- Chimera-dev - RBVI Mailing Lists

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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Zalman 3D
by Amédée des Georges 23 Mar '09

23 Mar '09

Dear Chimera developers, We just bought in the our lab (Frank lab) a new Zalman 3D monitor ( http://www.zalman.co.kr/Eng/product/Product_Read.asp?idx=219) Warren Delano has written an extension to get it to work with his Pymol. In our lab, we mainly use Chimera and it would be great if it became compatible with the Zalman system. The way the Zalman monitor works is by giving a different polarization to each row of the screen. The software just has to send the infos for each eye in alternating rows. Would that be something doable in Chimera? By advance thank you, Amedee

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_surface.SurfaceModel
by Randy Heiland 11 Feb '09

11 Feb '09

Hi gang, In trying to finish up my plugin port to the daily/Aqua version of Chimera, I'm confused over the replacement method for what used to be: _surface.Surface_Model.add_group I see that dir(_surface) now has SurfaceModel (without the underscore), but what's the replacement for add_group? >>> dir(_surface.SurfaceModel) ['__class__', '__delattr__', '__destroyed__', '__dict__', '__doc__', '__getattribute__', '__hash__', '__init__', '__new__', '__reduce__', '__reduce_ex__', '__repr__', '__setattr__', '__str__', 'addAssociatedModel', 'addGeometryChangedCallback', 'addPiece', 'associatedModels', 'bbox', 'bsphere', 'callGeometryChangedCallbacks', 'clipPlane', 'clipThickness', 'computeBounds', 'count', 'destroy', 'display', 'frontPoint', 'id', 'intersects', 'material', 'name', 'newPiece', 'openState', 'oslChildren', 'oslIdent', 'oslLevel', 'oslParents', 'oslTestAbbr', 'piecesAreSelectable', 'removeAssociatedModel', 'removeGeometryChangedCallback', 'removePiece', 'selLevel', 'subid', 'surfacePieces', 'useClipPlane', 'useClipThickness'] -Randy

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Question regarding MMTK
by Jean Didier Pie Marechal 11 Feb '09

11 Feb '09

Hi everyone, I have a question regarding the MMTK interfase. How complicate it is to get the hand on a the MMTK script and input files generated by chimera to perform the minimization ? Is it located in some subfolder? Is there a way to write it down so that I can perform further calculations outside the chimera environment? All the best, JD Dr. Jean-Didier Maréchal Lecturer Computational Bioorganic and Bioionorganic 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: Dimecres, Febrer 4, 2009 9:00 pm Assumpte: Chimera-dev Digest, Vol 61, Issue 1 > 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. alias menu (Richmond Timothy J.) > 2. Re: alias menu (Elaine Meng) > 3. Re: alias menu (Eric Pettersen) > > > -------------------------------------------------------------------- > -- > > Message: 1 > Date: Wed, 4 Feb 2009 14:09:53 +0100 > From: "Richmond Timothy J." <richmond(a)mol.biol.ethz.ch> > Subject: [chimera-dev] alias menu > To: <chimera-dev(a)cgl.ucsf.edu> > Message-ID: <874055BA140585479966DE1694AB0421F058B5(a)EX6.d.ethz.ch> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Chimera Developers, > > > > Perhaps I have missed it, but I would find a menu for selected > aliases very useful. Having returned to Chimera from PyMol > recently, it would be great to have an option for the alias command > that allowed the particular alias to be listed in a separate window > and ran the alias by clicking on the alias name listed there. > > > > Best regards, > > > > Tim > > > > ------------------------- > > > > ETH Zurich > > Prof. Timothy J. Richmond > > Institute of Molecular Biology and Biophysics > > HPK F 18 > > Schafmattstr. 20 > > 8093 Z?rich > > SWITZERLAND > > > > richmond(a)mol.biol.ethz.ch > > http://www.mol.biol.ethz.ch/groups/richmond > > > > +41 44 633 24 70 phone > > +41 44 633 11 50 fax > > > > > >

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alias menu
by Richmond Timothy J. 04 Feb '09

04 Feb '09

Dear Chimera Developers, Perhaps I have missed it, but I would find a menu for selected aliases very useful. Having returned to Chimera from PyMol recently, it would be great to have an option for the alias command that allowed the particular alias to be listed in a separate window and ran the alias by clicking on the alias name listed there. Best regards, Tim ------------------------- ETH Zurich Prof. Timothy J. Richmond Institute of Molecular Biology and Biophysics HPK F 18 Schafmattstr. 20 8093 Zürich SWITZERLAND richmond(a)mol.biol.ethz.ch http://www.mol.biol.ethz.ch/groups/richmond +41 44 633 24 70 phone +41 44 633 11 50 fax

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examples of 2-D plotting in plugins?
by Randy Heiland 14 Jan '09

14 Jan '09

Hi gang, For one of the Chimera plugins that I now maintain, I'm considering eliminating the use of matplotlib and wondering if Chimera's innards are capable of doing what I want. For starters, are there any example plugins, etc that demonstrate how one could do simple plotting and simple (image) contours? In addition, I'd need to handle mouse events, e.g. to retrieve x,y positions on the contour image. thanks, Randy

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