Hi everyone,
I have a simple problem that has come up before (4/2/2009 post), but I
haven't found a solution yet.
Maps written out from Coot and display in Pymol seem to be situated on
a different origin compared to the PDB coordinates. E.g., if I:
load my-structure.pdb
load my-map.map, map1, 1, ccp4
isomesh msh1,map1,1.0
A nice electron density map is rendered (no errors), but offset from
the my-structure.pdb coordinates (both map and coords were output from
Coot where they were overlaid correctly). It sometimes works to
explicitly indicate the residues around which to render the map:
isomesh msh1,map1,1.0,(chain a and resi 10),carve=3.0
In my current case however, an NCS-averaged map output from Coot is not
displaying at the desired location. To be clear, the map can be
displayed elsewhere in space, but it does not overlap with my
coordinates (these are not symmetry-generated molecules, they're part of
the ASU). As Robert Campbell indicated in response to the earlier post,
Pymol expects maps to be calculated to cover the whole molecule of
interest. My question is why does this map/model pair display correctly
in Coot while Pymol shows the map offset from the model? Is there a way
to tell Pymol to place the map at a different origin (i.e. so that it
overlays with the coordinates)?
I realize this may also be a Coot question, but I'm not sure of the
source of the problem yet so I'm posting here. I'll try the other bb if
necessary.
Thanks for your help,
-Andy Torelli
===========================================
Andrew T. Torelli Ph.D.
Postdoctoral Associate
Department of Chemistry & Chemical Biology
Baker Laboratory, Cornell University
Ithaca, NY 14853
===========================================
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