Miguel wrote:
...
set solvent on;
dots on;
# should generate a Connolly surface of the protein part as if alone
Q: Do you mean 'alone' as if the other atoms were not in the file?
Yes
If so, then that is not compatible with RasMol/Chime behavior.
but of much more use
Q: Is that what you want?yes, I want to be able to visualize binding pockets (where solvent and/or a ligand is in contact with the protein under experimental conditions)
Q: What do other people think?
restrict within(4.2, ligand );
# cut the surface to show only the binding pocket
select [HEM];
wireframe 80;
select [O2];
cpk;
# some nice rendering of the ligand
select protein;
cartoon
# some rendering of the protein part
should generate a nice surface of the HEM and O2 binding pocket of the
protein.
I did not understand this part ...
this is the less important part, just to complete the example Regards, Jan
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