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=1" which tells it to surface atoms irrespective of the ignore flag. Cheers, Warren -- mailto:war...@sunesis.com 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 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.
