidable to have wasted space around. Perhaps using a white background in the hope that white is less offending than black? Or is it a way to tailor the background according to the shape of the object? 2) "a stereoview might be helpful for better understanding". How to fulfill this request with chimera I have no idea. 3) "a molecular surface representation of the docking site would be useful". I read on passing about molecular surfaces on this forum. Is that feasible for the highly complex situation of 3D perspective with so many atoms at different "layers"? Thanks indeed for answering francesco pietra From odonnell at chem.fsu.edu Mon Feb 16 14:04:54 2009 From: odonnell at chem.fsu.edu (odonnell at chem.fsu.edu) Date: Mon, 16 Feb 2009 17:04:54 -0500 Subject: [Chimera-users] stereo view In-Reply-To: References: Message-ID: <20090216170454.1odps6s60coo8kkg@webmail.chem.fsu.edu> Hi Francesco, A couple of cents before the professionals respond with (very likely) better ideas: In response to 1) Black is best for contrast but uses a lot of ink and money. White should be fine. n response to 2) If you go to TOOLS=>VIEWING CONTROLS=>CAMERA, you can select various camera modes. CROSS-EYE stereo will put your chimera graphic into cross-eye stereo. You can save an image as it is displayed on the screen. But i find saving two images, stereo left eye and stereo right eye better. Place these side by side in another graphic program, (e.g Adobe illustrator) and voila, stereo viewing. With two single images you can switch them around to alternate between wall-eye and cross-eye. Also, with two images its easier to make the distance between them a certain length, as journals are usually stringent about how the stereo images are displayed. In response to 3)I'd to go TOOLS=>VIEWING CONTROLS=> SIDE VIEW and slide the back and front yellow planes. This will create a slab through your object removing other structural elements which might complicate the image. Also, try DEPTH CUEING under TOOLS=>VIEWING CONTROLS=> EFFECTS. tweak the "start ratio and yon intensity to further remove emphasis on unwanted objects. The Depth effects can make some really neat graphics Hope this helps. -Jason Quoting Francesco Pietra : > Hi: > > I would greatly appreciate advice about the following requests > (between "".."") by the referees (interaction between two proteins; > graphics by chimera): > > 1) "there is way too much wasted black space in figures". > > As the complex of proteins is elongated along one axis, I found it > unavoidable to have wasted space around. Perhaps using a white > background in the hope that white is less offending than black? Or is > it a way to tailor the background according to the shape of the > object? > > 2) "a stereoview might be helpful for better understanding". > > How to fulfill this request with chimera I have no idea. > > 3) "a molecular surface representation of the docking site would be useful". > > I read on passing about molecular surfaces on this forum. Is that > feasible for the highly complex situation of 3D perspective with so > many atoms at different "layers"? > > > Thanks indeed for answering > > francesco pietra > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. From meng at cgl.ucsf.edu Mon Feb 16 16:43:47 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 16 Feb 2009 16:43:47 -0800 Subject: [Chimera-users] stereo view In-Reply-To: <20090216170454.1odps6s60coo8kkg@webmail.chem.fsu.edu> References: <20090216170454.1odps6s60coo8kkg@webmail.chem.fsu.edu> Message-ID: Hi Francesco, All of Jason's suggestions are good (thanks Jason!), and I only wanted to add a few things: (1) while the window will always be a rectangle, you could resize it so that there is a different ratio between height and width. If your long molecule is oriented across, you could resize the window to be less tall so that the width:height ratio is greater. Don't worry if the window is then filling less of your screen -- you can specify as high a resolution as you want in the File... Save Image dialog. Of course, with a given window size, you should scale up your molecule(s) to fill it as much as possible. In agreement with Jason, I think usually a white background is better than black for publication purposes. How to change background color is described near the top of the "Tips on Preparing Images": (2) There is a section on saving stereo images near the bottom of that "Tips on Preparing Images" page (by the way, you can use "Help... Search Documentation" to look for help topics such as "stereo image"). I think journals usually show the "wall-eye" type of stereo, which can be achieved by saving one image in the wall-eye stereo mode, or by saving separate left and right views and placing them side by side with the left-eye view on the left and the right-eye view on the right. (3) just show the surface, adjust clipping and depth-cueing as Jason suggested, and use your artistic and scientific judgement as to whether it improves your image! There are additional suggestions for improving surface appearance in the "Tips on Preparing Images" page. 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 Feb 16, 2009, at 2:04 PM, odonnell at chem.fsu.edu wrote: > Hi Francesco, > A couple of cents before the professionals respond with (very > likely) better ideas: > > In response to 1) Black is best for contrast but uses a lot of ink > and money. > White should be fine. > > n response to 2) If you go to TOOLS=>VIEWING CONTROLS=>CAMERA, you can > select various camera modes. CROSS-EYE stereo will put your chimera > graphic into cross-eye stereo. You can save an image as it is > displayed on the screen. But i find saving two images, stereo left eye > and stereo right eye better. Place these side by side in another > graphic program, (e.g Adobe illustrator) and voila, stereo viewing. > With two single images you can switch them around to alternate between > wall-eye and cross-eye. Also, with two images its easier to make the > distance between them a certain length, as journals are usually > stringent about how the stereo images are displayed. > > In response to 3)I'd to go TOOLS=>VIEWING CONTROLS=> SIDE VIEW and > slide the back and front yellow planes. This will create a slab > through your object removing other structural elements which might > complicate the image. Also, > try DEPTH CUEING under TOOLS=>VIEWING CONTROLS=> EFFECTS. tweak the > "start ratio and yon intensity to further remove emphasis on unwanted > objects. The Depth effects can make some really neat graphics > > Hope this helps. > > -Jason > > Quoting Francesco Pietra : > >> Hi: >> >> I would greatly appreciate advice about the following requests >> (between "".."") by the referees (interaction between two proteins; >> graphics by chimera): >> >> 1) "there is way too much wasted black space in figures". >> >> As the complex of proteins is elongated along one axis, I found it >> unavoidable to have wasted space around. Perhaps using a white >> background in the hope that white is less offending than black? Or is >> it a way to tailor the background according to the shape of the >> object? >> >> 2) "a stereoview might be helpful for better understanding". >> >> How to fulfill this request with chimera I have no idea. >> >> 3) "a molecular surface representation of the docking site would be >> useful". >> >> I read on passing about molecular surfaces on this forum. Is that >> feasible for the highly complex situation of 3D perspective with so >> many atoms at different "layers"? From bala.biophysics at gmail.com Tue Feb 17 02:48:05 2009 From: bala.biophysics at gmail.com (Bala subramanian) Date: Tue, 17 Feb 2009 11:48:05 +0100 Subject: [Chimera-users] configuration file for chimera Message-ID: <288df32a0902170248q46342e01ied5fa0daf9a19480@mail.gmail.com> Dear chimerians, Sorry if this question has been asked before. Where can i fix the default parameters for chimera. I explored the preferences option in favourites menu and set chose some preferences. In addition to that I want to the following like setting the color of carbon atoms as green as default setting the color of hydrogen atoms as white as default setting some macros setting the command line option when the chimera starts up (every time i go to favourites and click command line to invoke it) and other settings something like the configuration file used for vmd (.vmdrc ). Thanks in advance, Bala -------------- next part -------------- An HTML attachment was scrubbed... URL: From sdecarlo at ccny.cuny.edu Tue Feb 17 03:12:24 2009 From: sdecarlo at ccny.cuny.edu (Sacha De Carlo) Date: Tue, 17 Feb 2009 06:12:24 -0500 (EST) Subject: [Chimera-users] configuration file for chimera In-Reply-To: <288df32a0902170248q46342e01ied5fa0daf9a19480@mail.gmail.com> References: <288df32a0902170248q46342e01ied5fa0daf9a19480@mail.gmail.com> Message-ID: <20090217061224.BTD60587@pelican.admin.ccny.cuny.edu> Try Preferences Panel - Restore (button) or even better the Reset button on the left... S. ------------------------------------------ Sacha De Carlo, Asst. Professor Marshak Building Room 1335 The City College of NY (212) 650-6070/6582 E-mail: sdecarlo at ccny.cuny.edu http://www.planetesacha.com/Work.htm ------------------------------------------ From meng at cgl.ucsf.edu Tue Feb 17 09:31:24 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 17 Feb 2009 09:31:24 -0800 Subject: [Chimera-users] configuration file for chimera In-Reply-To: <288df32a0902170248q46342e01ied5fa0daf9a19480@mail.gmail.com> References: <288df32a0902170248q46342e01ied5fa0daf9a19480@mail.gmail.com> Message-ID: <0DF8D665-57C4-4526-9FF8-A691E2126A43@cgl.ucsf.edu> Dear Bala, (1) which tools (Command Line, etc.) automatically start at Chimera startup: use Preferences, Tools category. You can choose "Favorites... Preferences" and then go to the Tools category, or go to it directly by choosing "Tools... Add to Favorites/Toolbar". Either way you will want to check the "Auto Start" column for "Command Line" and any other tools you want to appear at startup. Remember to click Save if you want the settings to apply to later uses of Chimera. (2) initial molecule appearance: use Preferences, New Molecules category. It sounds like you already saw this, and have found that the options there are somewhat limited. There is no way in this dialog to say carbons should be green, for example. However, at least the things you mentioned can be done by combining some of these New Molecules preference settings with a startup command script. In the New Molecules preferences, change "per-atom coloring" to "by element" and click Save. Then make a Chimera command script that defines your various macros (I imagine you could do this with the "alias" command) and changes the carbon element color to green. You specify the name/ location of any startup scripts in Preferences, Command Line category (again remember to click Save). Note that since the script is read at startup, it will not do any good to insert commands that do things to structures such as color carbons green, because there will not be any structures right at startup. Instead you must literally redefine the carbon element-coding color as green with the command: colordef C green I just tried this whole procedure to make sure it works. Each element color is simply named with the element symbol, see The default hydrogen color is already white. I should say that the longer-term goal is to allow people to define their own presets as well as which settings should apply to new molecules -- a more complete and flexible approach than is available currently -- so how one would go about this is expected to change. However, all of the above is how you would do it in today's Chimera. 8-) 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 Feb 17, 2009, at 2:48 AM, Bala subramanian wrote: > Dear chimerians, > > Sorry if this question has been asked before. Where can i fix the > default parameters for chimera. I explored the preferences option in > favourites menu and set chose some preferences. In addition to that > I want to the following like > > setting the color of carbon atoms as green as default > setting the color of hydrogen atoms as white as default > setting some macros > setting the command line option when the chimera starts up (every > time i go to favourites and click command line to invoke it) > and other settings something like the configuration file used for > vmd (.vmdrc ). > > Thanks in advance, > Bala From goddard at cgl.ucsf.edu Tue Feb 17 10:22:49 2009 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Tue, 17 Feb 2009 10:22:49 -0800 Subject: [Chimera-users] Volume->Fit in Map question In-Reply-To: <78E31D46-D8C1-4D7B-A70A-212E8E445624@salilab.org> References: <78E31D46-D8C1-4D7B-A70A-212E8E445624@salilab.org> Message-ID: <499B0079.8010606@cgl.ucsf.edu> Hi Keren, There is not an option to move the map instead of the atomic model when fitting. In what circumstances would that be useful? Tom Keren Lasker wrote: > hello, > > Is there a way to fit a density map to a pdb rather than a pdb to a > density map ? > Or in other words, that in the end of the fitting procedure the map > would move to best fit the model rather than the other way around. > > > thank you, > Keren Lasker. > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > From hu.guiqing at gmail.com Wed Feb 11 14:54:35 2009 From: hu.guiqing at gmail.com (G.