I'm am a very new PYMOL user. I'm trying to calculate and display and
electrostatic map, similar to what I used to get in GRASP. My version
of PYMOL I downloaded (yesterday) has the APBS plugin already installed.
It's the subtleties of displaying the surface that has me confused.
I displayed my molecule. From the 'Plugin' drop down I selected 'APBS
tools'. In 'APBS Location' tab I entered the path for apbs_tools.py for
the APBS binary location (is that correct?). I left the APBS psize.py
location blank.
After 'set grid' and 'run APBS', I was told I needed to load a map, so I
loaded my CNS 2FomFc map. 'Run APBS' ran just fine, I went to the
'Visualization' tab.
At this point I'm confused. I've hit various 'update' buttons, the
'Molecular Surface' on show is completely white. I've toggled values on
the visualization tab, and nothing seems to happen (even after hitting
the 'update' buttons).
I'm hoping there is something basic I'm missing and would appreciate any
pointers.
Many thanks,
Marilyn
Marilyn D. Yoder
Division of Cell Biology and Biophysics
5007 Rockhill Rd.
University of Missouri-Kansas City
Kansas City, MO 64110-2499
phone: 816-235-1986
fax: 816-235-1503
