March 2008 - 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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Re: [chimera-dev] [Chimera-users] list of atoms attributes
by Eric Pettersen 01 Apr '08

01 Apr '08

On Feb 22, 2008, at 7:28 AM, Jean-Didier Maréchal wrote: > Hi again, > > When using the python shell, I am often struggling to find the > attribute for the atoms I work on. > for at my list with the selected atoms, I caught that at[i].name gives > the atom name of the entry at[i], at[i].residue provides with the name > residue.chain, etc. > > Where can I find in the programmer's guide the full list of available > attributes? What would be the way to ask for the serialNumber from the > IDLE? > > Thanks lot > JD Hi JD, dir(a) will list the attributes of 'a'. help(a) will produce documentation for the attributes of 'a' that come from the C++ layer (but not ones that were added in the Python layer). 'a' could be a class rather than an instance. For example, help(chimera.Atom) lists the methods/attributes of Atom and provides some info about them. We do what we can to keep the programmer's guide up to date, but for attributes (since they get added/changed pretty frequently) it is better to query with help()/dir() than to fall back on the relatively static programmer's guide documentation. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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Wrapping Chimera in a Java program
by Fabrice Jossinet 31 Mar '08

31 Mar '08

Dear developers, I would like to launch Chimera from my Java program. I would like to send messages to Chimera to highlight in its own display selections I do in my Java program's display. I already did that with PyMOL using a pipe communication. So, several questions: - is it possible to start Chimera from a classical python distribution (not the embedded python of Chimera)? One of my ideas is to start Chimera from Jython, a Java implementation of Python - is it possible to communicate with Chimera using a pipe ? - and the most general question: is it possible to communicate with Chimera from the outside? Thank you for your answers Fabrice -- Dr. Fabrice Jossinet Laboratoire de Bioinformatique, modelisation et simulation des acides nucleiques Universite Louis Pasteur Institut de biologie moleculaire et cellulaire du CNRS UPR9002, Architecture et Reactivite de l'ARN 15 rue Rene Descartes F-67084 Strasbourg Cedex France Tel + 33 (0) 3 88 417053 FAX + 33 (0) 3 88 60 22 18 f.jossinet(a)ibmc.u-strasbg.fr fjossinet(a)gmail.com http://www-ibmc.u-strasbg.fr/arn/Westhof/index.html http://fjossinet.u-strasbg.fr/

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new keyword arg for added commands
by Eric Pettersen 26 Mar '08

26 Mar '08

If you have code that adds commands to Chimera using the addCommand () function, there is a new keyword to that function so that animation scripts can work better. The keyword is 'changesDisplay' and is a boolean that defaults to True. If your command typically changes the display in the main graphics window somehow the keyword should be True, otherwise False. It's needed so that as a script is executed, Chimera knows after each line whether a new frame is necessary or not. For instance, for the 'alias' command the value is False since after executing that command in a script you would not want to record a new frame in an animation. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu

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fit map in map -- also fit a/pix at the same time ?
by stefan.backstrom＠medchem.umu.se 26 Mar '08

26 Mar '08

Hi. Would it be possible to optimize the a/pix, or scale value when one is fitting either a map in map, or model in map ? Often it seems as if the scale is not 100 % correct between a crystal structure and a cryo-EM reconstructinon, and it would be nice to be able to choose to fit the scale of the EM-map at the same time as the fit rotation and translation. Best wishes, Stefan Bäckström Medical Biochemistry and Biophysics Umeå University Sweden

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iPhone SDK
by Tom Ferrin 11 Mar '08

11 Mar '08

The iPhone SDK was announced last week. Turns out the iPhone includes a lot of the same OS layers as does the Mac. I didn't see anything about Python, but there is a hardware accelerated OpenGL ES in there. Also the standard set of development tools (interface builder, xcode, etc) and a package called "Instruments" that let's you capture on a Mac lots of execution trace information on the iPhone via an interface cable. One novel user interface component: the iPhone includes a 3D accelerometer with software interface. The video I watched showed a shoot-em-up space wars game where you steered by moving the phone around. Someone is bound to come up with an interactive molecular viewer; I suspect Warren DeLano is working on Pymol right now. --tom

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Chimera-dev March 2008