Re: [PyMOL] surface properties

-- Andreas Henschel Bioinformatics Group TU Dresden Tatzberg 47-51 01307 Dresden, Germany Phone: +49 351 463 40063 EMail: a...@biotec.tu-dresden.de

Re: [PyMOL] Get coordinates of the mesh

Hi Horacio, you can save as wrl (VRML) or povray (as posted earlier). The former can be read by vtk (vtkVRMLImporter or so), from here you have a rich set of sophisticated algorithms such as decimate. google for vtkDecimate, vtkDecimatePro There are bindings for a couple of languages, also

Re: [PyMOL] rotate about an abitrary axis

/pymol-users -- Andreas Henschel Bioinformatics Group TU Dresden Tatzberg 47-51 01307 Dresden, Germany Phone: +49 351 463 40063 EMail: a...@biotec.tu-dresden.de from pymol import cmd from pymol.cgo import * def centerOfMass(selection, createSphere=True): ## assumes equal weights (best called

Re: [PyMOL] Distances and Python scripts

-- Andreas Henschel Bioinformatics Group TU Dresden Tatzberg 47-51 01307 Dresden, Germany Phone: +49 351 463 40063 EMail: a...@biotec.tu-dresden.de

Re: [PyMOL] mutagenesis script

. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Andreas Henschel Bioinformatics Group TU Dresden Tatzberg 47-51 01307

Re: [PyMOL] PyMOL compilation from source

: i have no idea about your error but i can provide you RPMs for Opensuse 10.2 i586 and x86_64, if you need them for other SuSE distributions, I can try to add them to my repository. Would that be feasable? Regards, Michael Andreas Henschel wrote: Hi all, did anyone of you come across

[PyMOL] PyMOL compilation from source

, Andreas -- Andreas Henschel Bioinformatics Group TU Dresden Tatzberg 47-51 01307 Dresden, Germany Phone: +49 351 463 40063 EMail: a...@biotec.tu-dresden.de

Re: [PyMOL] building centroids for residues

move the structure around afterwards? Any pointers much appriciated :) Cheers, Siv -- Andreas Henschel Bioinformatics Group TU Dresden Tatzberg 47-51 01307 Dresden, Germany Phone: +49 351 463 40063 EMail: a...@biotec.tu-dresden.de

Re: [PyMOL] center of mass and distances

mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Andreas Henschel Bioinformatics Group TU Dresden Tatzberg 47-51 01307 Dresden, Germany Phone: +49 351 463 40063 EMail: a...@biotec.tu-dresden.de

Re: [PyMOL] error on debian w/ pymol -c foo.pml

-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Andreas Henschel Bioinformatics Group TU Dresden Tatzberg 47-51 01307 Dresden, Germany Phone: +49 351 463 40063 EMail: a...@biotec.tu-dresden.de

Re: [PyMOL] 1letter code by default

a one letter code I can send you some stuff we use. Best, Andreas andrea carotti wrote: Hi all, a very basic question: is possible to set the 1letter code by default in pymol? Thanks in advance Andrea -- Andreas Henschel Bioinformatics Group TU Dresden Tatzberg 47-51 01307 Dresden

Re: [PyMOL] distance atom-protein surface

://lists.sourceforge.net/lists/listinfo/pymol-users -- Andreas Henschel Bioinformatics Group TU Dresden Tatzberg 47-51 01307 Dresden, Germany Phone: +49 351 463 40063 EMail: a...@biotec.tu-dresden.de

Re: [PyMOL] Coloring structure by hydrophobicity

-residue lookup table. I'm looking at a set of structure predictions, and it would be nice to easily see that a fold exposes a large patch of hydrophobic surface to solvent. Thanks, Andy -- Andreas Henschel Bioinformatics Group TU Dresden Tatzberg 47-51 01307 Dresden, Germany Phone

Re: [PyMOL] APBS and Pymol

-- Andreas Henschel Bioinformatics Group TU Dresden Tatzberg 47-51 01307 Dresden, Germany Phone: +49 351 463 40063 EMail: a...@biotec.tu-dresden.de psize.py Description: application/python

[PyMOL] Colors, their code and their rgb

(color)) Instead of the color code I need the RGB value, ideally also of those that were just defined in that session. I figured out some, but the list is far from exhaustive. Any idea? would be most appreciated. Cheers, Andreas -- Andreas Henschel Bioinformatics Group TU Dresden Tatzberg 47-51

[PyMOL] Global vars in Plugin name space?

simply do it with scripts (which can access global vars), not plugins. But in general, is there some info on plugin name spacing (and should it be put to the Wiki Plugin tutorial)? Cheers, Andreas -- Andreas Henschel Bioinformatics Group TU Dresden Tatzberg 47-51 01307 Dresden, Germany Phone: +49

[PyMOL] pngs and structures simultaneously?

and have the full power of pymol scripting and molecule viewing. At least I can do it seperately... Just a thought. Also, any idea, how I can call a function with just pressing a single key? Cheers, Andreas -- Andreas Henschel Bioinformatics Group TU Dresden Tatzberg 47-51 01307 Dresden, Germany Phone

[PyMOL] Surface/mesh coordinates

Dear all, is there an obvious way to get hold of surface/mesh coordinates in a python object? Thanks, Andreas -- Andreas Henschel Bioinformatics Group TU Dresden Tatzberg 47-51 01307 Dresden, Germany Phone: +49 351 463 40063 EMail: a...@biotec.tu-dresden.de

[PyMOL] PyMOL in CAVE

is there a straightforward way of producing 5 simultaneous views and exporting them to different output devices? Thanks for any help! Andreas -- Andreas Henschel Bioinformatics Group TU Dresden Tatzberg 47-51 01307 Dresden, Germany Phone: +49 351 463 40063 EMail: a...@biotec.tu-dresden.de

[PyMOL] SQL in function with cmd.extend

() ## Many thanks -- Andreas Henschel Bioinformatics Group TU Dresden Tatzberg 47-51 01307 Dresden, Germany Phone: +49 351 463 40063 EMail: a...@biotec.tu-dresden.de

[PyMOL] Alignment objects

functionality? Ie which methods/values does it provide? Many thanks. Andreas -- Andreas Henschel Bioinformatics Group TU Dresden Tatzberg 47-51 01307 Dresden, Germany Phone: +49 351 463 40063