[PyMOL] Problem reading multiframe pdb file for animation

Dear PyMol experts: When using Open-Source PyMOL 0.99rc6 I read in a pdb file which has 40 coordinate sets (each is one frame in an animation) each beginning with: HEADER Output iset= n _G=r_0_01 then a list of the pdb coordinates and ending with: ENDMDL n ranges from 0 to 39. This

Re: [PyMOL] Problem reading multiframe pdb file for animation

Hi Peter, If you could send me the PDB (or one like it) I'd like to see it. The known flags for controlling how PyMOL loads multi-state files are: discrete= 0 or 1 If 0, then all states must have the same number of atoms and similar connectivity If 1, then all states are treated as

[PyMOL] Adding Hydrogens

Dear All I would like to ask if the PyMOL function to add hydrogens to an entire protein also has options, meaning is it possible to set the protonation state of individual residues specifically? Like in a list or something? h_add, His202:+1 or so? And, it can be relevant at what atom a residue

Re: [PyMOL] APBS values

I am replying since your question did not get addressed in the past, but know that I am not intimately familiar with PyMOL code or python. I do have a thought, though, if using a grid approximation would work. I have done some work with using MRC density map format in pymol, partly in

Re: [PyMOL] Adding Hydrogens

I've had good results with MolProbity ( http://molprobity.biochem.duke.edu/index.php?MolProbSID=6b810d461879ca495f8d7898629dc18ceventID=15) in the past. I had a script that would let me cycle through all of the HIS residues, add hydrogens, and cycle between states. It's broken at the moment. The

Re: [PyMOL] Problem reading multiframe pdb file for animation

Hi Peter, When using Open-Source PyMOL 0.99rc6 I read in a pdb file which has 40 coordinate sets (each is one frame in an animation) each beginning with: HEADER Output iset= n _G=r_0_01 Please replace your HEADER stamps with REMARK in your PDB file. Then load with multiplex=0.

[PyMOL] Summary: Problem reading multiframe pdb file for animation

The solution (thanks to Jason) is to change all instances of: HEADER to: REMARK in the pdb file. Then opening the file results in the correct behavior (as before) of loading one object with 40 frames. Regards, Peter Stern Dear PyMol experts: When using Open-Source PyMOL 0.99rc6 I read in

[PyMOL] 3D Projector successful cases

Dear PyMOL Users, We're looking forward to buy an active 3D Projector for PyMOL Visualization. I would like to know which 3D Projector setups are you using and can certify that work with PyMOL. Which combinations of projector, Glasses, Emitters, OS, etc ... Actually work for you. Any help

Re: [PyMOL] 3D Projector successful cases

Jason, Thank you very much. Have you tried to use it with a Mac ? We have a Mac Pro with a Quadro FX 5600 Card and would be great to use the projector from there. We already use it with Nuvision glasses 60GX and a CRT display. Best, David On 16/03/2011, at 17:47, Jason Vertrees wrote: Hi

Re: [PyMOL] 3D Projector successful cases

We've had great success with the ViewSonic PJD6531w (http://www.viewsonic.com/products/pjd6531w.htm). It's bright, clear So are you guys using the DLP link (3d sync) technology of the projector with DLP link capable glasses?

Re: [PyMOL] 3D Projector successful cases

Hi David, Thank you very much. Have you tried to use it with a Mac ? We have not tried it with a Mac. The only stereo I can currently get on the Mac is Zalman. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603)

[PyMOL] ray_trace_mode, 1 - white outline

For some reason I am getting white outlines in saved pymol sessions with ray_trace_mode, 1. Does anyone know what is causing this and/or a quick way to switch to the black outlines. This does not occur with new sessions, only when I open a saved session. Thanks! - Nathan

Re: [PyMOL] ray_trace_mode, 1 - white outline

Hi Nathan, set ray_trace_gain, 0 set ray_trace_color, black If your background color is something other than black, use that color instead. Cheers, -- Jason On Wed, Mar 16, 2011 at 1:27 PM, NATHAN THOMSEN nathan.thom...@ucsf.edu wrote: For some reason I am getting white outlines in saved