-Q. Hu) Date: Wed, 11 Feb 2009 17:54:35 -0500 Subject: [Chimera-users] surface view of large file in chimera Message-ID: <480905dc0902111454m38eb1210v2c7cbe39865e2c72@mail.gmail.com> Hello, I am trying to show a large file by surface view in chimera. But I found that the structure lost the detail and the surface was smoothed. I guess there is a sampling problem for large file. Is there any way to view the large file at the original resolution? Thanks. Guiqing -------------- next part -------------- An HTML attachment was scrubbed... URL: From kerenl at salilab.org Tue Feb 17 11:18:42 2009 From: kerenl at salilab.org (Keren Lasker) Date: Tue, 17 Feb 2009 11:18:42 -0800 Subject: [Chimera-users] Volume->Fit in Map question In-Reply-To: <499B0079.8010606@cgl.ucsf.edu> References: <78E31D46-D8C1-4D7B-A70A-212E8E445624@salilab.org> <499B0079.8010606@cgl.ucsf.edu> Message-ID: thanks Tom. The reason i wanted to do that was that i had various models with a specific configuration i wanted to preserve. Currently there is no way in chimera (at least non i am aware of) to ask to fit one model into the map but transform all other models according to the final transformation. So - i thought this can be resolved by fitting the map to a specific protein, but is this is a problem - is there a way to fit one model into a map and then transform few other models according to that transformation ? On Feb 17, 2009, at 10:22 AM, Tom Goddard wrote: > Hi Keren, > > There is not an option to move the map instead of the atomic model > when fitting. In what circumstances would that be useful? > > Tom > > > Keren Lasker wrote: >> hello, >> >> Is there a way to fit a density map to a pdb rather than a pdb to >> a density map ? >> Or in other words, that in the end of the fitting procedure the >> map would move to best fit the model rather than the other way >> around. >> >> >> thank you, >> Keren Lasker. >> _______________________________________________ >> 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 Feb 17 12:39:50 2009 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Tue, 17 Feb 2009 12:39:50 -0800 Subject: [Chimera-users] Volume->Fit in Map question In-Reply-To: References: <78E31D46-D8C1-4D7B-A70A-212E8E445624@salilab.org> <499B0079.8010606@cgl.ucsf.edu> Message-ID: <499B2096.4050100@cgl.ucsf.edu> Hi Keren, Yeah, there is currently not a fitting option to fit one model and drag other models along with the model being fit keeping their relative orientations. It's hard to include all the desired flexibility in the graphical user interface without making it so confusing it is unusable. So I see this capability as being more appropriate for a command version of the fitting tool. That command does not exist yet. Here are ideas to deal with the problem now. Fit the one PDB into the map, then adjust the transforms of the other PDB models using the "matrixcopy" command. This approach assumes that the PDB models all have the same transformation placing them in the Chimera coordinate system -- that is, you haven't moved one PDB model relative to another after opening them in Chimera. If you fit pdb #3 into the map you would use the commands "matrixcopy #3 #1" and "matrixcopy #3 #2" to update the relative position of PDB models #1 and #2. I just now enhanced the matrixcopy command so that in tonight's build you could do this in one command "matrixcopy #3 #1-2". Another less flexible trick for handling this case is to first just open the PDB you want to fit, then open the map, but don't open the other PDB models. Do the fit. Then open the remaining PDB models. When they are opened they will be placed relative to the fit PDB model because it has the lowest model id number. Tom Keren Lasker wrote: > thanks Tom. > The reason i wanted to do that was that i had various models with a > specific configuration i wanted to preserve. > Currently there is no way in chimera (at least non i am aware of) to > ask to fit one model into the map but transform all other models > according to the final transformation. > So - i thought this can be resolved by fitting the map to a specific > protein, but is this is a problem - is there a way to fit one model > into a map and then transform few other models according to that > transformation ? > On Feb 17, 2009, at 10:22 AM, Tom Goddard wrote: > >> Hi Keren, >> >> There is not an option to move the map instead of the atomic model >> when fitting. In what circumstances would that be useful? >> >> Tom >> >> >> Keren Lasker wrote: >>> hello, >>> >>> Is there a way to fit a density map to a pdb rather than a pdb to a >>> density map ? >>> Or in other words, that in the end of the fitting procedure the map >>> would move to best fit the model rather than the other way around. >>> >>> >>> thank you, >>> Keren Lasker. >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users at cgl.ucsf.edu >>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> > From meng at cgl.ucsf.edu Tue Feb 17 12:44:38 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 17 Feb 2009 12:44:38 -0800 Subject: [Chimera-users] surface view of large file in chimera In-Reply-To: <480905dc0902111454m38eb1210v2c7cbe39865e2c72@mail.gmail.com> References: <480905dc0902111454m38eb1210v2c7cbe39865e2c72@mail.gmail.com> Message-ID: Hi Guiqing, I assume you are talking about volume data (such as a density map) since the resolution of a molecular surface would not be adjusted automatically. If so, you can just change the "step" in the Volume Viewer dialog to "1" to make sure the contour surface is based on the full data instead of a subsample. There is another setting that automatically adjusts resolution when a large data set is opened. In the Volume Viewer dialog, choose Features... Data display options. Then there should be more options shown in the dialog, including "Adjust step to show at most..." You can either change the number to something bigger, or just uncheck that option if you don't think your large datasets will be too slow to handle on your computer. If you want those settings to apply to later uses of Chimera, choose "Features... Save default dialog settings" from the Volume Viewer dialog. 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 Feb 11, 2009, at 2:54 PM, G.-Q. Hu wrote: > Hello, > > I am trying to show a large file by surface view in chimera. But I > found that the structure lost the detail and the surface was > smoothed. I guess there is a sampling problem for large file. Is > there any way to view the large file at the original resolution? > > Thanks. > Guiqing From meng at cgl.ucsf.edu Tue Feb 17 14:23:28 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 17 Feb 2009 14:23:28 -0800 Subject: [Chimera-users] color changes In-Reply-To: <499B28D4.4020508@lmb.uni-muenchen.de> References: <480905dc0902111454m38eb1210v2c7cbe39865e2c72@mail.gmail.com> <499B28D4.4020508@lmb.uni-muenchen.de> Message-ID: On Feb 17, 2009, at 1:15 PM, Jean-Paul Armache wrote: > hello, > i have one question concerning color manipulation in chimera. > every pdb file one opens gets a specific color (if set so). so, > having a few of them open, one can distinguish > between them color-wise. > now, when one selects the files, it is possible to change the color > via actions->color. this indeed changes all > of the things selected, and if the whole pdb was selected, all the > chains there. when one looks then into the > model panel, the old colors are still there - untouched. this would > be reasonable in the case when only parts > of the pdb were selected and re-colored. however if one selects > whole files and changes the colors - is it > possible to have these colors changed also in the model panel? and > is it possible to revert to the old color > once changed through this action menu? > > best regards, > jean-paul armache Hi Jean-Paul, It is because there is a coloring hierarchy: the Model Panel shows the model color, but you can also set atom colors, whichoverrule and hide the model color. As you found, Actions... Color and the "color" command set the atom colors (otherwise you would not be able to make different parts of the same model different colors). If you already colored the atoms of a model, you can "uncolor" some or all of them to reveal the model color using the command "~color". Another way is to choose "Actions... Color... from editor" and then click the "No Color" button in the Color Editor. (The Color Editor can be found in the menu under Tools... Utilities) You can change the model color with the command "modelcolor" or by clicking on the square color wells in the Model Panel to call up the Color Editor. 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 Wed Feb 18 00:41:52 2009 From: chiendarret at gmail.com (Francesco Pietra) Date: Wed, 18 Feb 2009 09:41:52 +0100 Subject: [Chimera-users] defining a putative binding site Message-ID: Hi: I need to define a putative binding site for a smaller protein upon a larger one. The task is creating a table of likely interactions between residues of the larger proteinseparated by less than 5 A from those of the smaller protein. Deriving from molecular dynamics, all residues for both proteins are in the same pdb file, alongside lipid, water, etc. I wonder whether the most appropriate way is to separate in two different pdb files the lines belonging to the two different proteins. Then: sel #0:20,30-40,55 & #1:1701-1793 z<5 where "0" is the larger and "1" is the smaller protein. If OK, can the results be obtained in a table form? Thanks francesco pietra From meng at cgl.ucsf.edu Wed Feb 18 09:00:22 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 18 Feb 2009 09:00:22 -0800 Subject: [Chimera-users] defining a putative binding site In-Reply-To: References: Message-ID: Hi Francesco, Your approach sounds OK to me. Then if you want a list of the selected residues, choose "Actions... Write List" and in that dialog, change the little menus at the bottom to Write "selected" "residues" (I assume you didn't want each atom to be listed). You can either click Log to send the list to the Reply Log or save the list to a file. 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 Feb 18, 2009, at 12:41 AM, Francesco Pietra wrote: > Hi: > I need to define a putative binding site for a smaller protein upon a > larger one. The task is creating a table of likely interactions > between residues of the larger proteinseparated by less than 5 A from > those of the smaller protein. Deriving from molecular dynamics, all > residues for both proteins are in the same pdb file, alongside lipid, > water, etc. > > I wonder whether the most appropriate way is to separate in two > different pdb files the lines belonging to the two different proteins. > Then: > > sel #0:20,30-40,55 & #1:1701-1793 z<5 > > where "0" is the larger and "1" is the smaller protein. If OK, can the > results be obtained in a table form? > > Thanks > > francesco pietra > From meng at cgl.ucsf.edu Wed Feb 18 12:06:52 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Wed, 18 Feb 2009 12:06:52 -0800 Subject: [Chimera-users] defining a putative binding site In-Reply-To: References: Message-ID: Hi Francesco, If you want detailed information about which atoms contact which, and the distances between them, use the "Find Clashes/Contacts" tool, or its command version "findclash", as discussed in several previous posts: There are links in those posts to the manual pages and a tutorial with an example. Some of those discussions were about finding contacts for a ligand, but the findclash feature is general and can be used on whatever set of atoms/residues you want. Again, you can save results to a file or write them to the Reply Log. 