Hi Rakesh,
My guess is that PyMOL is getting confused by your map's name when
loaded into PyMOL as an object. When you call isomesh/isosurface the
2nd parameter is the name of the map object loaded into PyMOL, not the
filename you loaded from.
I made some slight modifications to that set of commands reflecting a
newer PyMOL build (1.3r1); you should be able to copy/paste this:
# 1. Fetch PDB file
fetch 1w2i, async=0
# 2. Fetch 2fofc map if on EDS server
fetch 1w2i, type=2fofc, async=0
# 3. Zoom in the active site
select active, (resi 14-20,38) and chain A
zoom active
hide all
show stick, active
# 4. Locate and Display the active site water
select active_water, ( (resi 38 and name ND2 and chain A) around 3.5)
and (resn HOH)
show spheres, active_water
alter active_water, vdw=0.5
rebuild
# 5. Display the electron density around the active site atoms at
sigma level=1.0
isomesh mesh1, 1w2i_2fofc, 1.0, active, carve=1.6
Cheers,
-- Jason
On Tue, Oct 19, 2010 at 5:56 PM, Rakesh Joshi <[log in to unmask]> wrote:
> 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
>
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) [log in to unmask]
(o) +1 (603) 374-7120
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