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Use Swiss PDB Viewer (or O) to generate
crystal symmetry mates of the protein of interest that pack against it in the crystal and output the symmetry mates you are
interested in into a new pdb file. Then run the surface area calculations on
the complex and the separate proteins. Oleg Tsodikov From:
[EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Hi all: Recently, a question was asked on the BB about calculating solvent
accessibilities (SA) in CCP4. Similarly, I am interested in retrieving SA
values for protein atoms in a pdb file, however I want to take into
consideration the crystal packing environment (in other words, how the
symmetry-related molecules effect the solvent probe accessibility to the
"origin" molecule). I've got absolute SA values from NACCESS but
can't figure out how to address the packing issue with this or with SURFACE
and/or CONTACT in CCP4. Is there a way to do this in CCP4/CCP4i or is this a
ccp4mg capability? Other programs available that can address this? Thanks in advance for any suggestions and have a happy Thanksgiving
everyone! Brad Bennett -- |