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 Feb 18, 2009, at 10:55 AM, Francesco Pietra wrote: > Hi Elaine: > > By doing as indicate in your and my post, only residues (45 residues) > for model 0 (the bigger protein) are listed. Then I also commanded: > > sel #1:1701-1793 & 0:20,30-40,55 z<5 > > i.e., inverting the order of the two models. That gave a list of > residues (18 residues) for only model 1 (the smaller protein). > > Probably all that is useful information. But, is any way (one touch, > as above) to get information about which-to-which? > > I am not too lazy, I am prepared on the basis of the above two > listings, to use the zone command residue per residue, should this be > the way. > > (the numbers for the above residues are just for a split example; > actually I set all residues - even for areas that I knoe are not > involved - in the zone command for both proteins) > > Thanks > francesco > From emailanindito at yahoo.co.in Thu Feb 19 14:41:34 2009 From: emailanindito at yahoo.co.in (Anindito Sen) Date: Fri, 20 Feb 2009 04:11:34 +0530 (IST) Subject: [Chimera-users] multiple coloring Message-ID: <190185.96736.qm@web94911.mail.in2.yahoo.com> Dear All Please share with me as how to put multiple? color to several pdb structures docked in a density map. Best Andy Dr. Anindito Sen (Ph.D) Research Associate , Dept. of Biochemistry and Molecular Genetics University of Virginia Box 800733 Charlottesville, VA 22908 -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Thu Feb 19 16:44:02 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 19 Feb 2009 16:44:02 -0800 Subject: [Chimera-users] multiple coloring In-Reply-To: <190185.96736.qm@web94911.mail.in2.yahoo.com> References: <190185.96736.qm@web94911.mail.in2.yahoo.com> Message-ID: Hi Andy, I am not sure I understand the question. If you mean you just want to color each molecule model a different color of the rainbow in one step, see Rainbow (under Tools... Depiction). The Model Panel (under Favorites in the menu) also has a "rainbow" button. More generally, you would select a protein (or chain, or part of a chain) to color, then use Actions... Color to choose the color for that, then go on to the next protein or part of protein. There are many, many different ways to select things: Ctrl-click on the structure followed by pressing the up arrow key, or using the Select menu, or using the "select" operations on the right side of the Model Panel, etc. These things could also be done with commands or a command script. 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 Feb 19, 2009, at 2:41 PM, Anindito Sen wrote: > Dear All > > Please share with me as how to put multiple color to several pdb > structures docked in a density map. > > Best > Andy From meng at cgl.ucsf.edu Sun Feb 22 18:56:39 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Sun, 22 Feb 2009 18:56:39 -0800 Subject: [Chimera-users] coloring the clipped surface In-Reply-To: <5012527.1235350114675.JavaMail.hbahudha@fau.edu> References: <5012527.1235350114675.JavaMail.hbahudha@fau.edu> Message-ID: <28B6F711-AE03-44BB-96F1-1381D87E821A@cgl.ucsf.edu> On Feb 22, 2009, at 4:48 PM, Harinathachari Bahudhanapati wrote: > Dear Elaine, > Chimera is getting more exciting to work with than > ever. I think you guys are the best in the field. > About per-model clipping... > > When I tried, I was not able to find how to color the clipped plane > based on atom B-factors? I was able to give a color (single color) > only > but not based on atom B-factors or other attributes like SAS, SES, > electropotential. > I am not sure if modeled PDB files still have B-factor details. I saw > an image on the chimera website on the feature highlights (B-factor > coloring) and I wondered if I can get few more details on this > feature. > I am trying to make a few pictures for my paper. > Thank you elaine, > sincerely, > Hari > Dear Hari, Thanks for your kind words! Yes, there is a trick to coloring planar surface caps by B-factor or some other attribute, as in that figure: First, color the atoms by the attribute (Tools... Depiction... Render by Attribute), which would also color the actual molecular surface but not the planar cap where it is clipped. Then, select the atoms and use Color Zone (also under Tools... Depiction) to color the planar cap to match the nearby atoms. Render by Attribute: Color Zone: I've been wanting to write a tutorial on how to make that figure, but haven't had the time! I also increased the "mesh subdivision factor" in the Surface Capping dialog to 3. Coloring by electrostatic potential is different than coloring by an atom attribute. To color the planar cap by electrostatic potential, you would use Electrostatic Surface Coloring, but it requires a potential map previously created with some other program such as DelPhi. 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 Mon Feb 23 09:43:51 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 23 Feb 2009 09:43:51 -0800 Subject: [Chimera-users] drawing parallelepiped In-Reply-To: References: <20090216170454.1odps6s60coo8kkg@webmail.chem.fsu.edu> Message-ID: On Feb 23, 2009, at 3:31 AM, Francesco Pietra wrote: > > For mono view figures, I wonder whether Chimera allows enclosing the > model in a parallelepiped. This would confer a sense of depth to a > very complex model (a complex of two proteins, partly in a lipidic > membrane. Hi Francesco, There are a few different possibilities: (a) make a PDB file with "atoms" at the corners and the desired bonds (described in CONECT lines), show as wire or stick. The Crystal Contacts tool uses that trick, but is unlikely to generate what you want in this case. You could try creating it interactively with markers and links using Volume Tracer, but probably just creating a PDB file in a text editor would be easier. (b) make a file in BILD format describing the parallelpiped outlines -- requires similar information as the above: coordinates of points at the corners and which points should be connected both (a) and (b) require you to figure out coordinates for the corners yourself... (c) a devious but easy way if you don't mind a rectangular box (all angles 90 degrees) is to use the "molmap" command to create a density map from the displayed atoms, but hide that map's contour surface and just show the box around it. For example, use the command: molmap @/display 2 Then in the Volume Viewer dialog that appears, choose "Features... Data display options" and turn on "Show outline box" and also choose "File... Remove Surface." In that dialog you can also specify the color and linewidth of the outline. For conveying depth, you can also try adjusting the clipping planes in the Side View. If you put the back one closer to the atoms, the depth cueing "fog" will be more obvious. 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 shimes at umd.edu Tue Feb 17 21:01:13 2009 From: shimes at umd.edu (Sarah Himes) Date: Wed, 18 Feb 2009 00:01:13 -0500 (EST) Subject: [Chimera-users] Letter Reference for Amino Acid Atoms Message-ID: <20090218000113.AJC64859@po4.mail.umd.edu> Hi, My name is Sarah Himes. I'm a graduate student at the University of Maryland. I'm researching alkaline phosphatase for an advanced course. I'm using the file 1ALK in Chimera. I'm pretty familiar with Chimera but I had a question regarding the letter notation of amino acid atoms when you scroll over them. Here are some examples: His370 (NE2) Ser102 (CB) Ser102 (N) Asp327 (OD1) Asp327 (OD2) Glu322 (OE2) My question is, what do the letters in parentheses mean, what do they correspond to? When these letters show up in Chimera, there are no parentheses. I look forward to hearing from you shortly. Thank you for your time. Sincerely, Sarah Himes shimes at umd.edu 240-285-1251 -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at cgl.ucsf.edu Mon Feb 23 10:00:58 2009 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Mon, 23 Feb 2009 10:00:58 -0800 Subject: [Chimera-users] drawing parallelepiped In-Reply-To: References: <20090216170454.1odps6s60coo8kkg@webmail.chem.fsu.edu> Message-ID: <49A2E45A.8000004@cgl.ucsf.edu> There is a hidden capability to draw a bounding box for each model but there is no user interface for it. To use it start the Python shell Tools / General Controls / IDLE and type chimera.viewer.showBound = True It shows a separate box for each model and does not let you show boxes for some models and not others. Tom Elaine Meng wrote: > On Feb 23, 2009, at 3:31 AM, Francesco Pietra wrote: > >> For mono view figures, I wonder whether Chimera allows enclosing the >> model in a parallelepiped. This would confer a sense of depth to a >> very complex model (a complex of two proteins, partly in a lipidic >> membrane. >> > > Hi Francesco, > There are a few different possibilities: > > (a) make a PDB file with "atoms" at the corners and the desired bonds > (described in CONECT lines), show as wire or stick. > The Crystal Contacts tool uses that trick, but is unlikely to generate > what you want in this case. You could try creating it interactively > with markers and links using Volume Tracer, but probably just creating > a PDB file in a text editor would be easier. > > (b) make a file in BILD format describing the parallelpiped outlines > -- requires similar information as the above: coordinates of points > at the corners and which points should be connected > > > both (a) and (b) require you to figure out coordinates for the corners > yourself... > > (c) a devious but easy way if you don't mind a rectangular box (all > angles 90 degrees) is to use the "molmap" command to create a density > map from the displayed atoms, but hide that map's contour surface and > just show the box around it. For example, use the command: > molmap @/display 2 > > Then in the Volume Viewer dialog that appears, choose "Features... > Data display options" and turn on "Show outline box" and also choose > "File... Remove Surface." In that dialog you can also specify the > color and linewidth of the outline. > > For conveying depth, you can also try adjusting the clipping planes in > the Side View. If you put the back one closer to the atoms, the depth > cueing "fog" will be more obvious. > > 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 > From meng at cgl.ucsf.edu Mon Feb 23 10:09:12 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 23 Feb 2009 10:09:12 -0800 Subject: [Chimera-users] Letter Reference for Amino Acid Atoms In-Reply-To: <20090218000113.AJC64859@po4.mail.umd.edu> References: <20090218000113.AJC64859@po4.mail.umd.edu> Message-ID: Hi Sarah, The part inside the parentheses is the atom name, as read from the input file. I can tell because these are the standard atom names used in PDB files. However, I don't understand what where/what you are scrolling over or in which program (how you got those strings with parentheses in them) -- when I put the mouse over an atom in Chimera, I get information that does not contain any parentheses. 