Dear Pymol users,
I'm trying to run APBS v0.3.2 with pymol 0.98beta27, by first clicking
the Set grid button, then clicking run APBS, but I get the error message
shown below.
coarsedim is [119.03399429321288, 109.91349792480469, 143.63640098571776]
finedim is [90.019996643066406, 84.654998779296875, 104.49200057983398]
center is [105.73299789428711, 140.44650268554688, -1.4549999237060547]
finegridpoints is [193, 193, 225]
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: 53 atoms did not have properties assigned
ObjectMapLoadDXFile-Error: Unable to open file!
Another problem I've come across when trying to load phi maps exported
from Grasp is described below:
1) Load a pdb x
2) Load Grasp phi map for x
3) Run APBS tools, visualize, set phi map x to correlate with molecule
x, set values for say -16kt/e, 0, 16 kt/e, and show the surface, this
looks as it should.
4) Now load pdb y which is in the vicinity of x
5) Load Grasp phi map for y.
6) Run APBS tools, visualize, set phi map y to correlate with molecule
y, set values for say -16kt/e, 0, 16 kt/e, and show the surface, this
looks as it should for pdb y but the remaining isosurface from phi map y
gets mapped onto pdb x and the x surface no longer looks like it should.
..so is there anyway to load two phi maps and map them to the surfaces
of their correlating molecules without exceeeding their respective
surface boundaries?
Thanks,
Sabuj Pattanayek
