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 <CCP4BB@JISCMAIL.AC.UK> (on behalf of Rakesh Joshi ><rjo...@purdue.edu>) >Subject: [ccp4bb] help with pymol error message >To: CCP4BB@JISCMAIL.AC.UK > >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
