April 2009 - Chimera-dev - RBVI Mailing Lists

add h
by Virginie Lafont 01 May '09

01 May '09

Hi, I am a new user of chimera and I already have a question. I have an protonated aspartic acid in my protein and I was wondering, is it possible to add hydrogen atom to aspartic acid with chimera? Thanks Virginie

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scripting rotation around a bond
by Jean Didier Pie Marechal 29 Apr '09

29 Apr '09

Dear all, I'd like to generate from my script an ensemble of structures obtained by the rotation of a subgroup of the molecule around a given bond. Said in another way, I want to do something similar to the adjust torsion tools without getting to the interfase but defining myself the value of the angle I want to test. I can't figure out what is the module to load and how to use it and it seems there is no command line for this (rotation seems to accept only the atom specification for the bond as an argument). Could you give me a hand on this? By the way, I wanted to get the to the programmers's guide but I can't. You removed it from your server correct? 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 ----- Missatge original ----- De: chimera-dev-request(a)cgl.ucsf.edu Data: Divendres, Abril 24, 2009 9:00 pm Assumpte: Chimera-dev Digest, Vol 63, Issue 7 > 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. Re: stereo: Linux, nvidia Quadro FX 5600 (Randy Heiland) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Fri, 24 Apr 2009 13:45:42 -0400 > From: Randy Heiland <heiland(a)indiana.edu> > Subject: Re: [chimera-dev] stereo: Linux, nvidia Quadro FX 5600 > To: Greg Couch <gregc(a)cgl.ucsf.edu> > Cc: "chimera-dev(a)cgl.ucsf.edu" <chimera-dev(a)cgl.ucsf.edu> > Message-ID: <9CE3734E-31AE-45C3-B5DC-80BC2D67856C(a)indiana.edu> > Content-Type: text/plain; charset="us-ascii" > > Just thought I'd add to this thread, in hopes that it may save > others > some time... > > On Apr 24, 2009, at 11:22 AM, John Matthews wrote: > > > Hello Randy, > > > > Unfortunately, the CE3s are not compatible with the new 120Hz LCDs > > from Viewsonic and Samsung. We are currently looking at a few > > possible solutions. When we have something, we'll post it on our > > website. > > > > Thanks, > > > > > > John Matthews | Sr. Engineer > > RealD > > 5335 Sterling Drive > > Boulder, CO 80301 > > (P) 303.545.5843 x121 | (F) 303.448.9573 | jmatthews(a)reald.com > > www.reald.com > > > > > > > > > > -----Original Message----- > > From: Randy Heiland [heiland(a)indiana.edu] > > Sent: Friday, April 24, 2009 9:19 AM > > To: Real D Support > > Cc: Heiland Randy > > Subject: CrystalEyes and Viewsonic FuHzion > > > > Hello, > > > > I'd like to know if the CrystalEyes (CE-3) should work with the > > Viewsonic Fuhzion (120Hz) monitor? Just looking at the monitor thru > > them, it is very dark. Running glxgears in stereo does not work. > > > > If they should indeed work, then perhaps I need a different nvidia > > driver. > > > > Linux-x86_64 > > nvidia driver version: 180.29 > > GPU 0 (Quadro FX 5600) > > > > thanks, Randy Heiland > > > On Apr 17, 2009, at 12:46 PM, Greg Couch wrote: > > > I don't remember how we configured our Linux machine for stereo, > but > > the > > alternative to using the GUI to configure the X server for > stereo, > > is to > > read the documentation that came with the NVidia driver in > > /usr/share/doc/NVIDIA_GLX-1.0/README.txt and configure xorg.conf > > with a > > text editor. Look in "Appendix D. X Config Options" for the > > "Stereo" and > > "AllowDFPStereo" options. > > > > Good luck, > > > > Greg > > > > On Fri, 17 Apr 2009, Randy Heiland wrote: > > > >> Hello again gang, > >> > >> I'm guessing someone there can help me get past this - I know > Greg > >> has > >> offered advice elsewhere. > >> > >> My subject line says it all - I want to get stereo working on this > >> machine. Trying something more basic than chimera: > >> > >> $ glxgears -stereo > >> Error: couldn't get an RGB, Double-buffered, Stereo visual > >> > >> $ glxinfo -v|grep stereo > >> bufferSize=32 level=0 renderType=rgba doubleBuffer=1 stereo=0 > >> bufferSize=32 level=0 renderType=rgba doubleBuffer=1 stereo=0 > >> ... > >> > >> It's not obvious to me where/how one enables stereo via System- > >> >Prefs- > >>> More Prefs->nvidia x server settings > >> > >> The specs: > >> Linux-x86_64 > >> nvidia driver version: 180.29 > >> > >> GPU 0 (Quadro FX 5600) > >> mem 1536 MB > >> PCI Express 16x > >> X screens: Screen 0 > >> Display: Apple Cinema HDDisplay (DFP-1) > >> > >> GPU 1 (Quadro NVS 290) > >> 256 MB > >> PCI Express 16x > >> X screens: none > >> Display: none > >> > >> with an Apple 30" Cinema HDDisplay currently attached (and a > >> ViewSonic > >> Fuhzion, 120Hz as something else to experiment with). Currently > have>> CrystalEyes. > >> > >> I'd welcome any advice you might have. > >> thanks, Randy > >> > >> _______________________________________________ > >> Chimera-dev mailing list > >> Chimera-dev(a)cgl.ucsf.edu > >> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev > >> > >

