October 2012 - Chimera-users - RBVI Mailing Lists

Re: [Chimera-users] segmentation fault
by Tim Richardson 25 Oct '12

25 Oct '12

Hi, I'm getting segmentation faults when using chimera. I tried to produce a backtrace, but got an error: [tim@nest ~]$ gdb chimera core.3777 GNU gdb (GDB) Fedora (7.4.50.20120120-50.fc17) Copyright (C) 2012 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html > This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. Type "show copying" and "show warranty" for details. This GDB was configured as "i686-redhat-linux-gnu". For bug reporting instructions, please see: <http://www.gnu.org/software/gdb/bugs/>... "/usr/bin/chimera": not in executable format: File format not recognized [New LWP 3777] [New LWP 3787] Core was generated by `/opt/UCSF/Chimera-1.6.2/bin/python2.7 /opt/UCSF/Chimera-1.6.2/share/__main__.py'. Program terminated with signal 11, Segmentation fault. #0 0xb578ddc7 in ?? () (gdb) bt #0 0xb578ddc7 in ?? () #1 0x0963be90 in ?? () Backtrace stopped: previous frame inner to this frame (corrupt stack?) Could you advise how I might avoid a segmentation fault and what I'm doing wrong with the backtrace. Is there anything I can do short of installing a VM and running the windows version? Many thanks, Tim Richardson @timrich

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Regarding Metal Fixing in Protein
by Amit Jaiswal 24 Oct '12

24 Oct '12

Dear Sir /Mam, I am new to Chimera and thus facing problems in inserting Metal in my protein. I am using the Build structure command in Chimera but I am unable to move the metal from one place to the other. Please guide me out in fixing the metal. -- Yours Sincerely, ~~~~~~~~~~~~~~~~~~~~~~~~ Amit Jaiswal, Department of Bioinformatics, School of Life Sciences, Pondicherry Central University, Kalapet, Pondicherry, Puducherry - 605 014. Phone No.: +91 8124954834. ~~~~~~~~~~~~~~~~~~~~~~~~~

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pipes and planks
by Ishu Saraogi 23 Oct '12

23 Oct '12

Dear Chimera Users: I have been trying to makes pipes and planks in different colors for a co-crystal structure. I want each protein to be a certain color. The user manual says that I need to select "No colors" in the pipes and planks menu. However, this button is deactivated in my program. Has anyone else had that problem and is there a fix? I have tried using axes/planes command but it does not give me loops and sheets that I also need. Any advice will be greatly appreciated. Thanks! Ishu -- Ishu Saraogi, Ph.D. Postdoctoral Scholar California Institute of Technology 1200 E. California Blvd., MC 147-75 Pasadena, CA 91125-4100 USA Phone: (626)395 4071

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Label help
by Hansen, Bryan (NIH/NIAID) [F] 23 Oct '12

23 Oct '12

Hi all, I was wondering how to increase the font size of the label of an amino acid? I'm guessing this is really simple and I'm just missing something, but any tips are appreciated. Bryan

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scripting problem
by Strotz von Moos Dean 22 Oct '12

22 Oct '12

Hi, I have a question to the following code. I can not figure out why certain atom types are not understood (HG, QD etc). The atom types occur in the structure and I can select them through the terminal or add them as pseudo bonds through the pseudoBond reader. For a QD1 one for instance I get: KeyError: 'QD1' <module> grp.newPseudoBond(res[r1].atomsMap[A1][0],res[r2].atomsMap[A2][0]) Excerpt from the input file: 7 HA 7 H red #this is understood 7 H 7 QD1 yellow #error message for QD1 What is wrong with my code? The A1 = str(A1) ? How would I do it alternatively? All the best and many thanks Dean import chimera from chimera.colorTable import getColorByName from chimera.misc import getPseudoBondGroup from chimera import runCommand as rC # use 'rc' as shorthand for runCommand model = chimera.openModels.open('xxx.pdb') rC('show #0') rC('ribbon') rC('ribcolor gray') rC('background solid white') rC('unset depthCue') ins = open('pseudobondsToAdd.txt', "r" ) array = [] for line in ins: array.append(line) ins.close() for line in array: r1, A1, r2, A2, c = line.split() # Split the line on white space. r1 = int(r1) r2 = int(r2) A1 = str(A1) A2 = str(A2) c = str(c) res = model[0].residues grp = getPseudoBondGroup("mybonds", associateWith=model) grp.newPseudoBond(res[r1].atomsMap[A1][0],res[r2].atomsMap[A2][0]) grp.color = getColorByName(c) ETH Zürich Dean Strotz Laboratorium f. Physikalische Chemie HCI F 217 Wolfgang-Pauli-Str. 10 8093 Zürich E-Mail: dean.strotz(a)phys.chem.ethz.ch<mailto:dean.strotz@phys.chem.ethz.ch>

