- Chimera-users - RBVI Mailing Lists

problem with chimera 1.4
by lionel nauton 23 Oct '09

23 Oct '09

thank's for your answer Victor Sure that the Action Mark is active, my problem is for the distance, label or H-bond printing, they stay fixed when the models are moving.

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trying to process 1000 proteins via Chimera
by Bisn 21 Oct '09

21 Oct '09

Hello, We are Chimera users trying to process 1000 proteins, e.g., add hydrogen and charge. We want to do this via a Chimera for DOCK preparation. I know that Chimera accepts command line, but this is not realizable for processing 10000 molecules. Have you any idea of the task? Thanks! Jian Chen

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Calculation of RMSD between 2 PDB structures automatically
by Sumitro Harjanto 21 Oct '09

21 Oct '09

Hi, I have about 150 peptide structures in PDB format. I would like to compare each of them with a Template Structure (also in PDB format) and obtain an RMSD measurement for each comparison. These peptides are similar in structures to the template but may have very low sequence similarity/conservation. So my question is: 1. what is the command I should use given this scenario..? I was quite confused with the many different commands such as: rmsd, match, ensemblematch, matchmaker,... can anyone enlighten me on the differences among them. I would like to find one which can align/superimpose 2 peptides and calculate RMSD (Ca or backbone) 2. Is there a way to automate the process through scripting..? I'm still young with CHIMERA so please pardon my ignorance. =] Cheers, Sum

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Re: [Chimera-users] using CHIMERA to measure RMSD for large number of short peptides against a template structure
by Elaine Meng 21 Oct '09

21 Oct '09

On Oct 21, 2009, at 6:45 AM, Sumitro Harjanto wrote: > > Background: > Basically I would like to compare peptide to peptide and obtain the > RMSD between the two peptides using CHIMERA. These peptides may > have different lengths (eg 9-mer vs 10-mer) and they are not > conserved at all, in fact, they can be quite different in sequence. > They however have similar structures. > > Problem: > I have a dilemma in choosing which alignment method to use. If I > use matchmaker, which is based on sequence alignment, only selected > amino acid pairs will be measured (since the peptides are not > conserved); if I use match instead, the peptides have to be of > equal length, but they are not. Is there way to get around this > dilemma..? > I need the RMSD value to be exported from CHIMERA. I understand > that CHIMERA kept a log (replylog) for each session. Is there a way > for me to extract the content of this file? Or is there any other > way to keep a record of the RMSD values (since I would need to > automate this process to calculate RMSD for many pairs of peptides. > Thanks, > Sumitro Hi Sumitro, Matchmaker does not require the sequences to be identical, but generally it is intended for homologous proteins with at least partly conserved sequences and secondary structures. If you are working with short peptides, I agree that matchmaker will probably not give the matches that you want, so "match" would be the way to go. The "match" command does not require that the overall structures have the same number of atoms, only that you tell it to use equal numbers of atoms from the two models. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rmsd.html> For example, model 0 could be some protein with residues 1-500 in chain A and residues 1-250 in chain B, while model 1 is your peptide that only has 10 residues. In the match command you just say exactly which atoms and residues should be used. When the residues are of different types, you would normally just use their backbone atoms instead of the whole residues, which could have different numbers of atoms. Examples: match #1:1-10@ca #0:1-10.a@ca match #1:1-10@n,ca,c,o #0:425-434.b@n,ca,c,o match #1:2-9@ca #0:4.a,6-9.a,8-10.b@ca The RMSD values will be reported in the Reply Log (under Favorites menu). You can copy the text in it and paste to a file. Or, if you are running Chimera in "nogui" mode, this information can be redirected to a file as described in this previous post: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-September/ 003064.html> For more about scripting to process multiple structures, see previous posts such as: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-November/ 003261.html> <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-November/ 003262.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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Chimera 1.4 release candidate
by Elaine Meng 21 Oct '09

