[PyMOL] Error: unknown type

Hello List, Any ideas on why this script keeps failing in the newer PyMOL builds... http://pymolwiki.org/index.php/Zero_residues I keep getting the error message: Error: unknown type: '1hpv' where 1hpv is an actual pdb file/object I am running pymol 1.2b5 rev. 3706 (compiled from svn)

[PyMOL] Color By RMSD -- New Script

Hello List, A new PyMol script for coloring two objects by mutual RMS Deviation is now available on the PyMol wiki: http://pymolwiki.org/index.php/ColorByRMSD Hope some of you will find it useful... Many thanks to Jason Vertrees for help with turning the initial proof-of-principle into useful

Re: [PyMOL] figure of buried surface area

Hi Jiamu, Have you looked at VASCo : http://genome.tugraz.at/VASCo/ I have found it to be very useful and very capable. Contact interfaces, electrostatics (with Delphi) and many other features are available. And best of all, it works extremely well with PyMOL. Do read the manual carefully and

Re: [PyMOL] disjoint surfaces

Raluca, Something that helps is: tabbing into edit mode, selecting all vertices (ctrl-a) and removing doubles (Mesh Vertices Remove Doubles). Turning on smooth display also helps. What exactly are you having problems with? In what way are things disjointed ? Best, Shiven On Mon, Dec 21,

Re: [PyMOL] disjoint surfaces

On Mon, 21 Dec 2009 11:24:11 -0500  Shiven Shandilya shiven.shandi...@gmail.com wrote: Raluca, Something that helps is: tabbing into edit mode, selecting all vertices (ctrl-a) and removing doubles (Mesh Vertices Remove Doubles). Turning on smooth display also helps. What exactly

[PyMOL] PyMOL Blender

Hello List, An initial attempt at a PyMOL + Blender tutorial is now on the pymolwiki: http://pymolwiki.org/index.php/Blender Hope some of you will find it useful. Fellow Blenderheads, crits are welcome. Also, please help improve/add to the tutorial. Best, Shiven

Re: [PyMOL] PyMOL-users Digest, Vol 45, Issue 10

Hello Sing, Perhaps going over the basic tutorial will help make things clear: http://wwwuser.gwdg.de/~dseelig/plugin_tutorial.html Best, Shiven On Fri, Feb 19, 2010 at 1:13 PM, Kin Sing Stephen Lee s...@chemistry.msu.edu wrote: Dear all, Sorry I fixed the prepare_ligand4.py problem.  

Re: [PyMOL] Pymol and APBS

Hi Jon, Perhaps you could look at VASCo http://genome.tugraz.at/VASCo/ I have found it to work extremely well on Windows and Linux platforms. You not only get electrostatics but also hydrophobic surface coloring, and all without the APBS and Python hassles and headaches. Sorry to be knocking

Re: [PyMOL] Pymol and APBS

a personal note. Like everyone else writing to the list and answering questions, my aim was to help a fellow user get that job done. --- On Thu, Apr 15, 2010 at 12:00 PM, Michael Lerner mgler...@gmail.com wrote: On Thu, Apr 15, 2010 at 10:30 AM, Shiven Shandilya shiven.shandi

Re: [PyMOL] for evaluation only

hi victor, if you are on windows and need the latest pymol version, please take a look at christoph's pymol builds (thanks christoph!): http://www.lfd.uci.edu/~gohlke/pythonlibs/#pymol best, shiven On Thu, Apr 29, 2010 at 6:32 PM, Nathaniel Echols nathaniel.ech...@gmail.com wrote: On Thu,

Re: [PyMOL] New MacPros and PyMOL - Radeon only?

Dear Jason, I strongly support Adam's suggestion that the PyMOL website and the Wiki display a clear warning to people planning on using PyMOL with ATI/AMD graphics card. I have had numerous issues with ATI graphics cards + PyMOL over the years and nVidia is unquestionably the better choice when

[PyMOL] GLSL Shaders

Hi fellow PyMOLers, Thought some of you may be interested in this: http://pymolwiki.org/index.php/GLSL_Shaders Test, improve, share ... :-) Cheers!! -- Shiven -- Live Security Virtual Conference Exclusive live

Re: [PyMOL] Real-time black and white view possible?

Hi Martin, I guess you can do this using modified GLSL shaders … Two examples I posted on the PyMOL wiki a while ago: http://www.pymolwiki.org:/index.php/GLSL_Shaders Best, Shiven On Jun 12, 2014, at 5:10 PM, Martin Hediger ma@bluewin.ch wrote: Hi all I wonder if it's possible to

Re: [PyMOL] Cel shading in PyMOL

Hi Jacob, If you have the right mix of display drivers and Pymol version, you can try GLSL shaders. http://www.pymolwiki.org/index.php/GLSL_Shaders Unfortunately, it does not work flawlessly across platforms and I have not invested any more time figuring it out because the shader system in