Hi all, I am trying to get a model-density figure made where selected residues are shown with their densities whereas the nearby unmodeled densities are removed. I tried the "isomesh mesh" command as suggested by the tutorial:
1. Loading PDB file File -> Open -> 1w2i.pdb 2. Load the map file File -> Open -> 2fofc.map.xplor It takes a while to load the map file. 3. Zoom in the active site PyMOL> select active, (resi 14-20,38) and chain A PyMOL> zoom active PyMOL> hide all PyMOL> show stick, active 4. Locate and Display the active site water We know that the amide group of Asn38 is h-bond to an active water. PyMOL> select active_water, ( (resi 38 and name ND2 and chain A) around 3.5) and (resn HOH) The above command select any water molecules that is/are around 3.5A of the ND2 atom of resi 38 in chain A PyMOL> show spheres, active_water Well the Oxygen atom is now shown in its vdw radius. We can reduce the size of the sphere to 0.5A by: PyMOL> alter active_water, vdw=0.5 PyMOL> rebuild 5. Display the electron density around the active site atoms at sigma level=1.0 PyMOL> isomesh mesh1, 2fofc.map, 1.0, (resi 14-20,38 and chain A), carve=1.6 Because the residue atoms were previously defined as "active", you can simply type: PyMOL> isomesh mesh1, 2fofc.map, 1.0, active, carve=1.6 On doing this, I get an error message that reads" map or brick object<name of my file> not found". I can however open the entire density which tells me i have the file loaded correctly. My map file is a .ccp4 file. I do put in .map suffix when typing in the command. Any help will be welcome. Thanks in advance Rakesh