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 Feb 17, 2009, at 9:01 PM, Sarah Himes wrote: > Hi, > > My name is Sarah Himes. I'm a graduate student at the University of > Maryland. I'm researching alkaline phosphatase for an advanced > course. I'm using the file 1ALK in Chimera. I'm pretty familiar > with Chimera but I had a question regarding the letter notation of > amino acid atoms when you scroll over them. > > Here are some examples: > > His370 (NE2) > Ser102 (CB) > Ser102 (N) > Asp327 (OD1) > Asp327 (OD2) > Glu322 (OE2) > > My question is, what do the letters in parentheses mean, what do > they correspond to? When these letters show up in Chimera, there > are no parentheses. > > I look forward to hearing from you shortly. Thank you for your time. > > Sincerely, > Sarah Himes > shimes at umd.edu > 240-285-1251 From edm4 at u.washington.edu Mon Feb 23 16:41:59 2009 From: edm4 at u.washington.edu (E. Merkley) Date: Mon, 23 Feb 2009 16:41:59 -0800 (PST) Subject: [Chimera-users] Match -> Align used with a pair of homodimers Message-ID: Hello chimera friends: I am trying to get a structure-based sequence alignment for a pair of homologous proteins that are homodimers. If I proceed as described in the tutorial and in the 2006 BMC Bioinformatics paper, by first using Matchmaker, then using Match -> align, the Match -> Align fails to produce a reasonable alignment. The sequence identity from the Matchmaker output is 26.5%, but only 1.0 % from the Match -> Align step. If I delete the second monomer from each protein, Match -> Align works quite well. However, it seems like this alignment won't take into account any differences in the tertiary structure between the two proteins. That is, I think I want the global alignment of the whole dimer for the structural alignment, since the active sites is are at the interface. Any suggestions? I'm using version 1.2540, and my two proteins are PDB codes 1ds7 and 1nox (1nox dimer built from BIOMT matrix in Chimera and hand-edited to be 1 model with A and B chains). Thanks yet again, Eric From meng at cgl.ucsf.edu Mon Feb 23 17:51:22 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Mon, 23 Feb 2009 17:51:22 -0800 Subject: [Chimera-users] Match -> Align used with a pair of homodimers In-Reply-To: References: Message-ID: <48B8FE7A-9FAD-4CB6-A242-AEAA204416D4@cgl.ucsf.edu> Hi Eric, A couple of us independently tried the process and did not encounter the problem. Using default matchmaker and match->align parameters, the two alignments from match->align had 23% and 21% ID. However, I had a theory of where you might have gone astray. Here are the steps of the process: (1) generate 1nox dimer as a single model. Note this is much easier in newer versions of Chimera (1.3+): after creating the dimer using BIOMT, you can then use the "combine" command or the "copy/combine" action in the Model Panel to merge the two monomer models into one dimer model with chains A and B. No hand-editing! (2) have 1nox dimer and 1ds7 open in Chimera, use Matchmaker with default settings. This gives a sequence alignment of 1ds7 chain B and 1nox-dimer chain A with ~26% ID, as you said, and a pretty good- looking superposition: final iteration 101 atom pairs, 1.026 angstroms RMSD. (3) in Match->Align, you would choose 1ds7 chain B and 1nox-dimer chain A as one pair, Apply to get sequence alignment with 23% ID (default parameters in Match->Align). Choosing 1ds7 chain A and 1nox- dimer chain B as another pair, clicking Apply gives another sequence alignment with 21% ID. My theory is that maybe you chose A and A as one pair, B and B as another pair whereas the superposition really has each A chain on top of a B chain. 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 Feb 23, 2009, at 4:41 PM, E. Merkley wrote: > Hello chimera friends: > > I am trying to get a structure-based sequence alignment for a pair of > homologous proteins that are homodimers. If I proceed as described > in the > tutorial and in the 2006 BMC Bioinformatics paper, by first using > Matchmaker, then using Match -> align, the Match -> Align fails to > produce > a reasonable alignment. The sequence identity from the Matchmaker > output > is 26.5%, but only 1.0 % from the Match -> Align step. If I delete the > second monomer from each protein, Match -> Align works quite well. > However, it seems like this alignment won't take into account any > differences in the tertiary structure between the two proteins. > That is, > I think I want the global alignment of the whole dimer for the > structural > alignment, since the active sites is are at the interface. Any > suggestions? I'm using version 1.2540, and my two proteins are PDB > codes > 1ds7 and 1nox (1nox dimer built from BIOMT matrix in Chimera and > hand-edited to be 1 model with A and B chains). > > Thanks yet again, > Eric > From fabriceg at univ-reunion.fr Tue Feb 24 01:41:11 2009 From: fabriceg at univ-reunion.fr (fabriceg at univ-reunion.fr) Date: Tue, 24 Feb 2009 13:41:11 +0400 (RET) Subject: [Chimera-users] copy in a file the distance on the screen Message-ID: <10465.81.248.240.54.1235468471.squirrel@webmail.univ-reunion.fr> Dear Users, When analyzing a trajectory file, I would like to monitor a distance (or series of distances) and save it to a file for each frame (getting a time series). I can do it but the values remain on the screen only! I am sure there is a simple script for making this. Thanks for any answer. Best wishes. Fabriceg From chiendarret at gmail.com Tue Feb 24 08:26:42 2009 From: chiendarret at gmail.com (Francesco Pietra) Date: Tue, 24 Feb 2009 17:26:42 +0100 Subject: [Chimera-users] Fwd: stereo view In-Reply-To: References: <20090216170454.1odps6s60coo8kkg@webmail.chem.fsu.edu> <1632AD2E-1BAD-4732-8FAD-3A14A396C4C4@cgl.ucsf.edu> <0689FC94-2A44-49D3-ABA2-D23A0455DACB@cgl.ucsf.edu> Message-ID: It was a bad idea. What Jason initially suggested (save left-eye and right-eye) should work. What I have to manipulate images is only gimp, with which I am not very familiar. But it seems to have the capability of arranging the two saved files so as to get a stereo effect. There is even a (unofficial) plugin to remove unwanted space around. francesco ---------- Forwarded message ---------- From: Francesco Pietra Date: Tue, Feb 24, 2009 at 9:31 AM Subject: Re: [Chimera-users] stereo view To: Elaine Meng Hi Elaine: That makes problems as the referee just wants a stereo view of details of the binding site, which requires magnifying the figure. Is it any way to save a pdb file of the magnified zone alone? (to start from there to build a stereoview). Of course, the normal ?pdb saving of a magnified figure saves the coordinates for the whole. The only way I can conceive to get the coordinates of the binding site, and nothing else, is manually deleting rows from the pdb file. A tricky route because the chains start and return to the starting point and the binding site is on both strands. thanks francesco On Tue, Feb 24, 2009 at 1:27 AM, Elaine Meng wrote: > I guess you could also save separate left eye and right eye images and put > them farther apart. ?That might also mess up the stereo effect, though. > Elaine > > On Feb 23, 2009, at 4:26 PM, Elaine Meng wrote: > >> Hi Francesco, >> There is a certain separation needed or else your eyes cannot form the >> stereo image. ?You could try zooming out so the atoms don't take up the >> whole window, or adjusting parameters in the Camera tool (under Tools -> >> Viewing Controls) but I usually don't mess with those camera parameters >> because you could disrupt the stereo viewing if you change them very much. >> Elaine >> >> >> On Feb 23, 2009, at 3:06 PM, Francesco Pietra wrote: >> >>> Hi Elaine: >>> Is it any direct way to save stereoimages from magnified images? By >>> the normal route, the wall-eye couple of images are saved adjacent to >>> one another, with no space in between them. >>> >>> thanks >>> francesco >>> >>> On Tue, Feb 17, 2009 at 1:43 AM, Elaine Meng wrote: >>>> >>>> Hi Francesco, >>>> All of Jason's suggestions are good (thanks Jason!), and I only wanted >>>> to >>>> add a few things: >>>> >>>> (1) while the window will always be a rectangle, you could resize it so >>>> that >>>> there is a different ratio between height and width. ?If your long >>>> molecule >>>> is oriented across, you could resize the window to be less tall so that >>>> the >>>> width:height ratio is greater. ?Don't worry if the window is then >>>> filling >>>> less of your screen -- you can specify as high a resolution as you want >>>> in >>>> the File... Save Image dialog. ?Of course, with a given window size, you >>>> should scale up your molecule(s) to fill it as much as possible. ? In >>>> agreement with Jason, I think usually a white background is better than >>>> black for publication purposes. ?How to change background color is >>>> described >>>> near the top of the "Tips on Preparing Images": >>>> >>>> >>>> (2) There is a section on saving stereo images near the bottom of that >>>> "Tips >>>> on Preparing Images" page (by the way, you can use "Help... Search >>>> Documentation" to look for help topics such as "stereo image"). ?I think >>>> journals usually show the "wall-eye" type of stereo, which can be >>>> achieved >>>> by saving one image in the wall-eye stereo mode, or by saving separate >>>> left >>>> and right views and placing them side by side with the left-eye view on >>>> the >>>> left and the right-eye view on the right. >>>> >>>> (3) just show the surface, adjust clipping and depth-cueing as Jason >>>> suggested, and use your artistic and scientific judgement as to whether >>>> it >>>> improves your image! ?There are additional suggestions for improving >>>> surface >>>> appearance in the "Tips on Preparing Images" page. >>>> >>>> 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 Feb 16, 2009, at 2:04 PM, odonnell at chem.fsu.edu wrote: >>>> >>>>> Hi Francesco, >>>>> ?A couple of cents before the professionals respond with (very >>>>> likely) better ideas: >>>>> >>>>> In response to 1) Black is best for contrast but uses a lot of ink and >>>>> money. >>>>> White should be fine. >>>>> >>>>> n response to 2) If you go to TOOLS=>VIEWING CONTROLS=>CAMERA, you can >>>>> select various camera modes. CROSS-EYE stereo will put your chimera >>>>> graphic into cross-eye stereo. You can save an image as it is >>>>> displayed on the screen. But i find saving two images, stereo left eye >>>>> and stereo right eye better. Place these side by side in another >>>>> graphic program, (e.g Adobe illustrator) and voila, stereo viewing. >>>>> With two single images you can switch them around to alternate between >>>>> wall-eye and cross-eye. Also, with two images its easier to make the >>>>> distance between them a certain length, as journals are usually >>>>> stringent about how the stereo images are displayed. >>>>> >>>>> In response to 3)I'd to go TOOLS=>VIEWING CONTROLS=> SIDE VIEW and >>>>> slide the back and front yellow planes. This will create a slab >>>>> through your object removing other structural elements which might >>>>> complicate the image. Also, >>>>> try DEPTH CUEING under TOOLS=>VIEWING CONTROLS=> EFFECTS. tweak the >>>>> "start ratio and yon intensity to further remove emphasis on unwanted >>>>> objects. ?The Depth effects can make some really neat graphics >>>>> >>>>> Hope this helps. >>>>> >>>>> -Jason >>>>> >>>>> Quoting Francesco Pietra : >>>>> >>>>>> Hi: >>>>>> >>>>>> I would greatly appreciate advice about the following requests >>>>>> (between "".."") by the referees (interaction between two proteins; >>>>>> graphics by chimera): >>>>>> >>>>>> 1) "there is way too much wasted black space in figures". >>>>>> >>>>>> As the complex of proteins is elongated along one axis, I found it >>>>>> unavoidable to have wasted space around. Perhaps using a white >>>>>> background in the hope that white is less offending than black? Or is >>>>>> it a way to tailor the background according to the shape of the >>>>>> object? >>>>>> >>>>>> 2) "a stereoview might be helpful for better understanding". >>>>>> >>>>>> How to fulfill this request with chimera I have no idea. >>>>>> >>>>>> 3) "a molecular surface representation of the docking site would be >>>>>> useful". >>>>>> >>>>>> I read on passing about molecular surfaces on this forum. Is that >>>>>> feasible for the highly complex situation of 3D perspective with so >>>>>> many atoms at different "layers"? >>>> >>>> >> > > From meng at cgl.ucsf.edu Tue Feb 24 08:54:05 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 24 Feb 2009 08:54:05 -0800 Subject: [Chimera-users] Match -> Align used with a pair of homodimers In-Reply-To: <48B8FE7A-9FAD-4CB6-A242-AEAA204416D4@cgl.ucsf.edu> References: <48B8FE7A-9FAD-4CB6-A242-AEAA204416D4@cgl.ucsf.edu> Message-ID: Hi Eric, The steps in my previous message included Matchmaker fitting using only one monomer of each structure. In principle, you might want to do the initial fitting using both monomers (maybe that's what you were saying in your question and I didn't understand). However, in this case it doesn't make much difference because fitting a monomer superimposes the whole dimer pretty well. To use both chains in Matchmaker, you would choose the "Chain pairing" option "Specific chain(s) in reference structure with specific chain(s) in match structure." Then you can specifically the pairing of A with A and B with B (or A/B and B/A, equally valid): drag to choose both chains of 1nox dimer on the left, and then on the right, use the pulldowns to specify which 1ds7 chain should be paired with each. Otherwise using Matchmaker and Match->Align defaults: A/A,B/B pairing - Matchmaker 188 atom pairs 1.139 ang. RMSD, alignments from Match->Align ~23 and 21% ID. A/B,B/A pairing - Matchmaker 188 atom pairs 1.139 ang. RMSD, alignments from Match->Align ~23 and 21% ID. Compare to initial fit on only one pair (reported in previous mail) of 101 atom pairs 1.026 ang. RMSD, but essentially the same results from Match->Align. 