RE: [PyMOL] Coloring gradient
Thanks to all for the help so far. I'm getting there, but am currently
pondering
about the definition of the palette_dict. I wanted to add a color gradient
such
as grey_yellow, as the green_yellow didn't work as well as I was hoping for.
I'm not entirely sure what the color codes refer to.
i.e.
'yellow_blue' : ('c',3, 0, 83),
'blue_yellow' : ('c',3, 83, 0),
What do the parameters 'c', 3, 0 and 83 refer to, respectively? And is there
a
quick way to find the correct numbers matching a certain color for a
customized
gradient? Thanks for any further help.
Peter
--
Dr Peter Teriete
Laboratory of Molecular Biophysics
Department of Biochemistry
University of Oxford
South Parks Rd.
Oxford
OX1 3QU
Tel: +44 1865 275742
Fax: +44 1865 275182
count is the operator you're looking for:
spectrum count, green_yellow, selection=50-100/
Cheers,
Warren
--
mailto:war...@delsci.com
Warren L. DeLano, Ph.D.
Principal Scientist, DeLano Scientific LLC,
400 Oyster Point Blvd., Suite 213,
South San Francisco, CA 94080
Biz:(650)-872-0942 Tech:(650)-872-0834
Fax:(650)-872-0273 Cell:(650)-346-1154
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
Charles Moad
Sent: Tuesday, November 02, 2004 11:26 AM
To: Peter Teriete; pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Coloring gradient
I think I can help you except for one part. In short you
want the 'spectrum' command. For example, you can color a
chain R, based on the b-factor with the command:
spectrum b, green_yellow, chain R
The problem is that you must color based on a numeric value
that each atom has associated. So let's say you want to
color a helix from residue index 300-400. I tried:
spectrum resi, green_yellow, resi 300-400 spectrum
resi_number, green_yellow, resi 300-400
...and several other variations without success. Somebody
out there might no the answer to this problem.
-Charlie
Peter Teriete wrote:
Dear All,
I'm trying to color a protein cartoon structure from N- to
C-terminal
with a green to yellow gradient. Had a browse around and couldn't
quite find the correct command. Any pointers are welcomed.
Peter
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[PyMOL] Re: ribbon view of c-alpha only coordinates
Cathy, Set the ribbon_trace param to 1 to get a connected C-alpha trace, as in: load sample_CAs.pdb set ribbon_trace, 1 show ribbons Cameron === pymol-users-requ...@lists.sourceforge.net wrote (on 11/01/2004 09:05 PM): === Subject: [PyMOL] ribbon view of c-alpha only coordinates From: Cathy Lawson cathy.law...@rutgers.edu Date: Mon, 01 Nov 2004 12:05:51 -0500 To: pymol-users@lists.sourceforge.net Dear Fellow Pymolers, Some PDB files (notably models fitted into EM density) contain only C-alpha coordinates. When read into Pymol, Ive found that the coordinates appear as a constellation of individual atoms, and selecting a ribbon view doesn't connect them with lines. Anyone know a workaround to view C-alpha atom coordinates in Pymol as C-alpha traces? thanks, Cathy Lawson *** Catherine L. Lawson Laboratory for Structural Biology and Bioinformatics Department of Chemistry and Chemical Biology Rutgers University 610 Taylor Road, Piscataway, NJ 08854 cathy.law...@rutgers.edu tel 732 445 8074 fax 732 445 5312 http://rutchem.rutgers.edu/~lawson http://roma.rutgers.edu/~lsbb * -- Cameron Mura UCSD
Re: [PyMOL] stereo projection with PyMOL
On Mon, Nov 01, 2004 at 09:45:04PM +0100, EPF (Esben Peter Friis) wrote: We have great succes with PyMOL stereo on a two-projector system: - A Linux box with a Nvidia Quadro card provides the graphics (around $2000) - Two standard DLP projectors ($1500 each) - 2 Circular polarized filters ($300 total) - 30 Plastic circular polarized glassed ($375) - Projector stand and filter holder (about $700) - Non depolarizing screen ($2000) (prices just from memory :-) So you can be running for less than $9000 (even less if you go for a cheaper screen and a linear polarized solution). I doubt that you can get a decent CRT projector for that kind of money :-) The equipment was bought from REASOM (http://www.reasonco.com) and ProjectorPoint (http://www.projectorpoint.com). This 3D projection system is a real showoff, both internally and for costumer/guest presentations! Thanks Esben for the synopsis. It's encouraging to know someone has this working with PyMOL. I saw a presentation earlier this fall from someone involved in the GeoWall project (http://www.geowall.org) and ever since then have been thinking over ways to approach putting a system like this together (both technical as well as what kind of funding to try to use). What kind of uses does your system see? Is it predominately used by researchers, or by classes, or a good mix between the two? -- D. Joe Anderson, Asst. Sci.2252 Molecular Biology Bldg. BBMB Research Computing Support www.bb.iastate.edu/computing bbsupp...@iastate.edu
Re: [PyMOL] exporting surfaces
On Wed, Oct 20, 2004 at 09:15:55AM -0600, C Want wrote: I wrote a cheap hack a while back to produce STL output for the Connolly surfaces in pymol to help send some models to a 3D printer. Please see these previous messages for a 'patch' and some pictures: http://sourceforge.net/mailarchive/message.php?msg_id=5856368 http://sourceforge.net/mailarchive/message.php?msg_id=5933822 We have some 3D printer users in our Biochemistry department that still use this hack to get their models out of pymol. Speaking of which, thanks again for that code, Chris. I finally got around to patching and compiling pymol, printing out a few files, and tracking down a Zcorp 3D printer on campus here. The nice people who run it worked with me to print out a few parts as they refer to them. I printed 4 different PDB files, one I use in my demos in class, and one each from three structural biology groups in the department. The structure I use in class is a complex made up of two chains. I was gratified to see that when printed as separate chains, the two parts can be physically docked against one another pretty well. I had hoped that would be the case, but it's an entirely different matter to hold the two pieces in one's hands and to actually try to get them to fit! The print outs have been well received so far (I've had them for little over a week now) and we'll see if it gets enough interest for us to make more such models. One thing I did run into was trying to find a way of viewing the generated .stl files. In my searching, I thought I might be able to use a combination of GTS (http://gts.sourceforge.net) and GeomView (http://packages.debian.org/geomview) to do this, but when I tried to take the stl files through the first stage of the conversion, I got an error about the input not being a valid stl file. I'm hoping to get my hands on an stl file from another source (AutoCAD, maybe?) and seeing if I can tease out what the problem is. -- D. Joe Anderson, Asst. Sci.2252 Molecular Biology Bldg. BBMB Research Computing Support www.bb.iastate.edu/computing bbsupp...@iastate.edu