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Show molecular surface for one chain only
by Hurt, Darrell (NIH/NIAID) [E] 22 Oct '12

22 Oct '12

Hi Chimera folks, I have a peptide bound to a protein. They are two separate chains in single PDB. I want to show the molecular surface for the protein, but not the peptide (to see the surface where the peptide binds to the protein). This is easy (the default, actually) for small molecules. But when I select the chain of the protein and display its surface, the surface is "broken" around the peptide and I cannot see what I want. The rest of the surface is OK, but in the area of interest, I cannot see the surface. I tried the "Intersurf" command and it sort of works, but I want an MSMS molecular surface of the protein with the peptide sitting in it. Is there some trick for this other than separating the peptide from the protein and putting it into a separate model? Thanks, Darrell Darrell Hurt, Ph.D. Section Head, Computational Biology Bioinformatics and Computational Biosciences Branch (BCBB) OCICB/OSMO/OD/NIAID/NIH 31 Center Drive, Room 3B62B, MSC 2135 Bethesda, MD 20892-2135 Office 301-402-0095 Mobile 301-758-3559 http://bioinformatics.niaid.nih.gov (Within NIH) http://exon.niaid.nih.gov (Public) Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.

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Feature request: changing default color for H-bonds
by Miguel Ortiz Lombardía 21 Oct '12

21 Oct '12

Hi, I think the subject of the message is explicit enough... Perhaps the option of having a default color different than cyan for hydrogen bonds already exists, but I have failed to find it. I have this line in my .chimera/preferences file: 'FindHBonds': {'line width': 2.0}, So I tried to include something like 'color: (0.0, 0.0, 0.0, 1.0)' (or bond color or H-bond color...) in the FindHBonds dictionary, alas without success. Let me give some rationale: I prefer having a white background, against which cyan is not really very visible when the structure gets complex. Not to me eyes at least. Thank you! Best regards, -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR7257) CNRS, Aix-Marseille Université Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 mailto:miguel.ortiz-lombardia@afmb.univ-mrs.fr http://w2.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia

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coloring 3D maps according to local cross-correlation fit of docked PDB structures
by Jean-Francois Menetret 19 Oct '12

19 Oct '12

Dear users, we would like to color a Cryo-EM map according to the cross-correlation fit of docked PDB structures. Is that possible in Chimera ? Best wishes J-F Menetret

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H-bonds - molecules selection questions
by Marek Maly 19 Oct '12

19 Oct '12

Hello all, #1 I am just curious if it is in Chimera implemented possibility to select all the molecules which are connected via H-bonds with previously selected ("primary") molecule. If it is not implemented I would vote for putting it in the developers queue as it would allow to show easily and clearly (after action command "show selected only") just all the molecules from the given solution directly interacting with previously selected "primary" molecule and it would be a nice and useful feature I think. Perhaps the optimal solution would be to add into "H-bond Parameters" table an additional "clik choice" which would ensure (if marked) that together with visualizing of all H-bonds (defined in the table) will be also selected all molecules which are connected by that H-bonds. (as the supplementary option might be eventually selection of end residues only (not whole molecules) which might be also useful in some cases) #2 Similarly would be cool to have in menu-table "Select -> Zone..." except "Select all atoms/bonds of any residue in selection zone" also possibility like: "Select all atoms/bonds of any MOLECULE having at least one atom in selection zone". Then again using the action "show selected only" one might have quick and nice picture only of all and WHOLE molecules which are in the defined neighbourhood of the initially selected "primary" molecule. #3 Perhaps is it shame :)) but until now I was not able to find the right button to clear/delete previously visualized H-bonds. So my solution (probably not so much elegant) is that I simply select one atom (which is really not the candidate for H-bond ) like C atom and then I ask to visualize all H-bonds which has this atom as the one end. So naturally no H-bond is found and if I do not mark "Retain currently displayed H-bonds" also the previously visualized H-bonds are deleted. But perhaps there is more elegant solution, if not button so at least some command ? Thanks in advance ! Best wishes, Marek

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Three-dimensional surface trace
by Larsson, Per (pl6n) 18 Oct '12

18 Oct '12

Dear Chimera-users I have a problem that I'm not sure can be solved in Chimera, but I thought I'd put the questions out there. Have search the archives, but couldn't turn up anything really relevant. I have a set of pdb-structures (snapshots of the same protein from a molecular dynamics simulation). The protein sits in a membrane and has a bunch of floppy loops that protrude into the solvent region. My aim is to be able to make a plot (in 3D) of the space explored by these loops over the entire simulation, essentially to see if some regions of space are preferred over others. What I thought of doing was to calculate the surface regions traced out by the loops projected on the half-sphere formed by the membrane in the x-y-plane and z>0. I hope that makes sense! Is something like this even possible in Chimera, or should I look elsewhere for a solution (perhaps inventing my own method?) Thanks /Per Larsson, University of Virginia

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