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 Py

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 wrote: > Hi all > > I wonder if it's possible to have something

[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 eve

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 i

Re: [PyMOL] Running pymol without display

Hi Kim, The pymol wiki explains the various command line options/switches you can use to run pymol without a GUI and to execute specific operations non-interactively: http://pymolwiki.org/index.php/Command_Line_Options An example of using pymol for ray-tracing, without a GUI, is listed here: h

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] SDF with title displayed

Hi Om, Try doing this: load subset.sdf split_states subset, 1 dele subset set grid_mode, 1 label id 1, model I am guessing the resulting view is what you had in mind... You may have to increase the label_size to make the labels visible in grid_mode with the command: set label_size, 30 Best, Sh

Re: [PyMOL] Pymol and APBS

unity members on this. Thank you! With best regards, Shiven P.S. Apologies again if my criticism hit 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

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-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 wrote: > Dear all, > > Sorry I fixed the prepare_ligand4.py problem.  However, when I try to

[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] disjoint surfaces

ng. > Thank you, > Raluca > > > On Mon, 21 Dec 2009 11:24:11 -0500 >  Shiven Shandilya wrote: >> >> Raluca, >> >> Something that helps is: tabbing into edit mode, selecting all >> vertices (ctrl-a) and removing doubles (Mesh >Vertices >>> >&

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] 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 y

[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 c

[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) o

Re: [PyMOL] movie

Since this is your second message regarding the same problem... Did you try searching the the pymolwiki.org site? Or just google for commands/scripts to make a movie on pymol? Here is a link that may help: http://pymolwiki.org/index.php/Slerpy Best, Shiven On 2/1/07, shivesh kumar <2shiv...@gm

Re: [PyMOL] problem getting kabsch.py to run

On 10/15/06, Margaret Luk-Paszyc wrote: Hello -- Can someone please advise me? I'm a new user of PyMol trying to get the kabsch alignment script to work. I only installed the main pymol installer (v 0.99r6), and I have copied the kabsch.py script as the wiki said. However, I can't find this N