Mirek,
PyMOL isn't the optimal tool for measuring surface area -- perhaps
others on the list can suggest good alternatives.
The only kind of surface area PyMOL can measure well is solvent
accessible area, and it is a bit slow because all it does is sum up
partial areas associated with discrete dots on spheres (size = vdw +
solvent radius). The basic approach is:
# (1) make sure no atoms are ignored:
flag ignore, none
# (2) delete everything except what you want to measure (important!):
remove not polymer
# (3) adjust dot settings for solvent surface area measurement:
set dot_solvent, on
set dot_density, 4
# (4) visually preview what is being measured (optional):
show dots
# (5) computer the surface area value:
print cmd.get_area()
Cheers,
Warren
> -Original Message-
> From: Mirek Cygler [mailto:mi...@bri.nrc.ca]
> Sent: Monday, August 10, 2009 11:08 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] Measure surface area
>
> Hi,
> How can I get the measure in A2 of the surface area of the
surface I
> display with PyMol?
>
> Mirek
>
>
>
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