Martin, Just FYI, the gradient display in PyMOL you and I have been working on is still too immature to be considered supportable or supported. Indeed, prior to your post, you were one of the few PyMOL users even aware of it.
For everyone else, I suppose I should announce that one of the many new features pending for PyMOL 1.0 is the ability to display fieldlines in maps such as illustrated here: <http://pymol.sf.net/pmimag/fieldlines.jpg> The bugs are still being worked out, but usage parallels that of isomesh with ramp-based coloring by map potential. If you have SVN source, then "gradient ?" for usage. Note that this feature will not be supported by DeLano Scientific until after the 1.0 release. As for your question, "mdo" movie commands should be limited to localized state changes within PyMOL. Performing I/O or running external system calls (e.g. APBS) within a movie command is likely to not work, and may cause trouble, such crashes or hangs. The way to approach your need is to either precompute and preload all of your maps into PyMOL states (impractical for 600 maps), or to write a Python script which takes over from PyMOL in terms of sequencing, performing electrostatics, calculations, and rendering the movie. Cheers, Warren -----Original Message----- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Martin Höfling Sent: Friday, December 15, 2006 8:01 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] surface coloring fails with gradient loaded Hi there, i am trying to render fieldlines and sf potential together in a movie. The movie setup is like this: import os set gradient_spacing=5 load ProtOut.pdb,prot load trajshort.xtc,prot mset 1 -7 show surface set surface_solvent=1 for a in range(1,7): cmd.mdo(a,"delete flines;delete dxmap;delete dxmap2;delete rmp;delete rmp2;save prot.pdb,prot;os.system(\"pdb2pqr --ff=amber prot.pdb prot.pqr&>log.txt\");os.system(\"apbs apbs.in&>log.txt\");load apbsout.dx,dxmap;load apbsout.dx,dxmap2;ramp_new rmp,dxmap, [-1.5,-0.75,0];ramp_new rmp2,dxmap,[-10,0,10];gradient flines,dxmap,-10,10,prot,carve=15;color rmp,flines;set surface_color=rmp,prot") set ray_trace_frames=1 set cache_frames=1 mclear Is there anything wrong on this setup? the surface is always white. If i do a show surface in every frame, then it seems to me as if the surface is calculated for all frames (600 in total). This is too slow to do it on every step. Any ideas? Cheers Martin ------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV _______________________________________________ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
