This is probably a fairly basic question, but I'm stumped. I want to visualize electron densities along with my PDB file. So, say I'm interested in 2DJX. I go to the PDB and download 2DJX.pdb and 2djx-sf.cif. PyMOL doesn't seem to read the CIF file (?), so I downloaded and installed the PDB's tool sf-convert (http://sw-tools.pdb.org/apps/SF-CONVERT/index.html). I tried

sf-convert -i CIF -o Xplor -sf 2djx-sf.cif

but got some errors about the input format.

sf-convert -i mmCIF -o Xplor -sf 2djx-sf.cif

seemed to work (it produced a .Xplor file with what looks like data to me). However, PyMOL gives me errors when I try to load the resulting .xplor file.

This may not be directly related to PyMOL, but I'm hoping it's a common enough task that someone can point me in the right direction.



Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909
Rockville, MD 20852