- Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] coloring seperate domains
by Elaine Meng 23 Oct '08

23 Oct '08

On Oct 22, 2008, at 1:52 PM, Chin-Hsien (Emily) Tai wrote: > > We would like to use Chimera as a visualizing/figure drawing tool to > compare different domain parsing schemes and we are wondering how to > automate the process as much as possible. The tasks are: > 1.fetch a PDB > 2.select Chain (for example B) > 3.Invert (all models) > 4.Atoms/Bonds delete > 5.chain trace only > 6.backbone only > 7.Ribbon show rounded > > I am wondering if there is a simple way to combine step 1 to 4 to > display only specified chain in PDB? > Then rotate the structure to minimize domain overlapped area. > > Then color each domain according to different parsing schemes, for > example: > scheme1 "color red #0:1-38.A 150-190.A; color green #0:39-149.A; > color blue #0:192-347" > scheme2 "color red #0:1-30.A 160-195.A; color green #0:31-159.A; > color blue #0:196-347" > > Can Chimera read a script and displays different domains in > different colors? > Thanks for your advice in advance! > Cheers, > Emily, Dear Emily, You can definitely do all those steps in a script, except I'm not sure how to automatically orient the structure to best show the domains. I'll discuss the other parts first. A Chimera command script is just a text file containing the same things you would enter at the command line. If you name the file something.com or something.cmd it will automatically execute when opened in Chimera (with File... Open or the command "open"). Chimera can also execute python scripts (something.py) in the same way. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/indexcommand.html#cmdfile > There are many possibilities for either type of script, but here are some example Chimera commands: open 2mnr delete ~ :.a ribbon ribrep rounded ~disp color red :3-132 color dodger blue :133-359 copy png file 2mnr.png This set of commands fetches PDB structure 2mnr, deletes everything that is NOT chain A, displays ribbon, uses the rounded ribbon style, undisplays all atoms, colors the specified residue ranges, and saves an image in PNG format. You don't have to specify the chain in the coloring command since there is only one chain left. Each of these commands has a manual page if you want to see details (for example, there are other image formats such as TIFF). You can try the commands in the Command Line to see what works before putting them into a script. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/framecommand.html> For saving images, you might want to make the background white (set bg_color white) before using the script, or after opening each structure use the ribbons preset and then a publication preset (preset apply int 1; preset apply pub 1) instead of ribbon and ribrep rounded. <http://www.cgl.ucsf.edu/home/meng/docs/UsersGuide/print.html#tips> There are some fancier approaches that may facilitate processing a large number of structures. You can separate the structure-specific and general commands using aliases: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/alias.html> alias mypdb 2mnr alias mychain :.a alias dom1 :3-132 alias dom2 :133-359 ~alias dom3 ~alias dom4 alias output /Users/meng/Desktop/2mnr.png # # the following general commands could be put in a separate file # open mypdb delete ~ mychain preset apply int 1 preset apply pub 1 color red dom1 color dodger blue dom2 color yellow dom3 color magenta dom4 copy png file output close 0 This structure only has two domains, so I clear any previous dom3 and dom4 assignments from previous structures. There will be error messages when commands refer to nonexistent aliases, but they can be ignored. The reason you might want to separate the specific and general commands is that all of the general commands can then be put in a second command file (for example named "process.com" ) that is opened by the first script. The second script file could be in the same directory (folder) as the first, or you could specify its whole pathname. alias mypdb 2mnr alias mychain :.a alias dom1 :3-132 alias dom2 :133-359 ~alias dom3 ~alias dom4 alias output /Users/meng/Desktop/2mnr.png open /Users/meng/Desktop/process.com # # now go to next structure # alias mypdb 4enl alias mychain :.a alias dom1 :1-141 alias dom2 :142-436 ~alias dom3 ~alias dom4 alias output /Users/meng/Desktop/4enl.png open /Users/meng/Desktop/process.com [... etc.] Putting the general commands in a separate file minimizes the number of lines in the primary command file. However, it may still be tedious if you are processing a very large number of structures. Since I don't know python, I would probably write a script or program (in some other language) to make the long main Chimera command file. If you know python, another approach is to make the main script python instead of Chimera commands, and have it cycle through multiple structures. You could call the Chimera commands in my examples from inside the python script. Finally, now about orienting the structure to best show the domains. The only way I can think of with Chimera commands is to use "align" to put domains 1 and 2 front and back, then rotate 90 degrees, for example: align dom1 dom2 turn y 90 That worked pretty well in my tests. Those commands could be in the general script (process.com in my example), assuming all the structures have at least two domains, before the image-saving command. There are some other possibilities that require python; I'll get back to you if we come up with something good. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng(a)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

