[PyMOL] mixing ray_shadows states

I'm trying to make a high-quality figure showing ligand binding in a cleft, incorporating sticks, electron density, and some combination of cartoon/surface/lines for the protein. Ray-traced shadows make the perspective much clearer but also add visual "noise" - for instance, the electron densi

Re: [PyMOL] Another Nvidia question (7676 driver)!

Any body know how to fix this. Have people tested this driver? Should I load an earlier driver? When dealing with NVidia cards, I've found this is always the first thing to try whenever a problem arises. Their Linux drivers are updated to support new hardware and fix old bugs, but they often

[PyMOL] Another Nvidia question (7676 driver)!

Hi folks, Sorry for the slightly of topic question but I figure you guys know whats going on. I have a linux box with RHE WS 4 and I have just installed the nvidia driver (7676 x86) which at least works so far! The problem is that the screen will occasionally (and randomly) start flickering

[PyMOL] apbs and pymol in fink (OS X)

I have the same problem on a mac G5 dual processor with newly compiled pymol 0.98 and apbs 3.2, installed by fink. Also occurs with the standalone mac/xll hybrid executable, calling apbs 3.2 using the plug in menu. Interestingly, the programs work fine together on my mac G4 laptop, with singl

[PyMOL] Re: Slowwwww ray

Stuart, Stuart Endo-Streeter Default view, white with black background (sticks): Ray: total time: 15.68 sec. = 229.5 frames/hour. (15.68 sec. accum.) Surface ray (white w/ black background): Ray: total time: 32.67 sec. = 110.2 frames/hour. (48.35 sec. accum.) thanks a lot for the test. I g

RE: [PyMOL] saving multiple object in one pdb file

FYI: In the development code, I've added a new "segi" option to "symexp" that will automatically assign a unique segment ID to symmetry-generated molecules. This will allow a use case such as follows: % pymol load $PYMOL_PATH/test/dat/1tii.pdb symexp s, 1tii, 1tii, 20.0, segi=1 save packing.pdb,

Re: [PyMOL] saving multiple object in one pdb file

> My question is: how to save multiple objects from pymol as one nice pdb > file, for instance with each object with different chain name? alter SymgenObject,chain 'X' and repeat as needed for all objects (changing the chain as needed). Then use all of your objects as the selection for save (ak

RE: [PyMOL] Slowwwww ray

Michele, Did you just migrate from an older version? We switched PyMOL over to perspective-based rendering (WYSIWYG with OpenGL) as the default at some point in the past year. You can still render orthoscopically if you'd prefer: load 1alk.pdb show surface set orthoscopic set hash_max=160 ray

Re: [PyMOL] Slowwwww ray

Default view, white with black background (sticks): Ray: total time: 15.68 sec. = 229.5 frames/hour. (15.68 sec. accum.) Surface ray (white w/ black background): Ray: total time: 32.67 sec. = 110.2 frames/hour. (48.35 sec. accum.) About the times I've been seeing for equivalent work I've been doi

[PyMOL] Slowwwww ray

Hi, I have a 2GHz G5, 6GB RAM, running OS X 10.4.3 server. I started doing some modeling after about 6 months hiatus. I'm using MacPymol 0.99b29 (no flickering with this). But it's slower than molasses. I get: Ray: total time: 16.16 sec. = 222.8 frames/hour (32.15 sec. accum.). This is sim

Re: [PyMOL] problem with amber trajectory

Sorry Viktor and Warren, but I don't think your suggestions are applicable. I have only a single protein molecule in my trajectory, which I kept centered at the origin, so it never traverses the periodic boundary. I did strip all but 20 waters from it using ptraj and created the appropriate

Re: [PyMOL] apbs problem

I have the same problem on a mac G5 dual processor with newly compiled pymol 0.98 and apbs 3.2, installed by fink. Also occurs with the standalone mac/xll hybrid executable, calling apbs 3.2 using the plug in menu. Interestingly, the programs work fine together on my mac G4 laptop, with single pro

[PyMOL] apbs problem

Hi everyone, I am trying to run apbs from pymol (0.98) on window and always end up getting following error message. objectMap load DX file-error: unable to open file! Even after using improved plugin apbs tools.py , same error message.I also tried using externally generated .PQR file as an i

Re: [PyMOL] APBS

Hi Brian, Try this, the info is from the mailing list archive (http:// sourceforge.net/mailarchive/forum.php?forum_id=60)it just takes a bit of finding load x.pdb load whatever.dx, e_pot ramp_new e_lvl, e_pot, [-15, 0, 15], [ [1,0,0], [1,1,1] , [0,0,1] ] # this sets the scale and co