[PyMOL] RE: Surfacing Heme's (ie. HETATMS)

[DeLano, W. <wa...@su...>]

Hi Michel,

   PyMOL doesn't surface HETATM's by default.  A HEME is labeled a =
hetero-group in the PDB and is ignored by the surfacing routine (the =
ignore flag is set for those atoms).  To fix that, you need to clear the =
ignore flag for the HEM atoms:

flag ignore, hem/, clear
rebuild

Alternatively, if you didn't mind surfacing the waters as well, you =
could simply "set surface_mode=3D1" which tells it to surface atoms =
irrespective of the ignore flag.

Cheers,
Warren

--
mailto:wa...@su...
Warren L. DeLano, Ph.D.
Informatics Manager
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
S. San Francisco, CA 94080
(650)-266-3606  FAX:(650)-266-3501


-----Original Message-----
From: Michel Guertin=20

Dear Dr DeLano: A colleague showed me the possibilities of PyMol and I =
have been really impressed. However, before purchasing a license I have =
a question. I'm working on bacterial hemoglobins that displayed a tunnel =
connecting the surface of the protein to the heme distal site. With this =
colleague we asked PyMol to show the surface of myoglobin (test). I was =
surprised to find out that it showed the heme completely exposed to =
solvent: this is wrong. We looked at the manual, but found nothing about =
how PyMol build surfaces and if its possible to modify parameters.