I am creating a surface potential image (using the *.phi file)
following the instructions posted in this mailing list a while ago.
load rad52.pdb
load rad52.phi, e_pot
ramp_new e_lvl, e_pot
show surface, rad52
set surface_color, e_lvl, rad52
ramp_new e_lvl, e_pot, [-12,0,12], [ [1,0,0], [1,1,1],
Felix,
> I've read over the manual, and I think I understand the principle
behind a
> CGO. What I would like to do is generate a wall-&-floor type
background
> for an animation I'm putting together. I've followed the example
given by
> David Cooper
(http://ginsberg.med.virginia.edu/~dcoop/Help/
Hi Andreas
MEAD cannot create maps from a raw pdb-file. It requires a pqr-file, which
is a pdb file that has the Van der Waals radii in the B-factor column, and
the atom charges in the occupancy column.
Gromacs can assign partial charges and VdW-radii to a pdb-file and write out
a pqr-file.
I
As a novice to CGOs, I am turning to the Pymol power users out there to help
me get started.
I've read over the manual, and I think I understand the principle behind a
CGO. What I would like to do is generate a wall-&-floor type background
for an animation I'm putting together. I've followed
PyMOLers,
In response to user requests, I have added support for BRIX ("O" maps)
and FLD (AVS Field) map formats in the current development version.
Are there any other map formats which people would use heavily if PyMOL
were able to support them?
Thanks,
Warren
--
mailto:war...@delanoscien
Hi Esben,
I tried to follow your instructions to create and display an
electrostatic surface potential. I used 1UBQ.pdb as input. In Mead, I
encountered the following error when running
potential -epsin 2 -CoarseFieldOut 1UBQ 1UBQ
Starting potential for molecule named 1UBQ
with interior dielectri
Yu Chen, I think it is because of "endianess". My phi files were
generated by Delphi on an SGI in the GRASP format. My PyMOL 088 on
Linux does not seem to mind it. I think Warren has fixed the problem of
endianess and it should be fine in the next release.
Kaushik.
On Thursday, July 10, 2003,
Thanks everybody for suggestiones, and Warren for fixing the problem. I
will see if we could generate some phimap not 65x65x65.
Ksushik, I don't know why your Delphi is working fine, here is my output
from load phimap, which it should be cause of the endianess:
PHIMapToStr: now starting phimap