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Re: [Chimera-users] Chimera-users Digest, Vol 66, Issue 20
by Ibrahim Moustafa 22 Oct '08

22 Oct '08

Hi All, I figured it out. The problem turned to be the resolution of the files that did not play in the powerpoint. Editing the movie to have a lower resolution enabled the file to play fine in the powerpoint. I wonder if there can be an option to determine the resolution in the output file from Chimera to avoid such problems with powerpoint and also, this can be added to the tips on Chimera site for making the movie for use in powerpoint: "make sure of the produced file to match the projector and the computer. Usually, something like 800x600 should work" Thanks to Elaine for her help. Ibrahim On 10/22/08 3:00 PM, "chimera-users-request(a)cgl.ucsf.edu" <chimera-users-request(a)cgl.ucsf.edu> wrote: > Send Chimera-users mailing list submissions to > chimera-users(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users > or, via email, send a message with subject or body 'help' to > chimera-users-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-users-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-users digest..." > > > Today's Topics: > > 1. Question about movie in powerpoint (Ibrahim Moustafa) > 2. Re: Question about movie in powerpoint (Elaine Meng) > 3. Re: orthogonal views (Elaine Meng) > 4. Re: orthogonal views (Tom Goddard) > 5. Re: orthogonal views (Greg Couch) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 22 Oct 2008 13:05:51 -0400 > From: Ibrahim Moustafa <I.moustafa(a)psu.edu> > Subject: [Chimera-users] Question about movie in powerpoint > To: "chimera-users(a)cgl.ucsf.edu" <chimera-users(a)cgl.ucsf.edu> > Message-ID: <C524D5AF.343C%I.moustafa(a)psu.edu> > Content-Type: text/plain; charset="us-ascii" > > Dear Chimera team who is always giving the best support, > > I have a question regarding movie playing in power point and hope you can > help. > > I'm setting a power point presentation and want to play some movie (.avi > MSMPEG-4v2), created in Chimera, in the presentation. The movie play fine; > however, if I'm in the presenter view mode it does not play and gives me a > black screen. > I tried to re-insert the movie, change the view size, put everything in the > same place...but none of these solved the problem. > > The funny thing is that other movies bigger in size can play fine in the > presenter view mode. These have the same format (avi MSMPEG-4v2) and created > using the same program. > > Do you have any idea how to resolve this issue? Any advice is more than > welcome. > > Also, I noticed that sometimes the movie, that is known to be working > fine, does not work for unknown reason. > Especially in the case of 2 movies in the same slide. Any tips to have two > movies in the same slide to work in a more robust way is really appreciated. > > Really appreciating your help, thanks; > Ibrahim

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orthogonal views
by Thomas C. Marlovits 22 Oct '08

22 Oct '08

Hi Chimera's ... is there an easy way to create orthogonal views at the same time of a molecule ? The idea is to open a (pdb) file and visualize the molecule from orthogonal directions at the same time in one viewer. Rotation/ movemements of the molecule should be done then on all three views at the same time of course. Maybe you have already implemented such an option (similar to the stereo viewing ...) Tx, -T. ------------------------------------------------------------------------ ------- Thomas C. Marlovits, PhD, M.A.S. Research Group Leader IMP-IMBA Research Center - Research Institute of Molecular Pathology (IMP) - Institute of Molecular Biotechnology, Austrian Academy of Sciences (IMBA) Dr. Bohr-Gasse 3 Room IMBA/6.02 A-1030 Vienna Austria, Europe fone: (++43-1) 79044-4630 fax: (++43-1) 79044-4401 email: marlovits(a)imp.univie.ac.at

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Question about movie in powerpoint
by Ibrahim Moustafa 22 Oct '08

