September 2003 - Chimera-dev - RBVI Mailing Lists

...some questions
by Lars Kunert 26 Sep '03

26 Sep '03

Hi I have got a couple of questions. After loading a couple of molecules (files) into chimara: >>>opened = chimera.openModels.open('xxx.mol2') How do I access the name of the file, the model was loaded from? How can I find out if a model/molecule is active and on the screen? If not , who can I make it active, and zoom to it? How do I display a set of spheres, together with with some edges connecting them. I do like to show some kind of pseudo-molecule/graph. Can I display an ellipsoid? - Do I have to construct it from triangles? I want to display a binding pocket, can I limit the amount of data displayed before the proterin is shown the first time? I have got some problems with the calculation of surfaces (1dwd always crashs...). Is it possible to limit the surface-calculation to an connected area (pocket). By the way, the tutorials are great, but the reference manual will probably need some efford... Thanks a lot for your help, Lars

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colors...
by Lars Kunert 26 Sep '03

26 Sep '03

Hi I do like to color some molecules/atoms I figured out, that I create a color like this: >>c=chimera.Color() >>c=(1,0,0,1) But when I apply this to all the atoms of a molecule, I end up with the following error-message: >>> for a in m.atoms: a.color=c Traceback (most recent call last): File "<pyshell#66>", line 1, in ? for a in m.atoms: RuntimeError: __wrappy__ is missing >>> I suppose, that colors like "red"are predefined somewhere, where? Are the different color-levels modell/molecule/atom are just fancy stuff for the interactive user? - I colored a molecule first (interactive) "byatom" and then tried to alter the coloring by hand: >>m.color=c it did not work, I had to alter the color atomwise... is color-byatom a function? How can I call it? Is there a way to "switch on"a history function in the buildin IDLE? Copy and paste do also not work within the IDLE. I allways have to copy and paste via an editor...

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mol2-parser reorders entries
by Lars Kunert 24 Sep '03

24 Sep '03

Hi! I do like to reference chimera-atoms from my extension. I have the problem that chimera reorders the atoms (and probably also the bond entries) of mol2 files. Which of the following workarounds would you suggest: - resort all my mol2-files -> will only work if the resorting ist stable - use a dictionary -> puts some unwellcome functionallity into my python-wrapper - refer by name -> mol2-atom names do not have to be unique and will be slow without a dictionary or is there a way to switch it of??? Thanks Lars

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Re: chimera
by Thomas Goddard 16 Sep '03

16 Sep '03

Hi Matt, Below is example python code to start Chimera and open PDB 1zzz. For it to work you have to set the LD_LIBRARY_PATH environment variable before running python to include the chimera/lib directory. If you start it from your own Python program you can pass Python objects directly to Chimera. This is simplest if your program uses Tkinter, since Chimera needs the Tkinter event loop to run in order to update the graphics and accept user input. Tom # # Need to set LD_LIBRARY_PATH environment variable to <chimera-home>/lib # before running python2.2. # # On linux your python2.2 must have the dl module. This module is not # standard on linux. It is included in the Python included with Chimera. # chimera_home = '/usr/local/chimera-1700' import sys import os.path sys.path.insert(0, os.path.join(chimera_home, 'share')) sys.path.insert(0, os.path.join(chimera_home, 'lib')) os.environ['CHIMERA'] = chimera_home import chimeraInit chimeraInit.init([], eventloop = False) import chimera chimera.openModels.open('1zzz', 'PDBID') # Will download from web. chimera.tkgui.eventLoop() # Doesn't return until Chimera quits -------------------------- > Date: Tue, 16 Sep 2003 22:12:26 -0500 > From: Matthew Dougherty <matthewd(a)bcm.tmc.edu> > To: goddard(a)cgl.ucsf.edu > Subject: chimera > > Tom- > > I was wondering if I can run chimera using an embedded python. > If so can I send python data objects to it through my main program? > > Matt > > ------------------------------------------ > Matthew Dougherty/713-747-5433 > National Center for Macromolecular Imaging > Baylor College of Medicine >

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should we change the chimera help files on Windows?
by Greg Couch 16 Sep '03

16 Sep '03

>From the python devlopment mailing list summary: "This discussion also brought up the question of whether a .chm help file for the Windows distribution would be worth using instead of including the HTML distribution of the documentation as it stands now. It was agreed that it was a good thing to have since it allowed for better searching. Tim Peters also discovered the install went faster since it would not have to copy a ton of individual HTML files." Better searching would be nice, although we do provide searching on the web site. Faster installs would be nice, too. So I'm not proposing that we do this anytime soon, but that we keep this idea in the back of our heads. And if someone comes across a tool that maintains two forms of help files (html and cbm), please share that information. - Greg

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automatic checkForChanges
by Eric Pettersen 02 Sep '03

02 Sep '03

I'd like to suggest that chimera.openModels.{open,add,close} all automatically run chimera.update.checkForChanges() as they finish (suppressable by supplying a 'checkForChanges=False' keyword argument to the functions). Right now, developers who aren't "in the know" will write scripts that loop through structures, opening and closing them and performing operations, and because they don't know to call checkForChanges the scripts will typically fail due to running out of memory. Also, some other operations (surfacing) will fail if checkForChanges isn't called after a model is opened. There are other times when checkForChanges needs to run, but those are relatively rare compared to these openModels functions. It seems to me that making this change makes normal scripting less error-prone while allowing for the uncommon case of wanting to suppress the checkForChanges. Opinions? Eric Pettersen UCSF Computer Graphics Lab pett(a)cgl.ucsf.edu http://www.cgl.ucsf.edu

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Chimera-dev September 2003