[PyMOL] Difference between open source and licensed versions?

Are there any functional differences between the open source version vs the pre-packaged version? What are the differences? Also, I see no svn tags marking where the pre-packaged code came from. Is this intentional or are the two code bases completely different? How does one go about getting

[PyMOL] Multi file wizard and import path

Hi, I'm writing a wizard that consists of a bunch of files in a folder. I want the folder name to be the name of the wizard. Will this work? Do I need a file in the folder with the same name as the folder (wizard name)? Are wizard file and class names case sensitive (for the wizard command to wo

[PyMOL] pymol pair_fit script size limit ?

Hi, I am trying to run a pair_fit script: pair_fit \ 1p80_A & i. 79 & n. ca, 1gwe_A & i. 12 & n. ca,\ 1p80_A & i. 80 & n. ca, 1gwe_A & i. 13 & n. ca,\ 1p80_A & i. 81 & n. ca, 1gwe_A & i. 14 & n. ca,\ ... ... I get this error: Error: invalid arguments for pair_fit command. as soon as the script

Re: [PyMOL] handedness flip in editing mode

Thank you very very much, it's perfect and exactly what I was looking for (a replacement for connect object of insightII to perform manual alignments easily). Thank you again, Indraneel On Thu, Sep 21, 2006 at 02:35:31PM -0700, Warren DeLano wrote: > Indraneel, > > FYI -- the apparent handedness

[PyMOL] handedness flip in editing mode

Hi, In editing mode, the handedness flips when I press shift and rotate the object (RotO). This is in effect only during the rotation of the object. Normal rotation (Rota) shows the correct handedness when shift is released. Effectively, the first clicked atom in RotO mode comes to the front (conc

[PyMOL] Re: wizard path option

On Tue, Feb 28, 2006 at 10:38:40AM -0800, Warren DeLano wrote: > Indraneel, > > At present, wizards need to be located in the > $PYMOL_PATH/modules/pymol/wizard directory -- changing this would be > nontrivial, since all wizards are assumed to reside in the > "pymol.wizard" namespace. So this mea

[PyMOL] wizard path option

Hi, I notice that imp.find_module() uses wizard.__path__ instead of the default sys.path. Is there a problem in using wizard.__path__+sys.path ? I guess changing wizard.__path__ is probably a bad idea. How should one run wizards not located in the pymol tree (eg during testing)? TIA, Indraneel

[PyMOL] how to extract corresponding residue pairs after alignment ?

Hi, Is there any way to extract corresponding residue/atom pairs after alignment? eg. the atoms that are used to create the cgo when "object" option is specified. (I guess this is probably in op1.ai1VLA and op2.ai1VLA in layer3/Executive.c ?) Thanks in advance, Indraneel -- http://prodata.swmed

[PyMOL] Discreet cartoon representation for overlapping secondary structure ?

Hi, Is changing cartoon representation a major work? My program PALSSE defines overlapping Secondary Structural Elements and it would be nice if I could see cartoons without having consecutive elements merged. It is technically possible for consecutive helices or consecutive strands or helices an

[PyMOL] get color of atom ?

Hi, How can I find out the color of an atom? Also, how should I call it from a python script? (Is there a function that will let me access the C variables?) get , /x///1/CA does not work. (where is any item in settings.py that has anything to do with color) TIA, Indraneel -- http://prodata.

[PyMOL] Selecting residue from object

Hi, How can I select residues from a particular object? eg. select newObj, (resi 2-4) from-object-oldObj2 "in" does not work and I could not figure out how to use "byobj" or what it means. TIA, Indraneel -- http://prodata.swmed.edu

[PyMOL] (raw) input parsing in python shell

Hi, I am having a problem passing arguments to my function from the python shell (works fine when arguments are put on the shell from where python was started using raw_input() ) I want to do this: press ctrl-S to start a function input a line of text on the python shell function stores this tex

Re: [PyMOL] sudden flip / skip / jump while rotating stereo

> . South San Francisco, CA 94080 USA > . Biz:(650)-872-0942 Tech:(650)-872-0834 > . Fax:(650)-872-0273 Cell:(650)-346-1154 > . mailto:war...@delsci.com > > > > -Original Message- > > From: pymol-users-ad...@lists.sourceforge.net >

[PyMOL] sudden flip / skip / jump while rotating stereo

Hi, I could not find anything on this in the archives or google. While rotating a stereo image using the mouse, the molecule suddenly flips back by about 90 degrees. Seems like I get to see only one side of a molecule if rotated on one axis. I can get to see the other side if the molecule is made

[PyMOL] zoom size

Hi, Is there a way to zoom by a fixed distance with respect to the viewport? Something like the window command in molscript, so that different molecules can be viewed/rendered at the same scale. Thanks, Indraneel Majumdar -- Univ of Texas SouthWestern Medical Center at Dallas Tel: 214-648-2499