Vladimir,
Michael and I have been working on streamlining the process for
using ABPS with PyMOL and are almost at the point where PyMOL can generate
the necessary PQR file (for proteins at least) from an ordinary PDB file
lacking hydrogens, c-terminal carboxylates, etc. PyMOL can also now read
the ".dx" file output from APBS as a map file.
For example, using the latest Windows beta release (0.96beta13):
PyMOL>load $PYMOL_PATH/test/dat/il2.pdb
Executive: object "il2" created.
PyMOL>from chempy.champ import assign
PyMOL>remove hydro
PyMOL>assign.missing_c_termini()
PyMOL>assign.formal_charges()
PyMOL>h_add
PyMOL>assign.amber99()
PyMOL>stored.sum = 0
PyMOL>iterate all, stored.sum += formal_charge
Iterate: iterated over 2090 atoms.
PyMOL>print stored.sum
-1
PyMOL>stored.sum = 0
PyMOL>iterate all, stored.sum += partial_charge
Iterate: iterated over 2090 atoms.
PyMOL>print "%1.4f"%stored.sum
-1.0000
PyMOL>alter all, chain=''
Alter: modified 2090 atoms
PyMOL>save test.pqr
Save: wrote "test.pqr".
The resulting file "test.pqr" should be good to go for input into APBS.
Right now, Amber99 is the only forcefield that can be assigned inside of
PyMOL (inc. partial charges, bohr radii, atom types, and atom names) and
only for canonical protein residues.
After performing the calculation:
load apbs_map.dx
ramp_new e_pot, apbs_map, [-10,0,10]
show surface
set surface_color, e_pot, il2
etc.
Soon it should be possible to do all of the above using Michael's plug-in
without having to make any changes to PyMOL source code.
Cheers,
Warren
--
mailto:war...@delsci.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
> -----Original Message-----
> From: pymol-users-ad...@lists.sourceforge.net
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
> Vladimir Daric
> Sent: Tuesday, July 06, 2004 2:08 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] Showing electrostatics on surface ?
>
> I want to use PyMol to show electrostatics on surface.
>
> I tried to recompile PyMol with Michael Lerner's modified
> files ant to run his scripts but I couldn't make them work
> with actual version of Pymol.
>
> Is there a way to generate pkl files (like the one used in
> the Electrostatics demo) ?
>
> (I use APBS for electrostatic matrix calculation )
>
> Thanks.
>
> --
>
> Daric Vladimir
> Unité de Biochimie Structurale
>
> Institut Pasteur
> 25 rue du Dr. Roux, 75724 Paris, France
>
> Tel. +33 (0)1 40 61 35 46
> Fax. +33 (0)1 45 68 86 04
>
> http://www.pasteur.fr/recherche/unites/Bstruct
> -----------------------------------------------
>
>