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stereo: Linux, nvidia Quadro FX 5600
by Randy Heiland 24 Apr '09

24 Apr '09

Hello again gang, I'm guessing someone there can help me get past this - I know Greg has offered advice elsewhere. My subject line says it all - I want to get stereo working on this machine. Trying something more basic than chimera: $ glxgears -stereo Error: couldn't get an RGB, Double-buffered, Stereo visual $ glxinfo -v|grep stereo bufferSize=32 level=0 renderType=rgba doubleBuffer=1 stereo=0 bufferSize=32 level=0 renderType=rgba doubleBuffer=1 stereo=0 ... It's not obvious to me where/how one enables stereo via System->Prefs- >More Prefs->nvidia x server settings The specs: Linux-x86_64 nvidia driver version: 180.29 GPU 0 (Quadro FX 5600) mem 1536 MB PCI Express 16x X screens: Screen 0 Display: Apple Cinema HDDisplay (DFP-1) GPU 1 (Quadro NVS 290) 256 MB PCI Express 16x X screens: none Display: none with an Apple 30" Cinema HDDisplay currently attached (and a ViewSonic Fuhzion, 120Hz as something else to experiment with). Currently have CrystalEyes. I'd welcome any advice you might have. thanks, Randy

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Re: [chimera-dev] [Chimera-users] [Chimera-Users] help with IDLE
by Eric Pettersen 21 Apr '09

21 Apr '09

Hi Chris, I don't know if it works the same on all platforms, but on my mac if I copy text from somewhere I can paste it into IDLE with IDLE's Edit- >Paste menu item. --Eric On Apr 20, 2009, at 7:25 PM, christopher lau wrote: > Thanks Eric, > > Is there any way to paste commands copied from another application > or script into the IDLE shell? > > -Chris > > On Mon, Apr 20, 2009 at 10:36 AM, Eric Pettersen <pett(a)cgl.ucsf.edu> > wrote: > On Apr 19, 2009, at 5:57 PM, cdlau(a)ucsd.edu wrote: > >> Dear Sir/Miss, >> >> I am using the IDLE extensively and I have noticed I cannot paste >> text or >> <arrow up> to run previous commands. I was wondering if anyone >> knew how >> to change these features or if it is possible. I explored the >> options>configure IDLE, but haven't found any preference changes that >> change these problems I am having. Thanks for your help in advance. > > Hi Christopher, > To reuse/edit a command, either up-arrow to or mouse-click into the > command you want and hit return. A copy of the command will appear > at the current Python prompt. You can then edit it with the arrow > keys or the mouse and then hit Return to execute the modified command. > > --Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > >

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Re: [chimera-dev] [Chimera-users] [Chimera-Users] help with IDLE
by Eric Pettersen 20 Apr '09

20 Apr '09

On Apr 19, 2009, at 5:57 PM, cdlau(a)ucsd.edu wrote: > Dear Sir/Miss, > > I am using the IDLE extensively and I have noticed I cannot paste > text or > <arrow up> to run previous commands. I was wondering if anyone knew > how > to change these features or if it is possible. I explored the > options>configure IDLE, but haven't found any preference changes that > change these problems I am having. Thanks for your help in advance. Hi Christopher, To reuse/edit a command, either up-arrow to or mouse-click into the command you want and hit return. A copy of the command will appear at the current Python prompt. You can then edit it with the arrow keys or the mouse and then hit Return to execute the modified command. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Using chimera.BondRot
by Frederic RODRIGUEZ 16 Apr '09

16 Apr '09

Dear Chimera developers We want to generate structures (ligand+protein) in which we impose a variation (0 to 360 degrees, with step of 1 or 5, 10 degrees) of one or two dihedrals of the ligand. We want to use Chimera to select interactively, a list of dihedrals, and launch a script which do the rotations, produce PDB structures, save them. After we want to do another processing but using our own code (and perhaps including a new extension GUI, python, we work under Windows XP). We want to use BondRot functions, so we have explored module StructMeasure (and other related files ... BondObject.h) in order to understand how we can use this feature. We have done some experiments using a modified version of this extension so that we can select and rotate dihedrals as we want. If we make a script or a new extension, and let original StructMeasure module in place, we have problems. When we add a bond rotation using an expression such as: br = chimera.BondRot(bond) the panel AdjustTorsions of StructMeasure is always loaded. We would like to know if we can do our task without the use of chimera.BondRot , or if we can use it independently of StructMeasure dialog. thanks, Fred Rodriguez, Mansi Trivedi -- Frédéric Rodriguez Laboratoire de Synthèse et Physicochimie de Molécules d'Intérêt Biologique UMR 5068 CNRS / Université Paul Sabatier 118 Route de Narbonne 31062 TOULOUSE cedex 9, France vce: 05.61.55.85.66 - fax: 33 (0)5.61.55.60.11 elm: build(a)chimie.ups-tlse.fr

