[PyMOL] Convert pml script to Pymol Python script

Hi, I have a few pml scripts for pymol that I would like to rewrite properly in python, making use of Pymol's ability to interprete Python scripts. Do you know of an interpreter that converts pml scripts automatically to python scripts for Pymol? Since the number of tasks that you can do in pml i

[PyMOL] Pymol for Mac with xtc support

Hi, This is a specific question about how to compile Pymol for Mac with xtc support. The regular Pymol version that is compiled with "port" does not include support for xtc files (and thus can't play movies). However, the best thing about Pymol are its movie-making tools. How do you compile Pymo

[PyMOL] Making dashed line transparent

Hi, How can I make a dashed line transparent? Cheers, Matthias -- EditLive Enterprise is the world's most technically advanced content authoring tool. Experience the power of Track Changes, Inline Image Editing and ensu

[PyMOL] Secondary structure bug?

Hi I am making a movie in pymol that I prepared with g_morph g_morph -f1 start.pdb -f2 end.pdb -o movie.pdb -nofit (gromacs 4.5.4) Pymol does not assign the secondary structure. load movie.pdb dss, movie assigns incorrect secondary structure. In my case, dss models a complete transmembrane hel

[PyMOL] Delete frames in movie

Hi, I made a nice movie and it's fine and I would just like to delete a part of it or to insert some frames. How is that possible? Mset resets the whole movie and mview does not seem to do what I would like it to do... Best, Matthias -

[PyMOL] Render transparent cartoons

Hi, Apologies if that has come up before, but is it possible to ray-trace transparent cartoons? PyMol 1.4 (port on MacOs) does not seem to do that. The OpenGL cartoon however is transparent and looks fine. Best, Matthias -- Structural Bioinformatics and Computational Biochemistry Unit Dept. of B

[PyMOL] Compilation of PyMOL on Mac

Hi, I downloaded PyMol from https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol and tried to compile it with /sw/bin/python2.7 setup.py build The compilation works fine, but when it comes to linking, I get an error related to undefined symbols in an OpenGL library wrapper. Do you have an

Re: [PyMOL] Compilation of PyMOL on Mac

source. However the VMD Molfile plugin is still not working. The default builds of both MacPorts and Fink don't incldue the VMD Molfile plugin. Any suggestions? Best, Matthias On Thu, Aug 11, 2011 at 5:42 PM, Matthias Schmidt < matthias.rene.schm...@gmail.com> wrote: > Hi, >

[PyMOL] refresh molecule display in python script

Hi, I am loading a pdb file in a python script for pymol. The script has the following structure: def script do something cmd.load("file.pdb") do lot more cmd.extend("script", script) When the python script is completed, the molecule file.pdb is shown in the openGL display, but not before. Ho

[PyMOL] loop through pymol models

Hi, I would like to have a python script that runs in pymol and loops through all available loaded models. How do I get the number of models loaded in pymol? Thanks, Matthias -- This SF email is sponsosred by: Try Windo