July 2009 - Chimera-dev - RBVI Mailing Lists

Calculation voronoi volums in a prot.
by Jean Didier Pie Marechal 17 Jul '09

17 Jul '09

Dear all, We are trying to calculate voronoi's volumes around atoms in a protein. So far we used the interfase "Area/Volume from Web" but we have several troubles. So here the questions: 1. Is there a command line to do the server call automatically and display resulting volumes in the viewer? 2. We know that Qhull is one of the packages embedded in chimera. We try to see how to script voronoi calculation and read resulting volumes but failed so far. Do you have an example on how to generate the voronoi volumes maps from qhull in chimera? All the best, JD Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry @ Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal(a)uab.es

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Non-standard residues
by Alex Gawronski 15 Jul '09

15 Jul '09

Hello, Is there a way to select only standard residues with the "select" command? I was also wondering if this would work to minimize only H bonds: runCommand('select @H') runCommand('minimize freeze unselected nogui true') If not, how can it be done? When I try the inverse (selecting everything before Hs are added), I get "ValueError: underlying C++ Atom object is missing", which I assume occurs because atoms are removed by Dock Prep. Thanks in advance! Alex Gawronski Carleton University

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Non-standard residues
by Alexander Gawronski 14 Jul '09

14 Jul '09

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Generating images in chimera with the --nogui option
by Davide Baú 09 Jul '09

09 Jul '09

Hi, my name is Davide and I'm currently working on Marc Marti-Renom's group. I'm trying to generate an image using chimera with the --nogui option: chimera --nogui --nostatus --script cmd.py The file cmd.py contains the following lines: from chimera import runCommand > runCommand('open input.cmm') > runCommand('copy file image.png png') but I keep getting the following error message: Traceback (most recent call last): > File "/usr/src/chimera/share/__main__.py", line 65, in <module> > value = chimeraInit.init(sys.argv) > File "CHIMERA/share/chimeraInit.py", line 384, in init > chimera.openModels.open(a, prefixableType=1) > File "CHIMERA/share/chimera/__init__.py", line 1344, in open > File "CHIMERA/share/chimera/__init__.py", line 787, in _openPython > File "cmd.py", line 3, in <module> > runCommand('copy file image.png png') > File "CHIMERA/share/chimera/__init__.py", line 2025, in runCommand > File "CHIMERA/share/Midas/midas_text.py", line 62, in makeCommand > File "CHIMERA/share/Midas/midas_text.py", line 563, in doCopy > File "<string>", line 1, in <module> > File "CHIMERA/share/Midas/__init__.py", line 908, in copy > File "CHIMERA/share/chimera/printer.py", line 1182, in saveImage > AttributeError: '_chimera.NoGuiViewer' object has no attribute 'pilImages' > Error while processing cmd.py: > AttributeError: '_chimera.NoGuiViewer' object has no attribute 'pilImages' > (see reply log for Python traceback info) > cmd.py was generated from within chimera using the "record" command of chimera's "command line". If I delete the line "runCommand('copy file image.png png')", the script execute with no error. Is it possible to generate images using the --nogui option? Thanks a lot for your help! Best regards, Davide ____________ *Davide Baù* Structural Genomics Unit Bioinformatics & Genomics Department, Prince Felipe Research Center Avda. Autopista del Saler, 16 , 46012 Valencia, Spain Tel: +34 96 328 96 80 (ext. 1021) Fax: +34 96 328 97 01 Email: *dbau(a)cipf.es* Web: *http://sgu.bioinfo.cipf.es/dbau*

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Re: [chimera-dev] [Chimera-users] Display Molecule Name
by Greg Couch 02 Jul '09

02 Jul '09

So this is more of a chimera-dev question than a chimera-users question. If you have a Molecule object, m, it's textual "atom specification" would be (in Python): "#%d.%d" % (m.id, m.subid) Normally, if the subid is zero, we leave it out. To find out which molecules are currently being displayed can be harder: for m in chimera.openModels.list(modelTypes=[chimera.Molecule]): if not m.display: continue # molecule displayed, but constituents might not be # if that distinction is important (probably not for # ViewDock), then check bounding box valid, bbox = m.bbox() if not valid: continue # process molecule Hope this helps, - Greg On Thu, 2 Jul 2009, cdlau(a)ucsd.edu wrote: > Hi, > > Thanks for the response. This would not work for my case because I am > writing a plugin for ViewDock for use with a Tiled Wall Display. I was > hoping there was a setting that was available to show the molecule name > (if a setting does exist I can initiate it with runCommand). Does anyone > know if this is possible? > > Thanks, > > Chris > > On Thu, 2 Jul 2009, cdlau(a)ucsd.edu wrote: > > Hi, > > I was wondering if there was a way to display the molecule name that is > being shown in chimera. A simple display such as "molecule #0.10" below > the rendered molecule would be great. > > Thanks for your help, > > Chris > > Just place the mouse over the item you want to know more about and a popup > balloon will tell you about it. The text starts with the model number, > e.g., #0.10, and may or may not have additional information, i.e., for an > atom it includes the residue name and sequence number and the atom name. > > - Greg > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users >

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Chimera-dev July 2009