RE: [PyMOL] PyMol training

Dear PyMOL users, there will be a PyMOL training in the area of Berlin, Germany, soon. It is scheduled for October 19th, 15.00 at the beamlines of the BESSY II synchrotron. Please contact me for details. Kristian Rother Charite - Universitaetsmedizin Berlin kristian.rot...@charite.d

Re: [PyMOL] PyMol training

Hi, I've planned to write a french training document for PyMOL. I would enjoy that some people help me by reading my draft, before I release it. This document will be released under a Creative Common License (cc). Thanks, Jerome Pansanel Le Lundi 10 Octobre 2005 09:29, Kristian Rother a écrit

Re: [PyMOL] grid/cube representation

| | As a follow up to my last email asking whether there is a way to make 3D | grid representations of molecules I have found a picture of the kind | of thing I am after. Is there a way to make anything similar to this | http://www.techfak.uni-bielefeld.de/ags/ai/projects/docking/images/align

[PyMOL] PyMol does not compile with python 2.4.1

I've tried to compile PyMol 0.99beta15 (one from CVS) using: python setup.py install it fails while comiling layer0/Crystal.c the problem in gcc "-Wp,-D_FORTIFY_SOURCE=2" parameter, which fails compilation of PRINTF macro inside of Crystal.c If I compile Crystal.c without this parameter ev

[PyMOL] alpha helices as cylinders in Pymol

Hi, Is it possible to draw alpha helices as cylinders in PyMol? The effect I'm looking for is like the Molscript/render version of cylinders. Related to this, when I read into pymol an r3d script generated by molscript with helices drawn as flat ended cylinders, PyMol draws the cylinders as

[PyMOL] RGB values for preset colors in PyMol

Hi, Is it possible to get a listing of the RGB values for the present color palette used in PyMol? Related to this anyone know how to add user defined colors to the GUI interface. Thanks -- Mark Mayer Ph.D. LCMN NICHD NIH DHHS Bldg 35, Room 3B 1002 MSC 3712 35 Lincoln Drive Bethesda MD 20892

[PyMOL] Small problem or inconsistency in showing cgo objects?

Hi. I've run into a slight pymol UI problem with cgo objects and I'm wondering if I should be doing something differently or if it's a pymol idiosyncrasy. Here's a script: from pymol.cgo import * from pymol import cmd one = [ SPHERE, 0.0, 0.0, 0.0, 1.0 ] two = [ SPHERE, 2.0, 0.0,

Re: [PyMOL] alpha helices as cylinders in Pymol

Hi Mark, Try: set cartoon_cylindrical_helices,1 I think it should do the trick. For more cartoon related settings, type set cartoon_ and press ; pymol will then give you the list of all settings which match. Cheers, Tsjerk On 10/10/05, Mark Mayer wrote: > > Hi, > > Is it possible to draw al

[PyMOL] PyMol segmentation fault while starting from external python program

Launching PyMol form external python script will produce segmaentation fault. For example starting "launch.py" from "/pymol/examples/launching" -- $ python launch.py zsh: segmentation fault python launch.py -

[PyMOL] New PX beamline at APS

Dear Colleague, We are pleased to announce our first call for proposals for beam time at sector 23 of the APS. Beamline 23ID-D, currently operational, is the first of two undulator beamlines being constructed at GM/CA CAT, funded by NIGMS and NCI of the U.S. NIH. Proposals for beamtime should be

[PyMOL] Correction: New PX beamline at APS

Oops, please use the site http://www.gmca.aps.anl.gov/user_program/EnvelopeIDin.html For current beamline capabilities. Sorry for any confusion. Nukri Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT, Bld. 436, D007 Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fa

RE: [PyMOL] PyMol segmentation fault while starting from external python program

Dmitriy, Due to problem with multithreading (especially with the Tcl/Tk external GUI), we haven't been able to get the "import pymol" approach to work in a stable robust manner across different OSes and environments. So sight now, as per comments in "modules/pymol/__init__.py", the only support

RE: [PyMOL] RGB values for preset colors in PyMol

Mark, print cmd.get_color_indices() will retrieve the color indices print cmd.get_color_tuple(index-number) will retrieve individual RGB components. set_color color-name, [r,b,g] will create a new color that will appear in the GUI list. From the open-source GUI you can use the "add" button in

Re: [PyMOL] Small problem or inconsistency in showing cgo objects?

Hi, I was curious, and tried this out. Seems that "hide" means roughly the same as setting the representation to "none". "Enable/disable" are the equivalents to clicking on the "name-button". So, if you change the test script to have "cmd.disable('two')" at the end instead of 'hide', then