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 Feb 23, 2009, at 5:51 PM, Elaine Meng wrote: > Hi Eric, > A couple of us independently tried the process and did not encounter > the problem. Using default matchmaker and match->align parameters, > the two alignments from match->align had 23% and 21% ID. However, I > had a theory of where you might have gone astray. Here are the steps > of the process: > > (1) generate 1nox dimer as a single model. Note this is much easier > in newer versions of Chimera (1.3+): after creating the dimer using > BIOMT, you can then use the "combine" command or the "copy/combine" > action in the Model Panel to merge the two monomer models into one > dimer model with chains A and B. No hand-editing! > > (2) have 1nox dimer and 1ds7 open in Chimera, use Matchmaker with > default settings. This gives a sequence alignment of 1ds7 chain B > and 1nox-dimer chain A with ~26% ID, as you said, and a pretty good- > looking superposition: final iteration 101 atom pairs, 1.026 > angstroms RMSD. > > (3) in Match->Align, you would choose 1ds7 chain B and 1nox-dimer > chain A as one pair, Apply to get sequence alignment with 23% ID > (default parameters in Match->Align). Choosing 1ds7 chain A and 1nox- > dimer chain B as another pair, clicking Apply gives another sequence > alignment with 21% ID. > > My theory is that maybe you chose A and A as one pair, B and B as > another pair whereas the superposition really has each A chain on top > of a B chain. > > I hope this helps, > Elaine > > > On Feb 23, 2009, at 4:41 PM, E. Merkley wrote: > >> Hello chimera friends: >> >> I am trying to get a structure-based sequence alignment for a pair of >> homologous proteins that are homodimers. If I proceed as described >> in the >> tutorial and in the 2006 BMC Bioinformatics paper, by first using >> Matchmaker, then using Match -> align, the Match -> Align fails to >> produce >> a reasonable alignment. The sequence identity from the Matchmaker >> output >> is 26.5%, but only 1.0 % from the Match -> Align step. If I delete >> the >> second monomer from each protein, Match -> Align works quite well. >> However, it seems like this alignment won't take into account any >> differences in the tertiary structure between the two proteins. >> That is, >> I think I want the global alignment of the whole dimer for the >> structural >> alignment, since the active sites is are at the interface. Any >> suggestions? I'm using version 1.2540, and my two proteins are PDB >> codes >> 1ds7 and 1nox (1nox dimer built from BIOMT matrix in Chimera and >> hand-edited to be 1 model with A and B chains). >> >> Thanks yet again, >> Eric >> > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users From sergio.alberto.garay at gmail.com Tue Feb 24 09:21:35 2009 From: sergio.alberto.garay at gmail.com (Sergio Garay) Date: Tue, 24 Feb 2009 14:21:35 -0300 Subject: [Chimera-users] Sequence vs Sequence plot using minrms.... Message-ID: <74e2c5910902240921tf614da6x8fe2acfa16de0ae3@mail.gmail.com> Hi all I run minrms with defaults values on my two proteins and I was able to obtain many useful alignments. But when I load the results on chimera, it doesn?t show me the sequence vs sequence plot. Is there any particular way to do that? Or there is any special minrms command (option) to obtain this? All the other plot were right (rms vs sequece and the alignment plot). Any help will be appreciated. -- Dr. Sergio Garay Facultad de Bioquimica y Cs. Biol?gicas Universidad Nacional del Litoral Santa Fe - Argentina C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA Argentina Ph. +54 (342) 4575-213 Fax. +54 (342) 4575-221 -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Tue Feb 24 10:02:28 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 24 Feb 2009 10:02:28 -0800 Subject: [Chimera-users] Sequence vs Sequence plot using minrms.... In-Reply-To: <74e2c5910902240921tf614da6x8fe2acfa16de0ae3@mail.gmail.com> References: <74e2c5910902240921tf614da6x8fe2acfa16de0ae3@mail.gmail.com> Message-ID: Hi Sergio, That sequence vs. sequence plot was shown in the older tool AlignPlot, but is not included in the newer tool Minrms Plot. AlignPlot was removed a very long time ago, sometime between Dec 2004 and Oct 2005. You can get the Dec 2004 and older releases of Chimera from There have been many improvements and new features since then, so I recommend just naming the old version differently and/or putting it in a different place so that you can also have a current version of Chimera on your computer. I tried using the AlignPlot extension with a new version of Chimera, but that was unsuccessful (generated errors and did not work well). 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 Feb 24, 2009, at 9:21 AM, Sergio Garay wrote: > Hi all > > I run minrms with defaults values on my two proteins and I was able > to obtain many useful alignments. But when I > load the results on chimera, it doesn?t show me the sequence vs > sequence plot. Is there any particular way to do that? > Or there is any special minrms command (option) to obtain this? > All the other plot were right (rms vs sequece and the alignment plot). > > Any help will be appreciated. > From pett at cgl.ucsf.edu Tue Feb 24 11:36:51 2009 From: pett at cgl.ucsf.edu (Eric Pettersen) Date: Tue, 24 Feb 2009 11:36:51 -0800 Subject: [Chimera-users] copy in a file the distance on the screen In-Reply-To: <10465.81.248.240.54.1235468471.squirrel@webmail.univ-reunion.fr> References: <10465.81.248.240.54.1235468471.squirrel@webmail.univ-reunion.fr> Message-ID: <85DDBFDE-B1E1-4117-B0F0-7E135676373E@cgl.ucsf.edu> Hi Fabrice, I've attached a Python script below, that you can use in the "Define Script" MD Movie dialog to print any distances you're monitoring to the reply log. The Reply Log has a Save button which you can use to save the output into a file. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Feb 24, 2009, at 1:41 AM, fabriceg at univ-reunion.fr wrote: > Dear Users, > When analyzing a trajectory file, I would like to monitor a distance > (or series of distances) and save it to a file for each frame (getting > a time series). I can do it but the values remain on the screen only! > I am sure there is a simple script for making this. > Thanks for any answer. > Best wishes. > Fabriceg -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: mdDist.py Type: text/x-python-script Size: 183 bytes Desc: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From meng at cgl.ucsf.edu Tue Feb 24 15:38:50 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Tue, 24 Feb 2009 15:38:50 -0800 Subject: [Chimera-users] finding salt bridges In-Reply-To: <49A46BCF.7010404@mrl.ucsb.edu> References: <49A46BCF.7010404@mrl.ucsb.edu> Message-ID: <0FED6196-C98C-4DB6-B9C3-6EF2464C0B21@cgl.ucsf.edu> On Feb 24, 2009, at 1:51 PM, Jeremy Schmit wrote: > Does Chimera have a tool for identifying salt bridges? I was able > to use the findHbond tool to count intermolecular H-bonds in the > lysozyme crystal, but I can't seem to find an analogous tool for > salt bridges. In fact, the term "salt bridge" does not yield a > single result on the Chimera site. > Thanks, > Jeremy Hi Jeremy, There isn't a tool for specifically finding salt bridges, but you can consider them as a subset of hydrogen bonds. You could select only atoms in charged functional groups and then limit H-bond detection to that selection. Example commands to first select by atom type and then find the H-bonds: sel O2- | O3- | N3+ | Ng+ findhbond selRestrict both saveFile ~/mydir/myfile If the subunits of interest are different chains in the same model (same input file), you could then postprocess the output (for example, with "grep" on unix) to count only those between the chains. If each subunit is opened as a different model, you could add "intramodel false" to the findhbond command. There are analogous options on the FindHBond graphical interface: "Only find H-bonds with both ends selected" and find just the "inter-model" bonds. findhbond command: findhbond GUI: atom types: 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 bala.biophysics at gmail.com Wed Feb 25 03:37:58 2009 From: bala.biophysics at gmail.com (Bala subramanian) Date: Wed, 25 Feb 2009 12:37:58 +0100 Subject: [Chimera-users] slab representation of nucleic acid Message-ID: <288df32a0902250337y98a0704i715ad2fb78436137@mail.gmail.com> The slab representation of nucleic acid under Depiction is not working. I made the following settings *show backbone as* atoms/bonds, *show sugar as* atoms/bonds, *show base* as slab. But the representation is not displayed on the screen. What could be the reason. I myself have used it before and i am not aware why this happens now. Regards, Bala -------------- next part -------------- An HTML attachment was scrubbed... URL: From bala.biophysics at gmail.com Wed Feb 25 03:45:47 2009 From: bala.biophysics at gmail.com (Bala subramanian) Date: Wed, 25 Feb 2009 12:45:47 +0100 Subject: [Chimera-users] slab representation of nucleic acid In-Reply-To: <288df32a0902250337y98a0704i715ad2fb78436137@mail.gmail.com> References: <288df32a0902250337y98a0704i715ad2fb78436137@mail.gmail.com> Message-ID: <288df32a0902250345p64139eeay516ee3cd7b996c09@mail.gmail.com> Sorry for the posting the question. I have solved the problem. Actually the residues names were not of standard type. Bla On Wed, Feb 25, 2009 at 12:37 PM, Bala subramanian < bala.biophysics at gmail.com> wrote: > The slab representation of nucleic acid under Depiction is not working. I > made the following settings > > *show backbone as* atoms/bonds, *show sugar as* atoms/bonds, *show base*as slab. But the representation is not displayed on the screen. > > What could be the reason. I myself have used it before and i am not aware > why this happens now. > > Regards, > Bala > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jort at nmr.mpibpc.mpg.de Wed Feb 25 08:54:39 2009 From: jort at nmr.mpibpc.mpg.de (julien(GWDG)) Date: Wed, 25 Feb 2009 17:54:39 +0100 Subject: [Chimera-users] angles after match Message-ID: <49A577CF.1040703@nmr.mpibpc.mpg.de> Dear all, thank you for the very nice software. I continuously like it. I have the following problem. For different molecules, I would like to know what are the transformation that link them. I can do for example match #0 #1 matrixget - From this matrix I have the rotation information and the translation information. I would like to extract the angles. For that I need to know what convention you used. I guess those are Euler angles (?), but I need to know what is the order of rotation xyz, xzy... Finally how do you get ride of the gimbal lock problem if you use Euler angles. Thank you for your constant help. (Sorry if this question is a duplicate) many greetings julien From goddard at cgl.ucsf.edu Wed Feb 25 10:24:49 2009 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Wed, 25 Feb 2009 10:24:49 -0800 Subject: [Chimera-users] angles after match In-Reply-To: <49A577CF.1040703@nmr.mpibpc.mpg.de> References: <49A577CF.1040703@nmr.mpibpc.mpg.de> Message-ID: <49A58CF1.1070209@cgl.ucsf.edu> Hi Julien, In Chimera 1.4 daily builds since January 7 there is a command called "measure" that can report the relative orientation of two models: measure rotation #0 #1 prints in the reply log (menu Favorites / Reply Log) Matrix rotation and translation 0.22612416 0.31146762 -0.92296034 15.49596646 0.00745874 0.94692067 0.32138080 -1.29273361 0.97406993 -0.07955609 0.21179848 -13.27353380 Axis -0.20428607 -0.96657822 -0.15489914 Axis point 16.21434627 0.00000000 3.22513422 Rotation angle (degrees) 78.90585699 Shift along axis 0.13997704 giving the 3 by 4 transformation (3 by 3 rotation matrix plus translation in last column) or in a different format the rotation axis vector, a point on the rotation axis, a rotation angle and a shift along the axis. These numbers refer to the orientation of model #1 using the coordinate system of model #0. The command also makes a graphical depiction of the rotation axis. That becomes a new model which can be closed with Model Panel. I added a new optional parameter to "measure rotation" today to not show the graphical depiction: "measure rotation #0 #1 showAxis false". We do not use or provide Euler angles in Chimera. As you note there are problems with conventions and degeneracy with Euler angles. Tom julien(GWDG) wrote: > Dear all, > > thank you for the very nice software. I continuously like it. > > I have the following problem. > > For different molecules, I would like to know what are the > transformation that link them. > I can do for example > match #0 #1 > matrixget - > > From this matrix I have the rotation information and the translation > information. > I would like to extract the angles. For that I need to know what > convention you used. > I guess those are Euler angles (?), but I need to know what is the order > of rotation xyz, xzy... > Finally how do you get ride of the gimbal lock problem if you use