Re: [PyMOL] problems cloring sticks

2011-06-05 Thread David A. Horita
) 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 Salem, NC 27157, USA

[PyMOL] can't save pdb from within pymol

2011-01-27 Thread David A. 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.edumailto:dhor...@wfubmc.edu web: http://www1.wfubmc.edu/biochem/faculty/Horita.htmhttp://www1

[PyMOL] cd in windows

2010-09-20 Thread David A. Horita
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. Department

Re: [PyMOL] cd in windows

2010-09-20 Thread David A. Horita
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 double and single quotes as well as backslash space (I'd like to run a script that's

Re: [PyMOL] Feature Request/Ideas

2010-01-21 Thread David A. Horita
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. Department of Biochemistry Wake Forest University School

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

2009-06-09 Thread David A. Horita
, 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...@wfubmc.edu web: http://www1.wfubmc.edu

[PyMOL] hydrogen naming

2008-08-21 Thread David A. 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: http://www1.wfubmc.edu/biochem/faculty/Horita.htm http://www1.wfubmc.edu/biochem

[PyMOL] pymol nstall problems

2008-02-13 Thread David A. 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: http://www1.wfubmc.edu/biochem/faculty/Horita.htm http://www1.wfubmc.edu/biochem/faculty/Horita.htm/

[PyMOL] low-end graphics cards/laptops

2007-06-14 Thread David A. Horita
). 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 - David A. Horita, Ph.D

RE: [PyMOL] GUI

2006-01-20 Thread David A. Horita
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 27157-1016 Tel

[PyMOL] Ray, png

2006-01-03 Thread David A. Horita
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 27157-1016 Tel: 336 713-4194 Fax: 336 716-7671

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

2005-03-29 Thread David A. Horita
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

[PyMOL] rotating molecules

2004-10-27 Thread David A. Horita
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 Medicine Winston-Salem, NC

RE: [PyMOL] ray command

2004-04-05 Thread David A. Horita
that into another program)? -David Horita Mohammed, ray width, height png filename.png for example, for a 5x4 figure at 300 dpi: ray 1600,1200 png hires.png (or use Save image... from the File menu after the ray command) Cheers, Warren

FW: [PyMOL] selecting multiple atoms ie oxygen

2004-02-18 Thread David A. Horita
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

[PyMOL] unsetting cartoon_colors

2003-12-18 Thread David A. Horita
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: http://www.wfubmc.edu/biochem/faculty

[PyMOL] cartoons through nonstandard residues

2003-08-05 Thread David A. Horita
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: 336 716

[PyMOL] Nuvision stereo glasses?

2003-07-17 Thread David A. Horita
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 Fax: 336 716

[PyMOL] pkfrag

2003-05-08 Thread David A. Horita
. 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: 336 716-7671 email: dhor