Re: [PyMOL] Caching duplicate frames with mpng?

2007-05-22 Thread Tsjerk Wassenaar
Hi Nick, Unfortunately, there's nothing you can do about it. mpng just writes out the frames one after the other, with raytrace_frames set raytraycing each of them. cache_frames just puts each (rendered) frame in memory, so Pymol can cycle through them sort of smoothly after all frames are render

[PyMOL] Caching duplicate frames with mpng?

2007-05-22 Thread nick hatch
I'm rendering some longer movies that have long sequences of duplicate frames, eg: Molecule side view (5 seconds) Rotate/Zoom (3 seconds) Another view (5 seconds) I've noticed that when using the mpng command, these duplicate frames are rendered, one after another... Is there a setting I'm miss

Re: [PyMOL] surfaces for molecules with non-standard VDW's

2007-05-22 Thread Richard Gillilan
Thanks! That works. In the past I had actually wanted to set solvent radius fairly large, but had poor luck getting the results I wanted. Now it seems to solve this particular problem. Go figure. Richard On May 22, 2007, at 10:53 AM, Tsjerk Wassenaar wrote: Hi Richard, What about set

Re: [PyMOL] surfaces for molecules with non-standard VDW's

2007-05-22 Thread Tsjerk Wassenaar
Hi Richard, What about set solvent_radius,3 That seems to do the trick for me. Cheers, Tsjerk On 5/22/07, Richard Gillilan wrote: In the past I have used PyMol pretty successfully to visualize low- resolution x-ray solution scattering results in which each "atom" in a pdb file is actually

[PyMOL] surfaces for molecules with non-standard VDW's

2007-05-22 Thread Richard Gillilan
In the past I have used PyMol pretty successfully to visualize low- resolution x-ray solution scattering results in which each "atom" in a pdb file is actually a large sphere (say 4-6 Angstroms) representing some density. I would use >alter , vdw = 6.0 to set the sphere sizes appropriate

[PyMOL] Structural bioinformatics and computational biophysics ISMB satellite meeting

2007-05-22 Thread Rafael Najmanovich
On behalf of the 3DSig organising committee, I would like to bring to your attention the approaching deadline to submit an abstract to the forthcoming 3DSig 2007: Structural bioinformatics and computational biophysics ISMB satellite meeting to be held on July 19-20 in Vienna, Austr