Euler > angles. > > Thank you for your constant help. > (Sorry if this question is a duplicate) > > many greetings > > julien > > > _______________________________________________ > Chimera-users mailing list > Chimera-users at cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > From huiskone at biochem.mpg.de Wed Feb 25 12:10:26 2009 From: huiskone at biochem.mpg.de (Juha Huiskonen) Date: Wed, 25 Feb 2009 21:10:26 +0100 Subject: [Chimera-users] how to quickly delete several markers Message-ID: <49A5A5B2.4010205@biochem.mpg.de> Dear Chimera developers & users, I am visualizing template matching results of volume data in Chimera, and I have to discard hundreds of false positives matches, represented as markers. Now I select some markers and then delete the selected markers from the Volume Path Tracer menu. This is quite slow, and for me it would be really handy, if I could delete (all linked) markers just by clicking (one of them) them. Maybe "delete markers with mouse" feature could be added to Volume Path Tracer module? Or is there already a faster way to do this? Thanks a lot in advance for your suggestions! Juha -- Dr. Juha Huiskonen Max Planck Institute of Biochemistry Department of Molecular Structural Biology Am Klopferspitz 18 D-82152 Martinsried Germany Tel: +49 89 8578-2632 Fax: +49 89 8578-2641 GSM: +49 176 20786875 E-mail: huiskone at biochem.mpg.de http://www.helsinki.fi/~huiskone/ -------------- next part -------------- A non-text attachment was scrubbed... Name: huiskone.vcf Type: text/x-vcard Size: 386 bytes Desc: not available URL: From goddard at cgl.ucsf.edu Wed Feb 25 12:47:15 2009 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Wed, 25 Feb 2009 12:47:15 -0800 Subject: [Chimera-users] how to quickly delete several markers In-Reply-To: <49A5A5B2.4010205@biochem.mpg.de> References: <49A5A5B2.4010205@biochem.mpg.de> Message-ID: <49A5AE53.6020803@cgl.ucsf.edu> Hi Juha, There are always tricks! I use keyboard shortcuts to do this. You have to turn on keyboard shortcuts to use them (menu Tools / General Controls / Keyboard Shortcuts, then click Enable keyboard shortcuts). The shortcuts are 2-key sequences (no return key) typed in the graphics window and the relevant ones for your task are: Da - deletes selected markers/atoms sc - select all markers/atoms connected to the already selected ones by links/bonds So the typical use to delete a chain of markers is to select one with the mouse then type sc, then Da. The uppercase D is important. Upper case in shortcuts is used if the action has serious irreversible consequences. If you use the Chimera command-line that overrides the shortcuts. To get back to using shortcuts use the Chimera command "ac" and press return (that's a command not a shortcut, stands for accelerators). Here's a full list of shortcuts. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/accelerators/alist.html Your mouse mode would be nice. We need better support for alternate mouse modes in Chimera like a palette of modes as in paint programs. Tom Juha Huiskonen wrote: > Dear Chimera developers & users, > > I am visualizing template matching results of volume data in Chimera, > and I have to discard hundreds of false positives matches, represented > as markers. > > Now I select some markers and then delete the selected markers from > the Volume Path Tracer menu. This is quite slow, and for me it would > be really handy, if I could delete (all linked) markers just by > clicking (one of them) them. > > Maybe "delete markers with mouse" feature could be added to Volume > Path Tracer module? > > Or is there already a faster way to do this? > > Thanks a lot in advance for your suggestions! > > Juha > > _______________________________________________ > 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 Feb 26 05:22:22 2009 From: bala.biophysics at gmail.com (Bala subramanian) Date: Thu, 26 Feb 2009 14:22:22 +0100 Subject: [Chimera-users] searching chimera archieve Message-ID: <288df32a0902260522m3a98eb22uda75cb4d0876da54@mail.gmail.com> Dear Elaine, Long time back, I posted a question on *searching chimera archive for a keyword*. Just for an example, i gave "salt bridge" as a key word in the following link, but it dose nt show me the queries on salt bridge in chimera archive. I dnt undertand why ?. It would helpful for chimera loves like me not to repeat same queries and also to understand all ways of analyzing salt bridge based on previous queries. I am sorry if this question is not relevant to chimera technical issues. http://www.cgl.ucsf.edu/chimera/docs/feedback.html Cheers, Bala -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at cgl.ucsf.edu Thu Feb 26 11:00:48 2009 From: goddard at cgl.ucsf.edu (Thomas Goddard) Date: Thu, 26 Feb 2009 11:00:48 -0800 Subject: [Chimera-users] how to quickly delete several markers In-Reply-To: <49A5AE53.6020803@cgl.ucsf.edu> References: <49A5A5B2.4010205@biochem.mpg.de> <49A5AE53.6020803@cgl.ucsf.edu> Message-ID: <49A6E6E0.1070503@cgl.ucsf.edu> Hi Juha, I see, saving markers to an XML file is broken if atoms/bonds are deleted, for example using shortcut Da. Ok, I've fixed this -- try tonight's daily build (Feb 26 build available in about 12 hours). http://www.cgl.ucsf.edu/chimera/alpha-downloads.html Sorry I did not catch this earlier. I typically save markers in Chimera sessions (File / Save session) which is working with shortcut Da. But the XML output is of course useful when other programs will use the markers. Tom Juha Huiskonen wrote: > Hi Tom, > > Thanks for your response. However, I run into a problem.. I am sending > this only to you, since I am attaching some example files. (I also > updated Chimera to 1.3.2577 linux x86_64, but the problem persists.) > > My original markers are in (the file.cmm) If I use "Volume > Tracer->Delete markers" and then save the marker set (file > file_sel.cmm), everything is fine. If I then delete more markers, now > with the "sc" and "Da" accelators, I get an error: > > Invoked accelerator sc - Select connected atoms/bonds > Invoked accelerator Da - Delete atoms and bonds > Exception in Tk callback > Function: > (type: 'instancemethod'>) > Args: () > Traceback (innermost last): > File "CHIMERA/lib/python2.5/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py", > line 1747, in __call__ > None > File "CHIMERA/share/VolumePath/gui.py", line 294, in > save_marker_set_as_cb > None > File "CHIMERA/share/VolumePath/gui.py", line 325, in save_marker_sets > None > File "CHIMERA/share/VolumePath/markerset.py", line 707, in > save_marker_sets > None > File "CHIMERA/share/VolumePath/markerset.py", line 222, in save_as_xml > None > File "CHIMERA/share/VolumePath/markerset.py", line 339, in xyz > None > : underlying C++ Atom object is missing > > > I can still save the marker file, but it has not links (file_sel2.cmm). > > > Juha > > > Tom Goddard wrote: >> Hi Juha, >> >> There are always tricks! I use keyboard shortcuts to do this. You >> have to turn on keyboard shortcuts to use them (menu Tools / General >> Controls / Keyboard Shortcuts, then click Enable keyboard shortcuts). >> The shortcuts are 2-key sequences (no return key) typed in the >> graphics window and the relevant ones for your task are: >> >> Da - deletes selected markers/atoms >> sc - select all markers/atoms connected to the already >> selected ones by links/bonds >> >> So the typical use to delete a chain of markers is to select one with >> the mouse then type sc, then >> Da. The uppercase D is important. Upper case in shortcuts is used if >> the action has serious irreversible consequences. >> >> If you use the Chimera command-line that overrides the shortcuts. To >> get back to using shortcuts use the Chimera command "ac" and press >> return (that's a command not a shortcut, stands for accelerators). >> >> Here's a full list of shortcuts. >> >> >> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/accelerators/alist.html >> >> >> Your mouse mode would be nice. We need better support for alternate >> mouse modes in Chimera like a palette of modes as in paint programs. >> >> Tom >> >> >> Juha Huiskonen wrote: >>> Dear Chimera developers & users, >>> >>> I am visualizing template matching results of volume data in Chimera, >>> and I have to discard hundreds of false positives matches, >>> represented as markers. >>> >>> Now I select some markers and then delete the selected markers from >>> the Volume Path Tracer menu. This is quite slow, and for me it would >>> be really handy, if I could delete (all linked) markers just by >>> clicking (one of them) them. >>> >>> Maybe "delete markers with mouse" feature could be added to Volume >>> Path Tracer module? >>> >>> Or is there already a faster way to do this? >>> >>> Thanks a lot in advance for your suggestions! >>> >>> Juha >>> >>> _______________________________________________ >>> Chimera-users mailing list >>> Chimera-users at cgl.ucsf.edu >>> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >>> > Tom Goddard wrote: > Hi Juha, > > There are always tricks! I use keyboard shortcuts to do this. You > have to turn on keyboard shortcuts to use them (menu Tools / General > Controls / Keyboard Shortcuts, then click Enable keyboard shortcuts). > The shortcuts are 2-key sequences (no return key) typed in the graphics > window and the relevant ones for your task are: > > Da - deletes selected markers/atoms > sc - select all markers/atoms connected to the already > selected ones by links/bonds > > So the typical use to delete a chain of markers is to select one with > the mouse then type sc, then > Da. The uppercase D is important. Upper case in shortcuts is used if > the action has serious irreversible consequences. > > If you use the Chimera command-line that overrides the shortcuts. To > get back to using shortcuts use the Chimera command "ac" and press > return (that's a command not a shortcut, stands for accelerators). > > Here's a full list of shortcuts. > > > http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/accelerators/alist.html > > Your mouse mode would be nice. We need better support for alternate > mouse modes in Chimera like a palette of modes as in paint programs. > > Tom > > > Juha Huiskonen wrote: >> Dear Chimera developers & users, >> >> I am visualizing template matching results of volume data in Chimera, >> and I have to discard hundreds of false positives matches, represented >> as markers. >> >> Now I select some markers and then delete the selected markers from >> the Volume Path Tracer menu. This is quite slow, and for me it would >> be really handy, if I could delete (all linked) markers just by >> clicking (one of them) them. >> >> Maybe "delete markers with mouse" feature could be added to Volume >> Path Tracer module? >> >> Or is there already a faster way to do this? >> >> Thanks a lot in advance for your suggestions! >> >> Juha >> >> _______________________________________________ >> 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 conrad at cgl.ucsf.edu Thu Feb 26 12:38:26 2009 From: conrad at cgl.ucsf.edu (Conrad Huang) Date: Thu, 26 Feb 2009 12:38:26 -0800 Subject: [Chimera-users] searching chimera archieve In-Reply-To: <288df32a0902260522m3a98eb22uda75cb4d0876da54@mail.gmail.com> References: <288df32a0902260522m3a98eb22uda75cb4d0876da54@mail.gmail.com> Message-ID: <49A6FDC2.5060800@cgl.ucsf.edu> Searching Chimera mailing lists is implemented using Google. My first guess regarding the problem you encountered is that Google has not re-indexed our site yet. For example, the term "salt bridge" does not find anything, but "putative binding" returns a message that was posted earlier. There does seem to be some oddities, eg an even earlier message with "letter reference" in its title is not found by Google. Unfortunately, I'm not familiar enough with Google to be able to explain the problems. My suspicion is that the messages posted in the current month are found sporadically because the web pages are rebuilt regularly and perhaps Google is scanning us during the rebuilding process. Once the messages are rotated into static archives at the end of the month, they should be found consistently. I can only suggest that, if the search function is not returning hits for a recent message, you try viewing the threads in the archive for the current month. If you've noticed older messages not being found, please let me know and I will dig further. Conrad Bala subramanian wrote: > Dear Elaine, > > Long time back, I posted a question on *searching chimera archive for a > keyword*. Just for an example, i gave "salt bridge" as a key word in the > following link, but