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Re: [chimera-dev] [Chimera-users] PDB data
by Eric Pettersen 02 Apr '09

02 Apr '09

Hi Matt, You can find out about the (C++) attributes/methods of a class by using help() in the IDLE interpreter, e.g.: help(chimera.Residue) There is also declaration of the Python-visible attributes of Atom/ Residue/etc. in the source distribution in libs/_chimera/pyinterface. The more convenient way nowadays to get pyinterface is by browsing our SVN repository, i.e. from: /trunk/libs/_chimera/pyinterface – Chimera The other thing you might want to know that seems germane to your specific query is that the PDB headers are stored in the pdbHeaders dictionary in Molecule (key: header type [e.g. REMARK], value: list of strings). --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Apr 2, 2009, at 1:23 PM, Matthew Dougherty wrote: > I was writing some python code involving PDB data. > > looking at pre-existing code involving PDB: > > > m = om.open(pdb_path, 'PDB')[0] > rlist = m.residues > > for r in rlist: > > lc = 'monomer residue %d' % (r.id.position) > if r.isHelix: > lc += ' HELIX' > elif r.isSheet: > lc += ' SHEET' > > > > > > I was trying to track down the data structure for r/rlist, to see if > there are any other parameters I could use besides isHelix, isSheet, > and id.position. > where would that be located in the Chimera package? > > thanks, Matt > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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Re: [chimera-dev] [Chimera-users] reset/savepos
by Eric Pettersen 02 Apr '09

02 Apr '09

import Midas Midas.positions.keys() FYI, most command-line commands are implemented in the Midas module, usually in a function of the same name as the command. So the implementation of "reset" is in "def reset" in Midas/__init__.py. The implementation for commands that do the same things as tools (e.g. findhbonds, volume) are usually found in that tool's module though. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Apr 2, 2009, at 2:06 PM, Matthew Dougherty wrote: > thanks, > > > how would I get the same list in python? > > > On Apr 2, 2009, at 4:01 PM, Elaine Meng wrote: > >> Hi Matt, >> The command "reset list" will list the names of saved positions in >> the status line and Reply Log. >> Best, >> Elaine >> >> On Apr 2, 2009, at 1:37 PM, Matthew Dougherty wrote: >> >>> I have a chimera session file that is being passed around. >>> Different users are using savepos with no common nomenclature for >>> the >>> view_name. >>> >>> How can I get a list of all view_names? >>> >>> thanks, Matt >> >> >> >> > > _______________________________________________ > Chimera-users mailing list > Chimera-users(a)cgl.ucsf.edu > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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Re: [chimera-dev] [Chimera] #7111: problem with "toolbar buttons" programmer's example (was: Chimera bug report submission)
by Eric Pettersen 01 Apr '09

01 Apr '09

Hi Richard, The issue here is that Chimera executes Python scripts in temporary modules so that they don't interact with Chimera's own global namespace (they don't accidentally pick up names from the global namespace nor do they leave definitions there). After the script is executed, the temporary module is deleted from sys.modules. When that happens Python clears references in the module's globals dictionary by setting the values to None in an attempt to break circular references for garbage-collection and destructor-invocation purposes. So... the script's attempt to use those names later (when the toolbar button is pressed) produces the "'NoneType' object has no attribute 'compile'" error since when Python looks up "re" in the module's globals dictionary it gets 'None' back. The fix is to put "import re" inside the function definition (as well as an additional "import chimera" [an import is still required at the global level for code after the button-callback function]). I will need to update the example to account for this behavior. The example was written back when scripts were executed in Chimera's own namespace. --Eric On Apr 1, 2009, at 11:36 AM, Chimera wrote: > #7111: problem with "toolbar buttons" programmer's example > ----------------------------------------------- > +---------------------------- > Reporter: richard.marhoefer@… | Owner: pett > Type: defect | Status: accepted > Priority: normal | Milestone: > Release 1.4 > Component: Core | Version: 1.0 > (build 2540) > Severity: normal | Keywords: > Blockedby: | Project: chimera > Platform: all | Blocking: > ----------------------------------------------- > +---------------------------- > Changes (by pett): > > * status: new => accepted > * reporter: chimera-bug-report@… => richard.marhoefer@… > * component: => Core > * project: => chimera > * platform: => all > * version: => 1.0 (build 2540) > * milestone: => Release 1.4 > * owner: => pett > > > -- > Ticket URL: <http://socrates2.cgl.ucsf.edu/trac/chimera/ticket/7111#comment:2 > > > Chimera <http://socrates2.cgl.ucsf.edu/trac/chimera> > Chimera Issue Tracker

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Chimera-dev April 2009