I know people sometimes have good reasons, but people should be very careful about "carving" a map so close to the atoms - one could end up seriously misrepresenting the quality of the map.
=====================================
Phoebe A. Rice
Dept. of Biochemistry & Molecular Biology
The University of Chicago
phone 773 834 1723
http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123
http://www.rsc.org/shop/books/2008/9780854042722.asp
---- Original message ----
>Date: Tue, 19 Oct 2010 17:56:58 -0400
>From: CCP4 bulletin board <[log in to unmask]> (on behalf of Rakesh Joshi <[log in to unmask]>)
>Subject: [ccp4bb] help with pymol error message
>To: [log in to unmask]
>
>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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