[PyMOL] independent manipulation of two molecules

Hello, how is it possible to independently rotate or translate two molecules in pyMOL? I would like to display the interaction of two macromolecules but to do so, I first have to adjust their position relative to each other. Do I have to use different frames for loading, then positioning each in

Re: [PyMOL] independent manipulation of two molecules

Hi Michael, simply load both molecules in the same frame, and change to Mouse/3 Button Editing Mode. You have to select the molecule you want to translate/rotate by left clicking on an atom of it. Now, you have following options: shift+LMB+mouse_movement := rotate this molecule around the sele

[PyMOL] pymol and amd64 linux

I have been trying to build and install pymol-0.99rc from source because the binary version will not work on my system (there appears to be an incompatibility in my recently updated python install and the provided pymol - rebuilding on my pentiumpro system worked fine). I have managed to get t

[PyMOL] RE: wizard path option

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. FYI: module-name.__path__ has a different meaning than sys.path. Cheers, Warren --

[PyMOL] Set all settings to default

0.99 and 0.98 have different ray tracing and lighting models. When I read an old .pse file into .99, are the settings in the old file converted to the new style? Is there a way to reset all of the settings to default values, without modifying the objects themselves? Thanks, Mark _

[PyMOL] Castp plugin

Hi, I am using ver 0.99 and would like to install the castp plugin. i am not successful in installing under Linux/OSX. i am getting the following error. This PyMOL Executable Build incorporates Open-Source PyMOL 0.99rc1. Exception in plugin 'CASTpyMOL' -- Traceback follows... Traceback

[PyMOL] Sequence view print out

Hi all, I'm not sure if this has been asked before and I'm not sure if its possible...but here goes anyway. Is there a way to print/export the sequences in the viewer window? It would be an easy way to translate actual secondary structure to a sequence alignment Thanks J -- Joel Tyndall, P

RE: [PyMOL] Sequence view print out

Joel, Not yet...in fact, we're still not able to show an alignment in the sequence viewer. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(65

RE: [PyMOL] Set all settings to default

Hi Mark, Hmm. PyMOL attempts to migrate old settings into the new model, but it isn't perfect and one may need to fiddle with the various settings after migration. We'll need a new feature to reinitialize settings without deleting content so thanks for the suggestion! In the meantime, you can d

Re: [PyMOL] Set all settings to default

Warren, The problem is with ray tracing a surface from an old_session.pse. Much better results if you retrace it with the version that created it. Thanks for your help. Mark _ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry Biophysics Resea

[PyMOL] Question about surface property calculations

Hello all - As a grad student, I used Grasp to do extensive (albeit) simple calculations on surface properties. Grasp specifically assigned floats or ints to specific surface vertices (triangles) which could be assigned to subsets and calculated upon. I am interested in possibly doing sim

[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