Re: [PyMOL] Focus depth

Implementing DOF in PyMol wouldn't be trivial and I'm not sure it's a priority/necessity. There are excellent open-source (and proprietary) rendering engines out there that can render better and faster than PyMol. Why re-invent the wheel... my 2 cents' worth :) However, aside from exporting

Re: [PyMOL] WRL Output

My 2 cents' worth: How about skipping over the ancient and limiting WRL format and adopt a cross-platform solution. For example, Collada is gaining momentum in the 3D community (https://collada.org/public_forum/welcome.php) and provides an open standard digital asset schema for interactive 3D

[PyMOL] Command:turn

Greetings, Does anyone know if the camera commands (turn move) can be constrained to the reference (global) axes? I would imagine that the turn command (http://pymol.sourceforge.net/newman/ref/S1000comref.html#2_166) would cause a camera of 45 degrees about the reference axis: PyMOL turn x, 45

RE: [PyMOL] putty/sausage NMR figure

One way to do this would be to calculate RMSD between your models (using whatever package) and replace the B-factor column with those values (make sure you respect the PDB format (B-factors are in columns 61 - 66, with first column as 1 - see

RE: [PyMOL] transparent background

Set the ray_opaque_background to off The PNG file format supports transparency. Render your scene with the above, open up in an image editor and you should have a transparent background. JP -Original Message- From: pymol-users-ad...@lists.sourceforge.net

RE: [PyMOL] Cavity display?

Related the issue of inside-surface coloring, a useful feature to add to pymol would be the ability to flip surface normals for selected surfaces. Just a thought. JP Cartailler -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-

[PyMOL] map size/memory/crashing

Hello list, I've been working on making some figures from ultrahigh resolution data. I have some dense maps and pymol just bombs away when I try to 'ray' away. It's pymol 0.93, BRIX maps, tried it on two machines both with 1GB RAM (not enough, I know...), 6 month old P4's, win2000 and RH7.x.

[PyMOL] Alpha channel support gone?

What has happened to alpha channel support in PNG output? I could have sworn it used to be there. I'm now working in version 0.9. thanks Jean-Philippe Cartailler Vanderbilt University Medical Center S-3223 Medical Center North 1161 21st Avenue