Okay, I think I'm getting real close to having this working
(Mac G4 AlBook, OSX 10.3.5, Apple X11, X11PyMOL 0.97)
Here's my simple-minded approach so far, to get electrostatics in PyMOL
instead of the Honig Lab's online GRASS setup (which is also good).
1) maloc and apbs have been successfully compiled from source and
installed in /usr/local
2) M. Lerner's APBS Tools plugin 'About' tab says to load a structure;
the 'Visualization' tab says to load a "molecule and a map" So, I just
loaded a pdb file like I usually do, and displayed as cartoon
3) set the correct location of the apbs binary (/usr/local/bin/apbs),
clicked 'Set grid', then clicked 'run APBS'
4) those pink anchor handles in pymol started flashing around my
protein cartoon, then a pause, then the cartoon disappeared and the
pink anchors flashed around some more, then all went black. Nothing
happens when I click 'Update' under the Visualization tab.
5) PyMOL output:
________________________________________________________________________
_
coarsedim is [155.64339675903321, 159.7681230545044, 272.30599403381348]
finedim is [111.55493927001953, 113.98124885559082, 180.17999649047852]
center is [128.19829940795898, 61.232932090759277, 21.427999496459961]
finegridpoints is [225, 257, 385]
radiobutton said to generate it Use PyMOL generated PQR and PyMOL
generated Hydrogens and termini so i am returning pymol-generated.pqr
radiobutton said to generate it Use PyMOL generated PQR and PyMOL
generated Hydrogens and termini so i am returning pymol-generated.pqr
WARNING: 48 atoms did not have formal charges assigned
WARNING: 96 atoms did not have properties assigned
ObjectMapLoadDXFile-Error: Unable to open file!
________________________________________________________________________
_
supposing the WARNINGs are harmless, I'm not sure what to try next.
Maybe I need the electron density map after all?
--Michael
