[PyMOL] selecting surface residues only

n each residue.. Both of these require lots of time and some careful adjustment of the clipping plane if I want to be able to see anything.. If there's a quicker way, I'd love to know about it! Thanks in advance Jean

[PyMOL] PLUGIN PYMOL, FULL DOCUMENTATION

Hi I would like to get the full documentation related to the creation of plugins pymol I found this page, very usesful to start : http://www.pymolwiki.org:/index.php/Plugins_Tutorial But where could I found some more documentation and examples ? Best Regards Jean-Marc DAUGET Paris

[PyMOL] PLUGIN COMPATIBILITY WITH PYMOL VERSIONS

Hi Would you have some informations about the consequences of Pymol versions changes on the plugins previously created ? otherwise where could I find this informations ? Best regards Jean-Marc DAUGET Paris-Diderot University

[PyMOL] errors compiling fink pymol 0.98

error? Thank a lot for any responses. Jean-Christophe Making check in misc make t-printf t-scanf t-locale gcc-3.3 -DHAVE_CONFIG_H -I. -I. -I../.. -I../.. -I../../tests -I/sw/ include -g -O2 -mpowerpc -no-cpp-precomp -c `test -f t-printf.c || echo './'`t-printf.c /bin/sh ../../libt

[PyMOL] Red-Blue anaglyph in Pymol

Pymol. Thanks. Jean-Christophe ____ Jean-Christophe Amé, PhD Département Intégrité du Génome, UMR 7175-LC1 du CNRS École Supérieure de Biotechnologie de Strasbourg Pôle API Parc d'innovation, Boulevard Sébastien Brant BP 10413 67412 ILLKIRCH CEDEX France tel.: +33 (0)3 90

[PyMOL] Command:turn

Greetings, Does anyone know if the camera commands (turn & move) can be constrained to the reference (global) axes? I would imagine that the turn command (http://pymol.sourceforge.net/newman/ref/S1000comref.html#2_166) would cause a camera of 45 degrees about the reference axis: PyMOL> turn x, 4

Re: [PyMOL] WRL Output

My 2 cents' worth: How about skipping over the ancient and limiting WRL format and adopt a cross-platform solution. For example, Collada is gaining momentum in the 3D community (https://collada.org/public_forum/welcome.php) and provides an open standard digital asset schema for interactive 3D a

Re: [PyMOL] Focus depth

Implementing DOF in PyMol wouldn't be trivial and I'm not sure it's a priority/necessity. There are excellent open-source (and proprietary) rendering engines out there that can render better and faster than PyMol. Why re-invent the wheel... my 2 cents' worth :) However, aside from exporting

[PyMOL] Documentation and advice for external GUI Movies commands?

ut I can't figure out how to call Movie/Program/Static Loop/X-rock,. Thanks, Jean Jasinski, Ph.D. -- Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables un

[PyMOL] Alpha channel support gone?

What has happened to alpha channel support in PNG output? I could have sworn it used to be there. I'm now working in version 0.9. thanks Jean-Philippe Cartailler Vanderbilt University Medical Center S-3223 Medical Center North 1161 21st A

[PyMOL] map size/memory/crashing

Hello list, I've been working on making some figures from ultrahigh resolution data. I have some dense maps and pymol just bombs away when I try to 'ray' away. It's pymol 0.93, BRIX maps, tried it on two machines both with 1GB RAM (not enough, I know...), <6 month old P4's, win2000 and RH7.x. Th

RE: [PyMOL] Cavity display?

Related the issue of inside-surface coloring, a useful feature to add to pymol would be the ability to flip surface normals for selected surfaces. Just a thought. JP Cartailler > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > ad...@lists.source

RE: [PyMOL] transparent background

Set the ray_opaque_background to off The PNG file format supports transparency. Render your scene with the above, open up in an image editor and you should have a transparent background. JP > -Original Message- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...

RE: [PyMOL] colouring surfaces according to molecular properties

Speaking of, is there any way of extracting the polygons of the surface geometry (or points, for that matter)? JP -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Anders Madsen Sent: Tuesday, June 21, 2005

RE: [PyMOL] putty/sausage NMR figure

One way to do this would be to calculate RMSD between your models (using whatever package) and replace the B-factor column with those values (make sure you respect the PDB format (B-factors are in columns 61 - 66, with first column as "1" - see http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part