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gaussian interface: getting nuts with connectivity
by Jean Didier Pie Marechal 17 Jul '09

17 Jul '09

Dear all, I am trying to make chimera an interface for the quantum mechanical program gaussian. Pretty much everything seems to go smooth but I am getting crazy (stupid?) because I can't reproduce the geometry connectivity gaussian wants. I used tools of chimera I know for bond mapping and connectivity. But I can't get to the right connectivity format. I join you here an input file of gaussian (a ARG-ALA dipeptide). If you look at the file, the connectivity between the atoms is at the end and is in the following form: atom 1, atom 2, bond_order, atoms 3, bond_order (etc for all atoms linked to atom 1) ... atom 31 (to 37 = all terminal atoms). I have been using the different atoms attributes I know like neighbors, bonds and bondMap, but I can't see how to proceed neither I see how to use the bond order calculations as in the mol2 module. If you have time and can give me a hint, I would be extremely greatful Thank you very much, 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 ----- Missatge original ----- De: chimera-dev-request(a)cgl.ucsf.edu Data: Dijous, Juliol 9, 2009 9:00 pm Assumpte: Chimera-dev Digest, Vol 66, Issue 2 > Send Chimera-dev mailing list submissions to > chimera-dev(a)cgl.ucsf.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev > or, via email, send a message with subject or body 'help' to > chimera-dev-request(a)cgl.ucsf.edu > > You can reach the person managing the list at > chimera-dev-owner(a)cgl.ucsf.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Chimera-dev digest..." > > > Today's Topics: > > 1. Generating images in chimera with the --nogui option (Davide > Ba?) 2. Re: Generating images in chimera with the --nogui option > (Greg Couch) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Thu, 9 Jul 2009 17:32:22 +0200 > From: Davide Ba? <dbau(a)cipf.es> > Subject: [chimera-dev] Generating images in chimera with the --nogui > option > To: chimera-dev(a)cgl.ucsf.edu > Message-ID: > <3e4b67ca0907090832r4e46b826i5dfe81842b58685a(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > 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 > scriptexecute with no error. > > Is it possible to generate images using the --nogui option? > > Thanks a lot for your help! > > Best regards, > Davide > > ____________ > *Davide Ba?* > 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* > El document original ha estat eliminat per l'antivirus. El motiu ha estat: Fitxer adjunt amb extensió potencialment perillosa (vbs, vbe, js, jse,scr, exe, com, bat, lnk, ceo, htt, pif) Per a més informació vegeu: http://www.uab.es/si/virus_correu/

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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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Publishing an extension
by Sébastien Cuendet 29 Jun '09

29 Jun '09

Hi, At the Molecular Modelling Group (http://www.molecular-modelling.ch/) in Lausanne, Switzerland, we've developed a Chimera extension with 3 functionalities: * GUI for CHARMM setups: inspect, clean up and prepare molecules for use with CHARMM * GUI for the EADock docking software: setup a receptor, a ligand, choose the docking parameters that suit your needs, and run your docking * access to the S3DB database, a database containing more than 250 manually curated complexes The extension is reaching the end of the test phase and we plan on releasing it soon. However, coming closer to the release day brought up several questions: 1) We needed a slightly modified version of the writeMol2 function (in writeMol2.py), and had to include a modified version of the writeMol2 and midas package in our extension. Of course we're not claiming any intellectual property on any of those two modified files, but is it a problem to integrate them into our extension? 2) More or less the same situation appears for the rotamers window, from which we took a part to integrate it in part of our extension that allows a user to fix residues with missing atoms. We basically copied and pasted the code we needed. The problem is slightly different since this isn't a built-in function of Chimera, as opposed to writeMol2, for example. But again, is that a problem? 3) We plan to add some features to the awesome ViewDock extension that is already part of Chimera. However, we really only want to implement shortcut commands that are helpful when using EADock, but since ViewDock is already so complete, it makes no sense to start from scratch. We see two options: either extend the ViewDock extension with our features, or inherit a large part of the ViewDock extension and customize it in our own extension. Option 1 seems possible only if the owner of the ViewDock extension agrees to integrate our features in his extension and brings up questions of supporting/updating those features, whereas option 2 brings up the question already mentioned above. Could someone let us know what the standard policy is to deal with those issues? Thanks, Sébastien Cuendet

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Re: [chimera-dev] [Chimera-users] modeldisp
by Eric Pettersen 29 Jun '09

29 Jun '09

Hi Chris, I don't know how you opened your file, but if you opened it with chimera.openModels.open() then the return value is a list of models from that file, so... models = chimera.openModels.open("myfile.mol2") for i in range(len(models)): ... though perhaps more direct would be: models = chimera.openModels.open("myfile.mol2") for m in models: m.display = False for i, m in enumerate(models): ... setup stuff m.display = True ... more stuff m.display = False --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Jun 29, 2009, at 5:11 PM, cdlau(a)ucsd.edu wrote: > Hi, > > I am currently using the modeldisp command on the command line to > hide and > view various molecules within a single mol2 file. I was wondering > how I > would be able to access how many total molecules there were in a > single > mol2 file. For example, if the mol2 file is loaded into model 0, I > would > be using > > modeldisp #0.$i > > etc in a large loop where $i is changing. What command can I use to > return a value for the total number of molecules in the mol2 file so > I can > have this be the upper limit of $i? > > Thanks for your help, > > Chris > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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need some scripts from chimera source code
by ylei＠ecs.umass.edu 22 Jun '09

22 Jun '09

Hi all I am working on a project that requiring some program scripts concerning with 1) Compute Amber Energy Function 2) Read rotamer information from the Dunbrack Backbone-dependent Rotamer library 3) Read in Electron Density Map and get the density value for each 3-D point in the crystal I did check some related python files in the source code folder and can understand them to some extent, but for running these files, some modules (e.g. Chimera, Rotamers) are needed. However, I don't know how to install these modules, or maybe I should recompile Chimera from source code first(If so, then how, because I don't know the procedure either. BTW, my platform is mac osx)? Could someone show me which files I should use for the above mentioned three subjects and what kinds of modules I should install and how? Thank you so much and sorry for disturbing others. Yang

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need some scripts from chimera source code
by ylei＠ecs.umass.edu 19 Jun '09

19 Jun '09

Hi all I am working on a project that requiring some program scripts concerning with 1) Compute Amber Energy Function 2) Read rotamer information from the Dunbrack Backbone-dependent Rotamer library 3) Read in Electron Density Map and get the density value for each 3-D point in the crystal I did check some related python files in the source code folder and can understand them to some extent, but for running these files, some modules (e.g. Chimera, Rotamers) are needed. However, I don't know how to install these modules, or maybe I should recompile Chimera from source code first(If so, then how, because I don't know the procedure either. BTW, my platform is mac osx)? Could someone show me which files I should use for the above mentioned three subjects and what kinds of modules I should install and how? Yang

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