Re: [PyMOL] problems cloring sticks

graphics card) are the workarounds I use. Not a solution per se, but this seems to be an issue between OpenGL and Intel (although I've only seen problems with Pymol, and not vmd). -David David A. Horita, Ph.D. Department of Biochemistry Wake Forest University School of Medicine Winston S

[PyMOL] Ray, png

sions, and then used these to generate a high-resolution ray traced image with the same x/y ratio. I figure I'm missing something. Regards, --------- David A. Horita, Ph.D. Department of Biochemistry Wake Forest University School of Medicine Winston-Salem, NC 27157-10

RE: [PyMOL] GUI

Hi- I'd second this; my brain doesn't do well keeping track of whether I'm, for example, in maximum or reasonable performance mode. David ----- David A. Horita, Ph.D. Department of Biochemistry Wake Forest University School of Medicine Winston-Salem, NC

[PyMOL] low-end graphics cards/laptops

ll be satisfied). Many of the current crop of <5 lb notebooks use integrated graphics for price and battery life. If these units don't provide sufficient graphics power for Pymol/VMD/Deepview, the useful market shrinks substantially. Thanks, David ---------

[PyMOL] pymol nstall problems

se seen/fixed this problem? Thanks, Dave ----- David A. Horita, Ph.D. Department of Biochemistry Wake Forest University School of Medicine Winston-Salem, NC 27157-1016 Tel: 336 713-4194 Fax: 336 716-7671 email: dhor...@wfubmc.edu web: http://www1.wfubmc.edu/biochem/faculty/Horita.htm <http://www1.wfubmc.edu/biochem/faculty/Horita.htm/>

[PyMOL] hydrogen naming

- David A. Horita, Ph.D. Department of Biochemistry Wake Forest University School of Medicine Winston-Salem, NC 27157-1016 Tel: 336 713-4194 Fax: 336 716-7671 email: dhor...@wfubmc.edu web: http://www1.wfubmc.edu/biochem/faculty/Horita.htm <http://www1.wfubmc.edu/bioc

Re: [PyMOL] How to plot residu with a number > 9999

roblem with fixed-width fields, but that's another discussion... Regards, David --------- David A. Horita, Ph.D. Department of Biochemistry Wake Forest University School of Medicine Winston-Salem, NC 27157-1016 Tel: 336 713-4194 Fax: 336 716-7671 email: dhor...@wfub

Re: [PyMOL] Feature Request/Ideas

times where I've highlighted a collection of residues as spheres and then accidentally added spheres to the whole molecule instead of the next selection. Being able to get back from that (even one step) would be a time-saver. Dave - David A. Horita, Ph.D. Departmen

[PyMOL] isosurfaces

Hi, Is there any way to display an electrostatic isosurface (calculated by apbs) as either a nice-looking mesh or as a projection plane (as done by the SGI version of Grasp)? (Or some other format that is reasonably clear in 2 dimensions.) Thanks, David - David A

[PyMOL] cd in windows

Hi, How does one change directories in Windows when the directory name has a space in it? I've tried double and single quotes as well as backslash space (I'd like to run a script that's in such a directory). Thanks David ----- David A. Horita, Ph.D

Re: [PyMOL] cd in windows

rom: Edward A. Berry [mailto:ber...@upstate.edu] Sent: Mon 9/20/2010 2:03 PM Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] cd in windows David A. Horita wrote: > Hi, > How does one change directories in Windows when the directory name has a > space in it? I've tried do

[PyMOL] align

rst in the set. If I only load in a subset - say the 4 lowest energy, they may or may not include any given filename, so aligning them to an explicit name won't always work. Thanks, David --------- David A. Horita, Ph.D. Department of Biochemistry Wake Forest Unive

[PyMOL] can't save pdb from within pymol

) Thanks, Dave --------- David A. Horita, Ph.D. Department of Biochemistry Wake Forest University School of Medicine Winston-Salem, NC 27157-1016 Tel: 336 713-4194 Fax: 336 716-7671 email: dhor...@wfubmc.edu<mailto:dhor...@wfubmc.edu> web: http://www1.wfubmc.edu/biochem/faculty/H

[PyMOL] pkfrag

gh control. Selecting and protecting atoms doesn't seem to help, in this case. Thanks, Dave Horita ----- David A. Horita, Ph.D. Department of Biochemistry Wake Forest University School of Medicine Winston-Salem, NC 27157-1016 Tel: 336 713-4194 Fax: 336 716-767

[PyMOL] Nuvision stereo glasses?

the 15-pin VGA connector. Is this signal present on ATI cards (or even on dual-DVI-I output cards)? Thanks, Dave Horita ----- David A. Horita, Ph.D. Department of Biochemistry Wake Forest University School of Medicine Winston-Salem, NC 27157-1016 Tel: 336 713-4194 Fa

[PyMOL] cartoons through nonstandard residues

seem to go through the PTR without problem, and selenomets don't seem to cause trouble, either. Thanks, David Horita ----- David A. Horita, Ph.D. Department of Biochemistry Wake Forest University School of Medicine Winston-Salem, NC 27157-1016 Tel: 336 713-4194 Fax: 33

[PyMOL] unsetting cartoon_colors

n error about not knowing what color default is. Thanks, Dave Horita --------- David A. Horita, Ph.D. Department of Biochemistry Wake Forest University School of Medicine Winston-Salem, NC 27157-1016 Tel: 336 713-4194 Fax: 336 716-7671 email: dhor...@wfubmc.edu web:

FW: [PyMOL] selecting multiple atoms ie oxygen

Warren, Personally, I'd much rather have wild-card selections in atom names and have to deal individually with the ill-conceived PDB files than the other way around. Regards, David Horita -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sou

RE: [PyMOL] ray command

Hi, Regarding the use of the ray command, is there a way to automatically set either the x or y value to maintain the same aspect ratio as displayed in the window? For that matter, how do you determine the number of x and y points displayed (other than making a bitmap and loading that into anot

[PyMOL] rotating molecules

might have hit on the appropriate combination of protecting/freezing/creating objects/etc. once, but can't seem to repeat the routine. Thanks for any tips, David Horita --------- David A. Horita, Ph.D. Department of Biochemistry Wake Forest University School of Medicin

RE: vmd-l: vmd and Re: [PyMOL] pymol crashes with new [7167] nvidia driver

Hi, I Haven't tried VMD yet, but Windows XP-pro pymol crashes upon file open under the 71.84 drivers, but not the 70.78 drivers. (Quadro 1300, XP-Pro servicepack 2) David Horita -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.ne