Hi Jason, If you already created a .map from CCP4 and changed the extension to .ccp4. Then, to create a map in PyMol for your protein only is the following.
create chainA, (chain A & pdb name) #I think you can leave out the pdb name isomesh mesh1, your map, 1.0, (chainA), carve=1.5 If the chain contains other atoms beside the protein atoms. create chainA, (chain A & resi #-#) isomesh mesh1, your map, 1.0, (chainA), carve=1.5 Sincerely, Carlos >>> Jason Porta <jpo...@unmc.edu> 05/09/09 3:19 PM >>> Hi everybody, Sorry if this message was already asked (I could not find it in the archives). I am making a figure of a recently solved protein structure including the electron density. I would like the electron density to cover only the protein, and not the surrounding space where the symmetry-related atoms are. I remember this being a simple task with Xfit, but I cannot find a copy for Intel-based Macs. I have tried doing this using Coot and PyMol, but have had no luck as of yet. I have also tried using Mapmask in CCP4, which also did not work. Any suggestions would be greatly appreciated. Jason Porta Graduate Student Dept. Biochemistry & Molecular Biology University of Nebraska Medical Center Omaha, NE 68198
