Hello,
If possible, how does one color a PDB representation in PyMOL by the
B-factor field??
Thanks!
Cameron
--
--
Cameron Mura
Urey Hall, Rm. 4234
Department of Chemistry Biochemistry
University of California, San Diego
La Jolla, CA 92093-0365
--
--
Cameron Mura
Urey Hall, Rm. 4234
Department of Chemistry Biochemistry
University of California, San Diego
9500 Gilman Dr. Dept. 0365
La Jolla, CA 92093-0365
Email: cm...@mccammon.ucsd.edu
Phone: 858.534.0956
Fax: 858.534.7042
--
Hi Martin,
Visit Robert Campbell's repository of PyMOL scripts
(http://adelie.biochem.queensu.ca/~rlc/work/pymol/)...where you'll find
Python scripts to import into PyMOL for drawing unit cell edges
(draw_cell.py), symmetry axes (draw_symops.py), and lots of other stuff...
Cameron
Dear PyMOL and O list members,
I just got stereo working on my machine (PC, Red Hat 9, Radeon8500
(64MB) video card) after installing Xi Graphic's Summit v2.2 DX-Platinum
drivers to enable quad-buffered software stereo, but I noticed that 3D
stereo rendering in 'PyMOL' and 'O' seems a lot
For lots of image conversion/movie-making on your Windows PC --
including direct import of PNG sequences -- another piece of software to
consider is Logipole's Konvertor file convertor. I used this a while
ago when I was trying to go backwards from what most people are
describing here (i.e.,
hi, simple/stupid question -- is it possible to search the archives of
this mailing list??
If so, how does one go about it? I tried looking at
http://sourceforge.net/mailarchive/forum.php?forum=pymol-users, but
didn't see an obvious search mechanism...
Thanks,
Cameron
___
PyMOL-users mailing list
PyMOL-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/pymol-users
--
Cameron Mura
UCSD
@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/pymol-users
--
Cameron Mura
UCSD
___
PyMOL-users mailing list
PyMOL-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/pymol-users
--
Cameron Mura
UCSD
://ads.osdn.com/?ad_id=2562alloc_id=6184op=click
___
PyMOL-users mailing list
PyMOL-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/pymol-users
--
Cameron Mura
UCSD
---BeginMessage---
hi Michael,
quick question about your
python-numeric-devel-22.0-2mdk
libxml2-python-2.5.4-3.rh9
gnome-python2-1.99.14-5
python-numeric-22.0-2mdk
--
Cameron Mura
UCSD
an Oracle 10g class now,
and we'll give you the exam FREE.
http://ads.osdn.com/?ad_id=3149alloc_id=8166op=click
___ PyMOL-users mailing
list PyMOL-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/pymol-users
--
Cameron Mura
UCSD
is
analogous to the tube-style cartoons -- i.e., there are
'cartoon_saus_quality' and 'cartoon_saus_radius' settings.
Please let me know of any questions or problems with its usage.
Best regards,
Cam.
--
Cameron Mura
UCSD
Oops, sorry -- first link below should have been
http://mccammon.ucsd.edu/~cmura/PyMOL/; (no trailing ScriptsPatchesEtc/).
Cam.
=== Cameron Mura wrote (on 09/15/2004 07:50 PM): ===
Hi Warren others,
I've written a patch to the v0.97 source that enables sausage-style
cartoon representations
--
Cameron Mura
UCSD
*
--
Cameron Mura
UCSD
Hi,
Say, what do people think about the idea of creating a PyMOL Wiki to hold
nuggets of information like this? Or is there a better alternative to
Wiki now available?
I (still) think it's a great idea, and bet it would serve as an
indispensible resource to both novice and seasoned
Hi,
I should probably google about some more for an answer to this, but
maybe someone who's reading this already knows -- is a detailed
description of pymol's molecular editing functionality available
anywhere online (e.g., ctrl-right-click to select a bond and ctrl-d to
delete it, and so
Hi Hyun-Chul,
It's easy to use PyMOL to build protein fragments in standard geometries
(Build menu in the Tcl/Tk GUI window), but I'm not sure about DNA.
Three non-PyMOL methods that I'm aware of are:
(1) The program B (aka Biomer) from Dave Case's group at Scripps
Hi,
I'm wondering if any of you who've delved into the PyMOL source know
what the following line (and subsequent block of code) from the file
data/chempy/sidechains/generate1.py refers to:
for fyle in glob(source/*):
I assume it's something like a sidechain rotamer database, but isn't
Sarma,
I am trying to create a surface representation of a protein with
mutations that abolish activity in one color (say yellow) and the ones
that don't change activity in another (say green). The rest of the
residues colored gray.
I can change the color of the surface to gray or a rainbow
Hi,
Anyone out there have a spec file (or srpm) for building a pymol v0.98
RPM on CentOS-4 or Fedora Core 3?
I succeeded in building a monolithic pymol RPM (~11MB) on CentOS by
basically wrapping the standalone
pymol-0_98rc3-bin-linux-x86-glibc23.tgz, but this resulted in an
executable that
alexandra,
i was just able to load a molecule into pymol and set its tube radius to
XYZ by doing the following:
hide everything
cartoon tube, all
show cartoon, all
set cartoon_tube_radius, XYZ
another thing which you can try if you want variable (residue-specific)
tube thicknesses which are
hi,
i apologize for the somewhat off-topic post to both lists, but I figured
there may be many O and PyMOL users who use stereo with a monitor
connected through a KVM switch?
if so, please see the 2nd question in my email below...
thanks,
cameron
=== Cameron Mura wrote (on 07/15/2005 10
Projects Teams * Testing QA
Security * Process Improvement Measurement * http://www.sqe.com/bsce5sf
___
PyMOL-users mailing list
PyMOL-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/pymol-users
--
Cameron Mura
UCSD
492op=click
___
PyMOL-users mailing list
PyMOL-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/pymol-users
--
Cameron Mura
UCSD
Demetres Roger,
I've had the same problem w/ stereo on FC4 (tested only w/ an nVidia
Quadro 700 XGL card), and have been meaning to mail the list. The
problem occurs even after taking the typical steps to set-up the nVidia
drivers on the system (as described by Roger), and also occurs w/
Boost,
etc., I'm wondering if anyone else has seen anything like this...? or
has advice on how best to proceed? Any tips or suggestions would be most
greatly appreciated.
Thanks,
Cam
--
---
Cameron Mura
Assistant Professor
University
the code producing the
tracebacks. The important clues are somewhere in the middle.
Ralf
*From:* Cameron Mura cm...@virginia.edu
*To:* cctb...@phenix-online.org; Pymol-users
pymol-users@lists.sourceforge.net
*Sent:* Sunday
in space_group_info.group().all_ops():
With best regards,
Cam
--
---
Cameron Mura
Assistant Professor
University of Virginia
Department of Chemistry
McCormick Road, Box 400319
Charlottesville, VA 22904-4319
Email: cm...@virginia.edu
Web: http://muralab.org
Tel
30 matches
Mail list logo
