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
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