Kaushik,
Good questions.
(1) PyMOL doesn't show the solvent accessible surface, rather it shows the
solvent/protein contact surface. The solvent accessible surface area is
usually defined as the surface traced out by the center of a water sphere,
having a radius of about 1.4 angstroms
Maybe this has already been discussed but I was wondering if the
surface that PyMOL generates is solvent accessible surface area (SASA)
? If so what is the solvent probe radius? The reason I ask is some
atoms seem to have exposed surfaces when rendered with PyMOL whereas my
SASA program has it
Of course!
Before you load a PDB file, run the command:
set connect_mode,1
You can put this in your ".pymolrc" file if you want this to be the default
behavior.
Note that with this approach, you'll need to supply ALL connectivity
information, even for standard residues. At some point in the
Hi,
Is there command to by pass the distance based bonding
and use only the CONECT information for bonding.
When I changed the line
SettingSet_i(I,cSetting_connect_mode, 0);
to
SettingSet_i(I,cSetting_connect_mode, 1);
in layer1/Setting.c and recompile it.
it seems to do that. But is there a com
Dear Nukri,
> When I do
> select cont,(/molA//s/401 around 4)
> it sure selects all atoms from molA that are within 4 A from residue 401
> but it also selects
> ALL other atoms from the current session (but not displayed) that are
> within 4 A.
> What needs improvement - the program or my command