21 Oct '09

Hi everybody, Candidate builds for the Chimera 1.4 production release are now available. <http://www.cgl.ucsf.edu/chimera/download.html> As detailed in the release notes, <http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.4.html> many new features have been added since the 1.3 release. Please try the candidate and report any problems. Thanks, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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Incompatibility between --nogui and viewdock scripting ?
by Aurelien Grosdidier 20 Oct '09

20 Oct '09

Dear all, I'm trying to create a minimal chimera script that loads a PDB structure, then loads docking results (Dock format), saves the result and exits, as follows: open mystructure.pdb viewdock myresult.dock4 "Dock 4, 5 or 6" save result.py stop This works perfectly, when I launch Chimera (1.4rc 32-bits on Kubuntu 9.04 AMD64) : chimera --script mkview.com However, when I try to get rid of the display by adding the --nogui switch, chimera crashes with the following stack trace: ...Traceback (most recent call last): File "CHIMERA/share/chimeraInit.py", line 425, in init chimera.openModels.open(a, prefixableType=1) File "CHIMERA/share/chimera/__init__.py", line 1439, in open File "CHIMERA/share/Midas/ChimeraExtension.py", line 32, in func File "CHIMERA/share/Midas/midas_text.py", line 101, in processCommandFile File "CHIMERA/share/Midas/midas_text.py", line 132, in _processFile File "CHIMERA/share/Midas/midas_text.py", line 64, in makeCommand File "CHIMERA/share/ViewDock/ChimeraExtension.py", line 42, in cmdViewdock File "CHIMERA/share/ViewDock/base.py", line 97, in __init__ File "CHIMERA/share/chimera/baseDialog.py", line 523, in __init__ File "CHIMERA/share/chimera/baseDialog.py", line 244, in __init__ File "CHIMERA/share/ViewDock/base.py", line 286, in fillInUI TclError: invalid command name "tix" Error while processing mkview.com: TclError: invalid command name "tix" File "CHIMERA/share/ViewDock/base.py", line 286, in fillInUI See reply log for Python traceback. Any idea / workaround ? Cheers, -- Aurélien Grosdidier Molecular Modeling Group Swiss Institute of Bioinformatics PS: I already tried Xvfb with no luck (segfault, this might be a *buntu bug, though).

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minimize without addh and without GUI
by richardbonnet 19 Oct '09

19 Oct '09

Dear users Would you give me the best way to minimize the hydrogens in ligands with chimera used without GUI and without addh? I use : chimera --nogui --nostatus ligand_1.mol2 ./script.py here is script.py : from chimera import runCommand runCommand("select @H=") runCommand("minimize freeze unselected nsteps 1000") runCommand("write format mol2 0 out.mol2") However, chimera add wrong hydrogen because of the load of addh with minimize. I have a lot of ligands to process and I can not use GUI. thank you much for your help, Richard Bonnet Universite Auvergne

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Running chimera in Intel Core 2
by Dimitrios Evangelopoulos 19 Oct '09

19 Oct '09

Hi everyone, Just a question regarding running chimera on a Intel Core 2 cpu. Do you know if it is running propeprly? I just show that you mention that Chimera uses the Intel Pentium instruction set so wondering before download it. Thanks in advance. Best regards, Dimitrios Evangelopoulos, PhD student

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chimera 1.4 and Windows 7
by Boaz Shaanan 19 Oct '09

19 Oct '09

Hi, Has the latest production release (1.4) been also tested under Windows 7 ? Does it work OK ? Thanks, 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

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bond order
by Dan Gurnon 19 Oct '09

19 Oct '09

I was wondering if there are plans to enable the display of bond order in ball and stick mode? -- ____________________________ Daniel Gurnon, Ph. D. Assistant Professor of Chemistry DePauw University Greencastle, IN 46135 p: 765-658-6279 e: danielgurnon(a)depauw.edu

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