22 Oct '08

Dear Chimera team who is always giving the best support, I have a question regarding movie playing in power point and hope you can help. I'm setting a power point presentation and want to play some movie (.avi MSMPEG-4v2), created in Chimera, in the presentation. The movie play fine; however, if I'm in the presenter view mode it does not play and gives me a black screen. I tried to re-insert the movie, change the view size, put everything in the same place...but none of these solved the problem. The funny thing is that other movies bigger in size can play fine in the presenter view mode. These have the same format (avi MSMPEG-4v2) and created using the same program. Do you have any idea how to resolve this issue? Any advice is more than welcome. Also, I noticed that sometimes the movie, that is known to be working fine, does not work for unknown reason. Especially in the case of 2 movies in the same slide. Any tips to have two movies in the same slide to work in a more robust way is really appreciated. Really appreciating your help, thanks; Ibrahim -- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., University Park, Pennsylvania State University PA 16802 Tel. (814) 863-8703 Fax (814) 865-7927

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About Amber residue number renumbering
by Francesco Pietra 22 Oct '08

22 Oct '08

Hi Elaine: At the end of a long journey of ACE/NME capping a fractionated model, I would not leave the impression that I like the way Amber treats the layout of pdb files. With Chimera I had all HETATM capping groups on one side and the ATOM of protein stretches on another side, conserving the residue number they had in the unabridged model. Straightforward to relate to the starting crystallographic work Now, after Amber forced (forced against me) manipulation, the ACE/NMR residues are intermingled with the standard amino acid, all ATOM, and take part to the overall sequential numbering. As the number of atoms in ACE differs from NME, and the stretches are many, headache in relating residue numbers imposed by Amber to residue numbers in the original crystallographic work from which I started. Regards francesco pietra

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Error when fetching pdb by ID
by Kenward Vaughan 21 Oct '08

21 Oct '08

Hmm... is this my system or outside it? I'm at home behind a firewall and have never seen such an error before. I'm not sure where I should look for an answer... Fetch by ID. The error log: Opening 1ai2 Error reading 1ai2: Error during PDB fetch: [Errno socket error] (-2, 'Name or service not known') Done opening 1ai2 It doesn't fail at work, so I'm suspicious of my home network. ??? Both my workstation and gateway/firewall are Debian/Sid boxes. What port is the call made on?? Thanks for any ideas! Kenward -- ."^~;,_ Dr. Kenward Vaughan `:,'~~~~~ Professor of Chemistry \;:/ Chair, Physical Science Department |,;| Bakersfield College / ', \ 1801 Panorama Drive / o O \ Bakersfield, CA 93305 (oOoOOoOo) http://www2.bc.cc.ca.us/kvaughan ---========--- ???$$MM$$???

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Fwd: Pruning pdb graphically
by Francesco Pietra 21 Oct '08

21 Oct '08

Hi Elaine: LEaP does not understand capping, with a pdb file that Chimera understands perfectly. I have asked for light at both the Amber and Dock sites. Even Dock uses LEaP for amber score. LEaP adds and exta H to the terminal/beginning and OXT to the terminal/last. Moreover, it tries to join the first ACE with last NME. I have not tried separating the capping residue with TER. francesco ---------- Forwarded message ---------- From: Francesco Pietra <chiendarret(a)gmail.com> Date: Tue, Oct 21, 2008 at 10:34 AM Subject: Re: [Chimera-users] Pruning pdb graphically To: Elaine Meng <meng(a)cgl.ucsf.edu> Hi Elaine: I had fully protonated histidine and left the chain amino group of lysine in basic form! No excuse for that. Now the charge is 5.0000 so that I expect that dockprep (avoiding add-h!) will work. In my (brief) experience, Chimera is an excellent tool also for capping, especially if Add-H is revised for the cases of capped residues. In some cases (12 residues capped in my case) that is important. Also because I want to run MD under various pH conditions, so that capping will change (constant pH MD is not possible with Amber under explicit medium conditions). That Amber has updated to PDB rules is good news. Perhaps I was so suspicious because a few days ago I found a bug with the latest version of ambpdb (Amber's tool to get a pdb file from inpcr/prmtop): the N-hydrogen names for LEU as first residue are written incorrectly. A revised ambpdb is forthcoming. Regards francesco On Tue, Oct 21, 2008 at 12:49 AM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > > After looking at more parameter files, I now believe that Amber and PDB atom > names in standard residues, including hydrogens, are the same. My previous > information was old (I haven't run Amber for 10 years!), sorry about that. > You would still need to worry about correctly naming any atoms changed or > added with Build Structure, though. > > Besides the Amber *lib files mentioned before, you can also look up the > standard atom names in the links from this PDB page: > http://remediation.wwpdb.org/downloads.html > > Elaine > > > On Oct 20, 2008, at 2:39 PM, Elaine Meng wrote: > >> I forgot to mention that usually you don't need to worry about the atom >> names, as Add Charge knows which PDB names go with which Amber >> names/charges, and AddH uses the standard names. >> >> I think you only have to worry about the names of atoms that were changed >> or added "manually" in Build Structure, and if the nonhydrogen atoms have >> the standard names (PDB = Amber for nonhydrogen atoms in standard residues), >> AddH will use correct names for the hydrogens later added to those atoms. >> If you use hydrogens added by Build Structure, however, you have to fix >> their names. >> >> Elaine >> >> > >

