Dear Pymollers,
I am having a very strange set of results with carving an electron
density map around a protein or ligand in Pymol. First, let me say
that I have done this before (and can still do this) with a different
protein and map and it worked fine!
Generally I do the following:
load protein.pdb, main
load fofc.xplor
select ligand, B/1001/
show sticks, ligand
isomesh msh1, fofc, 2.0, ligand, carve=2.0
color cyan, msh1
In the past I did this just fine, and I can still get the old map to
carve around virtually any PDB file if I set the radius wide enough, so
the PDB file is NOT the source of the problem, nor is Pymol (I am using
MacPymol). So in the latest set of structures I am working on have
density maps generated in .ccp4 format (from ccp4) or .xplor format
(ported through Mapman and exported in .xplor format). The results are
as follows:
The maps load just fine if I use only the following part of the isomesh
command:
isomesh msh1, fofc, 2.0
The density shows up to whatever sigma I set and the size of the map is
whatever came out of ccp4. The problem comes with the carve command.
If I add any carve command ALL of the density disappears. It doesn't
make any difference what carve radius you use or sigma value for the
map. It also doesn't make any difference if you use ccp4 or xplor
format map files.
Yet the real kicker is that I have the old .xplor maps that still work
fine and can be carved to any part of a coordinate file that I want. I
have opened the old and new maps and compared them side-by-side and
they look superficially identical in format (same type of header info
and 7 columns of numeric data). When they load into Pymol they both
yield the same type of info through the text window:
The one that works says:
PyMOL>load omit.xplor
Crystal: Unit Cell 50.687 53.878 56.234
Crystal: Alpha Beta Gamma 89.489 63.605 62.610
Crystal: RealToFrac Matrix
Crystal: 0.0197 -0.0102 -0.0127
Crystal: 0.0000 0.0209 0.0053
Crystal: 0.0000 0.0000 0.0205
Crystal: FracToReal Matrix
Crystal: 50.6870 24.7863 24.9992
Crystal: 0.0000 47.8380 -12.3880
Crystal: 0.0000 0.0000 48.8246
Crystal: Unit Cell Volume 118388.
Executive: object "omit" created.
the one that does not work says:
PyMOL>load fofc.xplor
Crystal: Unit Cell 55.288 72.164 129.571
Crystal: Alpha Beta Gamma 90.000 90.000 90.000
Crystal: RealToFrac Matrix
Crystal: 0.0181 -0.0000 -0.0000
Crystal: 0.0000 0.0139 -0.0000
Crystal: 0.0000 0.0000 0.0077
Crystal: FracToReal Matrix
Crystal: 55.2880 0.0000 0.0000
Crystal: 0.0000 72.1640 0.0000
Crystal: 0.0000 0.0000 129.5710
Crystal: Unit Cell Volume 516963.
Executive: object "fofc" created.
It doesn't make any difference if it is a fo-fc, 2fo-fc, or any other
variation on a map type. The new maps don't seem to carve (or they
carve too much because ALL the density disappears!!).
Any help will be greatly appreciated!!
Thanks,
Kelley
Dr. Kelley Moremen
Professor
Complex Carbohydrate Research Center (Room 3055)
and Department of Biochemistry and Molecular Biology
315 Riverbend Road
University of Georgia, Athens, GA 30602-7229
Office (706) 542-1705 Fax: (706) 542-1759
Email: more...@uga.edu
(send email with large attachments to: more...@ccrc.uga.edu)
Website: http://bmbiris.bmb.uga.edu/moremen/lab/