it dose nt show me the queries on salt bridge in > chimera archive. I dnt undertand why ?. It would helpful for chimera > loves like me not to repeat same queries and also to understand all ways > of analyzing salt bridge based on previous queries. I am sorry if this > question is not relevant to chimera technical issues. > > http://www.cgl.ucsf.edu/chimera/docs/feedback.html > > Cheers, > 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 Feb 26 12:49:39 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 26 Feb 2009 12:49:39 -0800 Subject: [Chimera-users] searching chimera archieve In-Reply-To: <49A6FDC2.5060800@cgl.ucsf.edu> References: <288df32a0902260522m3a98eb22uda75cb4d0876da54@mail.gmail.com> <49A6FDC2.5060800@cgl.ucsf.edu> Message-ID: <605109E6-86FD-4D2F-B643-DD6EE9FDB075@cgl.ucsf.edu> Hi Bala, Although not helpful for your "salt bridge" example, in general I recommend searching the documentation (Help... Search Documentation in the Chimera menu) before searching the chimera-users archive. I will try to put something in the documentation that mentions salt bridges, although it may not happen right away (many many things need documentation!). Best, Elaine On Feb 26, 2009, at 12:38 PM, Conrad Huang wrote: > Searching Chimera mailing lists is implemented using Google. My first > guess regarding the problem you encountered is that Google has not > re-indexed our site yet. For example, the term "salt bridge" does not > find anything, but "putative binding" returns a message that was > posted > earlier. There does seem to be some oddities, eg an even earlier > message with "letter reference" in its title is not found by Google. > Unfortunately, I'm not familiar enough with Google to be able to > explain > the problems. My suspicion is that the messages posted in the current > month are found sporadically because the web pages are rebuilt > regularly > and perhaps Google is scanning us during the rebuilding process. Once > the messages are rotated into static archives at the end of the month, > they should be found consistently. > > I can only suggest that, if the search function is not returning hits > for a recent message, you try viewing the threads in the archive for > the > current month. If you've noticed older messages not being found, > please > let me know and I will dig further. > > Conrad > > Bala subramanian wrote: >> Dear Elaine, >> >> Long time back, I posted a question on *searching chimera archive >> for a >> keyword*. Just for an example, i gave "salt bridge" as a key word >> in the >> following link, but it dose nt show me the queries on salt bridge in >> chimera archive. I dnt undertand why ?. It would helpful for chimera >> loves like me not to repeat same queries and also to understand all >> ways >> of analyzing salt bridge based on previous queries. I am sorry if >> this >> question is not relevant to chimera technical issues. >> >> http://www.cgl.ucsf.edu/chimera/docs/feedback.html >> >> Cheers, >> Bala From newton at secsg.uga.edu Thu Feb 26 13:19:52 2009 From: newton at secsg.uga.edu (Gary Newton) Date: Thu, 26 Feb 2009 16:19:52 -0500 Subject: [Chimera-users] How to refer to Chimera in a Newsletter Message-ID: <10C86B13-7517-46E8-B105-AD80EB40B454@secsg.uga.edu> Hello... I am writing a newsletter for the SER-CAT synchrotron beamlines sector 22 at APS - the newsletter is called the "SER-CAT Spectrum" and is distributed primarily to beamline users. I have included a simple protein drawing produced by CHIMERA and indicated that the drawing was produced by CHIMERA. Should I include a trademark symbol or perhaps a copyright symbol after the name? Thanks for any advice. Best, Gary Newton University of Georgia Athens, GA From meng at cgl.ucsf.edu Thu Feb 26 14:09:51 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Thu, 26 Feb 2009 14:09:51 -0800 Subject: [Chimera-users] How to refer to Chimera in a Newsletter In-Reply-To: <10C86B13-7517-46E8-B105-AD80EB40B454@secsg.uga.edu> References: <10C86B13-7517-46E8-B105-AD80EB40B454@secsg.uga.edu> Message-ID: <0A3C300A-05A1-4922-926C-463C7CB43FFB@cgl.ucsf.edu> Hi Gary, No symbol is needed -- here is our standard info on how to cite UCSF Chimera: However, there is some wiggle room depending on how figure credits are usually done in your newsletter. The page above suggests an acknowledgement, literature citation, and URL, but if there is no provision for literature citations in your newsletter's figure credits, for example, you could just use the statement and possibly the URL. Thanks for using 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 Feb 26, 2009, at 1:19 PM, Gary Newton wrote: > Hello... > > I am writing a newsletter for the SER-CAT synchrotron beamlines sector > 22 at APS - the newsletter is called the "SER-CAT Spectrum" and is > distributed primarily to beamline users. > > I have included a simple protein drawing produced by CHIMERA and > indicated that the drawing was produced by CHIMERA. Should I include a > trademark symbol or perhaps a copyright symbol after the name? > > Thanks for any advice. > Best, > > Gary Newton > University of Georgia > Athens, GA From tef at cgl.ucsf.edu Thu Feb 26 14:11:58 2009 From: tef at cgl.ucsf.edu (Tom Ferrin) Date: Thu, 26 Feb 2009 14:11:58 -0800 Subject: [Chimera-users] How to refer to Chimera in a Newsletter In-Reply-To: <10C86B13-7517-46E8-B105-AD80EB40B454@secsg.uga.edu> References: <10C86B13-7517-46E8-B105-AD80EB40B454@secsg.uga.edu> Message-ID: <49A713AE.4080602@cgl.ucsf.edu> For a professional society publication such as this, it's fine to just indicate the image was produced by Chimera, without trademark or copyright symbol. It would be great if you could include the URL for our Chimera web site (www.cgl.ucsf.edu/chimera/) so that if someone wanted to follow-up and learn more, they'd have a place to go. Thanks! --tom --- Thomas Ferrin, PhD Professor of Pharmaceutical Chemistry and Biopharmaceutical Sciences Director, Resource for Biocomputing, Visualization, and Informatics University of California, San Francisco 600 16th Street, M/S 2240 San Francisco, CA 94158-2517 Phone: 415-476-2299 Fax: 415-502-1755 Email: tef at cgl.ucsf.edu Office: GH-N472 Gary Newton wrote: > Hello... > > I am writing a newsletter for the SER-CAT synchrotron beamlines sector > 22 at APS - the newsletter is called the "SER-CAT Spectrum" and is > distributed primarily to beamline users. > > I have included a simple protein drawing produced by CHIMERA and > indicated that the drawing was produced by CHIMERA. Should I include a > trademark symbol or perhaps a copyright symbol after the name? > > Thanks for any advice. > > Best, > > Gary Newton > University of Georgia > Athens, GA > _______________________________________________ > 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 Fri Feb 27 00:39:51 2009 From: damien.lariviere at fourmentinguilbert.org (=?ISO-8859-1?Q?Damien_Larivi=E8re?=) Date: Fri, 27 Feb 2009 09:39:51 +0100 Subject: [Chimera-users] Multiscale model of RNAP : fibrous aspect Message-ID: <49A7A6D7.1030606@fourmentinguilbert.org> Dear Elaine, I used the Multiscale Model tool to create a low resolution surface of the PDB 1L9U (TAQ RNA polymerase). The attached image is what I got with a resolution 4 : a fibrous structure. So, I wonder what such a fibrous aspect means or whether it means the tool has some difficulties to create the surface with this specific protein ? Thanks for your help Damien -------------- next part -------------- A non-text attachment was scrubbed... Name: RNAP_1L9U.jpg Type: image/jpeg Size: 93666 bytes Desc: not available URL: From sdecarlo at ccny.cuny.edu Fri Feb 27 04:49:40 2009 From: sdecarlo at ccny.cuny.edu (Sacha De Carlo) Date: Fri, 27 Feb 2009 07:49:40 -0500 (EST) Subject: [Chimera-users] Multiscale model of RNAP : fibrous aspect In-Reply-To: <49A7A6D7.1030606@fourmentinguilbert.org> References: <49A7A6D7.1030606@fourmentinguilbert.org> Message-ID: <20090227074940.BTN85141@pelican.admin.ccny.cuny.edu> Hi, What do you mean by difficulties of creating surfaces? I speak for a person coming from the cryo-em world, that T4 RNAP surface pretty much looks like a 4A 3D reconstruction based on cryo-EM data. Compare with Ludtke's GroEL structure at about 4 A (Ludtke et al., 2008, Structure 16:441-448). Maybe compare with surface renderings of the 4A X-ray structure of holoenzyme by Murakami (Science, 2002) or the first x-Ray structure of RNAP2 at ~5A by Darst? I am sure that the Chimera team will tell you more about how the surface is calculated, but it looks correct to me. Sincerely, - S ------------------------------------------ Sacha De Carlo, Asst. Professor Marshak Building Room 1335 The City College of NY (212) 650-6070/6582 E-mail: sdecarlo at ccny.cuny.edu http://www.planetesacha.com/Work.htm ------------------------------------------ From bala.biophysics at gmail.com Fri Feb 27 07:11:55 2009 From: bala.biophysics at gmail.com (Bala subramanian) Date: Fri, 27 Feb 2009 16:11:55 +0100 Subject: [Chimera-users] solvent accessible area Message-ID: <288df32a0902270711j2d6c5902vb15402a44548b55c@mail.gmail.com> chimerians, I want to calculate the solvent accessible surface area for each atom and write it in the pdb file, kindly tell me how to do it. This is something i used to do with GRASP. it calculates the sasa for each atom and it can be written as a pdb file with sasa in the last column. Thanks, hve nice weekend Bala -------------- next part -------------- An HTML attachment was scrubbed... URL: From goddard at cgl.ucsf.edu Fri Feb 27 09:57:34 2009 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Fri, 27 Feb 2009 09:57:34 -0800 Subject: [Chimera-users] Multiscale model of RNAP : fibrous aspect In-Reply-To: <49A7A6D7.1030606@fourmentinguilbert.org> References: <49A7A6D7.1030606@fourmentinguilbert.org> Message-ID: <49A8298E.3060300@cgl.ucsf.edu> Hi Damien, At 4 Angstroms you will see alpha-helices and beta-strands as you see here. But there is a special problem with the multiscale tool on PDB entry 1l9u. The trouble is that 1l9u has only backbone atoms N, CA, C. The multiscale tool uses to surface contour levels, one for models that include only CA atoms and one for models that contain additional atoms, usually all side-chain atoms. So 1l9u is using the contour level appropriate for models that include side-chain atoms. You can change these contour levels. In the Multiscale Models dialog on the line that says "Resurface - resolution 4" there is a check button that shows additional options. Change the "Threshold atom density" parameter from 0.02 to maybe 0.004 (closer to the CA-only level of 0.002) then press Resurface. The contour level is in number of atoms per cubic Angstrom. I've attached an image of what it looks like with that setting. (I used silhouette edges, a white background, and glossy lighting (Chimera 1.4 daily builds only) for my image.) Tom Damien Larivi?re wrote: > Dear Elaine, > > I used the Multiscale Model tool to create a low resolution surface of > the PDB 1L9U (TAQ RNA polymerase). The attached image is what I got > with a resolution 4 : a fibrous structure. So, I wonder what such a > fibrous aspect means or whether it means the tool has some > difficulties to create the surface with this specific protein ? > > Thanks for your help > > Damien > > ------------------------------------------------------------------------ > -------------- next part -------------- A non-text attachment was scrubbed... Name: 1l9u.png Type: image/png Size: 96681 bytes Desc: not available URL: From bshaanan at bgu.ac.il Fri Feb 27 10:11:23 2009 From: bshaanan at bgu.ac.il (Boaz Shaanan) Date: Fri, 27 Feb 2009 18:11:23 GMT Subject: [Chimera-users] solvent accessible area Message-ID: Hi Bala, The program areaimol in the ccp4 package will do just that (i.e. generate a pdb file with the sasa value in the b-factor column). ? Cheers, ?????????????? Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan? -------------- next part -------------- An HTML attachment was scrubbed... URL: From chiendarret at gmail.com Fri Feb 27 10:12:58 2009 From: chiendarret at gmail.com (Francesco Pietra) Date: Fri, 27 Feb 2009 19:12:58 +0100 Subject: [Chimera-users] Reverse of AddH Message-ID: Hi: Is it possible to remove all hydrogens by command, without intervening manually on the pdb file? I have to rmsd the starting (no H) pdb with the final structure after MD (with H). AddH command to the starting structure would place H not optimized, while MD has also changed the C-backbone conformation. Thanks francesco pietra From meng at cgl.ucsf.edu Fri Feb 27 11:35:27 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 27 Feb 2009 11:35:27 -0800 Subject: [Chimera-users] solvent accessible area In-Reply-To: <288df32a0902270711j2d6c5902vb15402a44548b55c@mail.gmail.com> References: <288df32a0902270711j2d6c5902vb15402a44548b55c@mail.gmail.com> Message-ID: Hi Bala, Chimera automatically calculates surface areas per atom and residue when you show the surface. They are attributes named "areaSES" (solvent-excluded) and "areaSAS" (solvent-accessible): You can color the structure using those values, or show them as sphere radii, or save them to an "attribute" file. It is possible to write a PDB file with the values in the B-factor column, but only by tricking Chimera into thinking they are B-factors, and you also lose digits to rounding that way, as well as the original B-factors. More details on how to do all of these things below. The issue is: why do you want the values in the B-factor column? I'm asking because I think Chimera has much better ways to handle and display all kinds of atom-associated and residue-associated values ("attributes"), as mentioned above. For example, open structure 2gbp and show its surface. Then open "Render by Attribute" (under Tools... Depiction). That dialog lists the attributes, and if you choose "areaSAS" you will see a histogram of the values in the structure. Render by Attribute allows showing the values on the structure with colors, etc, and saving the values to a file with File... Save Attributes. The file looks like this (I'm showing just the first several lines): attribute: areaSAS recipient: atoms :1.A at N 48.482898712158203 :1.A at CA 14.890939712524414 :1.A at CB 66.201515197753906 :1.A at C 1.1530930995941162 :2.A at N 1.2013516426086426 :2.A at CA 0.01819705031812191 :2.A at C 0.39648371934890747 :3.A at N 0.0 :3.A at CA 0.46803078055381775 If you instead want the totals per residue, in the Render by Attribute dialog choose attributes of "residues" and again choose attribute "areaSAS". This file format is the same as you could use to read in new attributes, with any name and values you want, and is described here: To write a PDB with the surface area values in the bfactor column: You could replace the real B-factors by the atomic areaSAS values using Attribute Calculator (calculate attribute "bfactor" for "atoms" with the Formula atom.areaSAS ) and then save the structure as a PDB file, but that is somewhat of a hack. 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 Feb 27, 2009, at 7:11 AM, Bala subramanian wrote: > chimerians, > > I want to calculate the solvent accessible surface area for each > atom and write it in the pdb file, kindly tell me how to do it. This > is something i used to do with GRASP. it calculates the sasa for > each atom and it can be written as a pdb file with sasa in the last > column. > > Thanks, > hve nice weekend > 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 Fri Feb 27 11:42:18 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 27 Feb 2009 11:42:18 -0800 Subject: [Chimera-users] Reverse of AddH In-Reply-To: References: Message-ID: <8D58BDF8-2D93-45E0-B208-D3B88A4535F3@cgl.ucsf.edu> Hi Francesco, command: delete element.H (or menu: Select... Chemistry... element... H, Actions... Atoms/ Bonds... delete ) 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 Feb 27, 2009, at 10:12 AM, Francesco Pietra wrote: > Hi: > > Is it possible to remove all hydrogens by command, without intervening > manually on the pdb file? > > I have to rmsd the starting (no H) pdb with the final structure after > MD (with H). AddH command to the starting structure would place H not > optimized, while MD has also changed the C-backbone conformation. > > Thanks > > francesco pietra > _______________________________________________ > 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 Feb 27 12:03:51 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 27 Feb 2009 12:03:51 -0800 Subject: [Chimera-users] Renaming chain directly in Chimera In-Reply-To: <49A8259A.6090808@fourmentinguilbert.org> References: <49A8259A.6090808@fourmentinguilbert.org> Message-ID: <61F1AFCE-FB49-4355-ACCF-6593AA7B8FC8@cgl.ucsf.edu> Hi Damien, For a more reliable response, please send mail to chimera-users at cgl.ucsf.edu rather than to me directly -- sometimes the others know the answer when I don't, and sometimes I'm away from work. Chimera doesn't provide a way to just choose some set of residues and give them any chain ID you want. It can reassign chain IDs if you are merging models, for example if you had two models that were both chain A, it could combine them into another model with chains A and B. However, I can't think of how that process could be used to do what you want in this situation. I've come across a few PDB-editing web servers, but I don't know which of these might do what you want. You may need to use SPDBV for pre- processing in this case. Here are the web servers in case they are of general interest: 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 Feb 27, 2009, at 9:40 AM, Damien Larivi?re wrote: > Dear Elaine, > > If a PDB structure contains 2 chains A and B, is it possible to > rename chain B as for example chain A directly in Chimera in order > to get one only chain ? Also, is it possible to rename part of > residues of a chain A (residues 256 to 312 for example) as chain B ? > > I ask this question because I often export low resolution surfaces > (obtained with Multiscale Models tool) in the vrml format or obj > format. However, I often have to color all the model (chains A and > B) in only one color and highlight a set of residues in another color. > > I know that I can do this by selecting the residues of interest, > coloring them by using Color zone, but the result is not exportable > in VRML (problem of vertex color or something like that). To avoid > export problem, it is very simple to rather rename chains and/or > reassign a letter to part of chain, which I do by using > SwissPDBviewer. So, can I do this in Chimera ? > > Thanks for your help > > Damien > From meng at cgl.ucsf.edu Fri Feb 27 12:50:57 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Fri, 27 Feb 2009 12:50:57 -0800 Subject: [Chimera-users] finding salt bridges Message-ID: > Hi everybody, I just realized my previous suggestion would not include the positively charged histidines, and I have not been able to think of a selector for just those nitrogens. > Example commands to first select by atom type and then find the H- > bonds: > > sel O2- | O3- | N3+ | Ng+ > findhbond selRestrict both saveFile ~/mydir/myfile Sorry about that, 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 goddard at cgl.ucsf.edu Fri Feb 27 13:26:23 2009 From: goddard at cgl.ucsf.edu (Tom Goddard) Date: Fri, 27 Feb 2009 13:26:23 -0800 Subject: [Chimera-users] Renaming chain directly in Chimera In-Reply-To: <61F1AFCE-FB49-4355-ACCF-6593AA7B8FC8@cgl.ucsf.edu> References: <49A8259A.6090808@fourmentinguilbert.org> <61F1AFCE-FB49-4355-ACCF-6593AA7B8FC8@cgl.ucsf.edu> Message-ID: <49A85A7F.1070405@cgl.ucsf.edu> Hi Damien, Chimera does export the colors in VRML including per-vertex colors on multiscale surfaces. I just tested this with the Octaga Player vrml viewer on Mac. As Elaine says Chimera is not able to edit chain ids of PDB models. Perhaps the effect you want can be achieved using the molmap Chimera command instead of the multiscale tool. This will only be useful if you are not using the symmetry replication capability of multiscale. You can create a surface for any set of residues at any desired resolution with molmap, for example, molmap #1:57-96.B 12 makes a 12 angstrom surface using residues 57 through 96 of chain B of molecule #1. To improve the smoothness of the surface add the grid spacing argument molmap #1:57-96.B 12 grid 2 Grid spacing defaults to 1/3 of resolution. The molmap command adds Gaussians for each atom to make a volume and displays a contour surface. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html Tom Elaine Meng wrote: > Hi Damien, > For a more reliable response, please send mail to chimera-users at cgl.ucsf.edu > rather than to me directly -- sometimes the others know the answer > when I don't, and sometimes I'm away from work. > > Chimera doesn't provide a way to just choose some set of residues and > give them any chain ID you want. It can reassign chain IDs if you are > merging models, for example if you had two models that were both chain > A, it could combine them into another model with chains A and B. > However, I can't think of how that process could be used to do what > you want in this situation. > > I've come across a few PDB-editing web servers, but I don't know which > of these might do what you want. You may need to use SPDBV for pre- > processing in this case. Here are the web servers in case they are of > general interest: > > > > > 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 Feb 27, 2009, at 9:40 AM, Damien Larivi?re wrote: > > >> Dear Elaine, >> >> If a PDB structure contains 2 chains A and B, is it possible to >> rename chain B as for example chain A directly in Chimera in order >> to get one only chain ? Also, is it possible to rename part of >> residues of a chain A (residues 256 to 312 for example) as chain B ? >> >> I ask this question because I often export low resolution surfaces >> (obtained with Multiscale Models tool) in the vrml format or obj >> format. However, I often have to color all the model (chains A and >> B) in only one color and highlight a set of residues in another color. >> >> I know that I can do this by selecting the residues of interest, >> coloring them by using Color zone, but the result is not exportable >> in VRML (problem of vertex color or something like that). To avoid >> export problem, it is very simple to rather rename chains and/or >> reassign a letter to part of chain, which I do by using >> SwissPDBviewer. So, can I do this in Chimera ? >> >> Thanks for your help >> >> Damien >> >> > > _______________________________________________ > 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 Sat Feb 28 12:40:43 2009 From: meng at cgl.ucsf.edu (Elaine Meng) Date: Sat, 28 Feb 2009 12:40:43 -0800 Subject: [Chimera-users] finding salt bridges In-Reply-To: References: Message-ID: Hi everybody, At long last, a complete explanation of using "findhbond" to find only salt bridges: > Select charged functional groups and then use the FindHBond option > to find only H-bonds with both ends selected. This option is in the > GUI and is also available as a keyword of the findhbond command: > > > > > Selecting charged functional groups: > The following command selects atom types in charged groups commonly > found in amino acids and nucleotides, excluding histidines: > select Ng+ | N3+ | N2+ | O2- | O3- > > That's better than using residue names, because it also gets the > free N-term and C-term and most charged ligand functional groups, > and it is not necessary to specify "side chain only" to exclude > neutral backbone hydrogen-bonding groups. However, we don't have a > thiolate sulfur atom type; if there is specific Cys thiolate you > wish to consider, you would have to add that sulfur to the selection > manually. > > Another caveat is that the selection command above does not include > histidines. You could use > > select Ng+ | N3+ | N2+ | O2- | O3- | :his at nd1,ne2 > > but that would get nitrogens in neutral histidine sidechains as well > as the positively charged. A more correct possibility with more > steps is to: add hydrogens (AddH tool or command addh), add charge > (Add Charge tool or command addcharge), and then use > > select Ng+ | N3+ | N2+ | O2- | O3- | :/amberName=HIP & @nd1,ne2 > > (The charge assignment process identifies which histidines are > doubly protonated and assigns them the AMBER residue name HIP.) There are additional atom types for charged functional groups, but they would not occur in proteins. If manmade ligands are involved, however, you may want to take a look at the list of atom types and possibly add N1+,P3+,S3+,S3- (no, that's not thiolate even though it sounds like it) to the selection command. Apologies for the earlier incomplete explanation. 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 Feb 27, 2009, at 12:50 PM, Elaine Meng wrote: > > I just realized my previous suggestion would not include the > positively charged histidines, and I have not been able to think of a > selector for just those nitrogens. > >> Example commands to first select by atom type and then find the H- >> bonds: >> >> sel O2- | O3- | N3+ | Ng+ >> findhbond selRestrict both saveFile ~/mydir/myfile >