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Residue Accessibility
by Luis Alberto Alvarez 21 Oct '08

21 Oct '08

Hello, I am trying to calculate the relative surface accessibility of residues (It will come to getting the solvent accessibility I guess) and the only information I found is from a post in the mailing list dating to 2005 ( http://www.cgl.ucsf.edu/pipermail/chimera-users/2005-October/000482.html)I am just wondering if there is anything new in this front or I should just follow the 2005 instructions. Thank you -- Luis Alvarez alvarez(a)lcp.u-psud.fr Laboratoire de Chimie Physique Université Paris-Sud à Orsay microscope: 01 69 15 30 31 (80% du temps) bureau: 01 69 15 56 15

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Presets and multiple structures
by James Nettles 16 Oct '08

16 Oct '08

Something that often comes up is that I have some number of aligned protein structures with nicely color coded secondary features and specific side chains. I then want to fit another molecule in this same space and apply a "preset" graphic mode to the new structure without undoing the previous molecular views. I expect this is possible, but I haven't gotten it to work yet. I've tried making only my molecule of interest "active" in the Model Panel, but the preset still effects everything. I'm using Alpha build 2557 2008/09/13 at the moment. Thanks, Jim ________________________________________________________ James Nettles, Ph. D. Assistant Professor Department of Pediatrics, Emory University School of Medicine Laboratory of Biochemical Pharmacology (LOBP) Computer Assisted Discovery Research Environment (CADRE) ________________________________________________________

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Building ACE, NME (peptide caps)
by Elaine Meng 16 Oct '08

16 Oct '08

On Oct 16, 2008, at 6:22 AM, Francesco Pietra wrote: > Hi Elaine: > Thanks. > Is it possible with Chimera to cap the the protein termini (once the > work below is carried out) with ACE and NMA residues? I have no > experience with such a procedure. > francesco Hi Francesco, I wouldn't recommend doing it in Chimera. If you are using AMBER anyway, do it with that program. In Chimera, you could do it by using Build Structure (under Tools... Structure Editing), Modify Atom section. It would take several cycles of atom modification, being careful to name the residues ACE and NME and to give the atoms the correct types and names as you build out. For the first atom in the new residue you would use "change modified residue's name to ACE" (or NME) and then for the rest of the atoms in the residue, leave the residue name unchanged. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.ht… > Then, because the names of hydrogens added while building aren't standard for those residues, either delete all the hydrogens and re- add them using AddH, or use Modify Atom to change the hydrogen names to what AMBER expects (shown below), or just write out the file and use a text-editor to change their names. It is easy to make mistakes in this long process. In addition, I just found a bug where addh still thinks the first amino acid has a free N-terminus even though it is capped by ACE, so if you use addh, you would then have to delete the two hydrogens on the first amino acid's nitrogen and then use Build Structure (Modify Atom) on that nitrogen to make it trigonal and get one hydrogen back, and then change the name of that hydrogen to H. THEN you would get correct charges from addcharge. The atom names that AMBER (and addcharge) expect: for ACE: C O CH3 HH31 HH32 HH33 for NME: N H CH3 HH31 HH32 HH33 If you are capping the residues to avoid terminal charges on residues that are not really the termini, there is no need to do this. AddH looks at the SEQRES information in the file to decide what is really a terminal residue. If it is not a real terminus (for example, the structure starts at residue 5 because 1-4 are disordered), the residue will still be treated as an internal residue starting with NH-CA- (etc.) not as NH3+-CA-(etc.). The C-terminus is handled similarly, (...)C(=O) if not a real terminus instead of (...)CO2 minus for the real C-terminus. Best, Elaine ----- Elaine C. Meng, Ph.D. meng(a)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

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