m: Paulo Martel
To: EPF (Esben Peter Friis)
Sent: 14-09-03 20:28
Subject: Re: [PyMOL] Electrostatic potential maps in PyMOL
Dear Esben,
no matter how hard I try, I cannot make pymol read a phi map converted
from avs with your utility. The .fld file was generated with the
potential program in
Dear Esben,
Gromacs can create pqr files, but does it in a very bad way - the radii
information comes from a very limited set of atoms, and not directly from
the forcefield parameters. A colleague of mine, Antonio Baptista, has
written an awk script that can generate a proper pqr file from a gro
Original Message-
From: Andreas Förster
To: EPF (Esben Peter Friis)
Cc: 'pymol-users@lists.sourceforge.net'
Sent: 10-07-03 21:25
Subject: Re: [PyMOL] Electrostatic potential maps in PyMOL
Hi Esben,
I tried to follow your instructions to create and display an
electrostatic surface potenti
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
: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-
ad...@lists.sourceforge.net] On Behalf Of Warren L. DeLano
Sent: Wednesday, July 09, 2003 2:20 PM
To: 'EPF (Esben Peter Friis)'; 'Kaushik Raha '; 'Yu Chen '
Cc: pymol-users@lists.sourceforge.net
Subject: RE: [PyMOL] Ele
e (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 Warren L. DeLano
> > Sent: Wednesday, July 09, 2003 2:20 PM
> > To: 'EPF
Peter Friis)'; 'Kaushik Raha '; 'Yu Chen '
> Cc: pymol-users@lists.sourceforge.net
> Subject: RE: [PyMOL] Electrostatic potential maps in PyMOL
>
> Yes, you have identified the problem: PyMOL 0.90 currently only reads
> PHI files in one of the two endian formats
Yes, you have identified the problem: PyMOL 0.90 currently only reads
PHI files in one of the two endian formats (not sure if it is big or
little).
The problem is, how it PyMOL to determine which format the incoming map
is in? The file format is so darn implicit, I haven't yet come up with
any
Chen
Cc: pymol-users@lists.sourceforge.net
Sent: 09-07-03 22:42
Subject: Re: [PyMOL] Electrostatic potential maps in PyMOL
Yu Chen, I have attached the output from the load command (which loads
the phimap). I don't see the error that you describe. Does this output
mean that it is working fi
Yu Chen, I have attached the output from the load command (which loads
the phimap). I don't see the error that you describe. Does this output
mean that it is working fine? I can generate a surface and color it
with the electrostatic potential too. But I am not sure if I can trust
the result
Hello, Kaushik
Yeah, we do had problems with DelPhi to PyMoL. I don't know what your
mean by "modified version of Delphi..." We bought the latest Delphi from
their website, and used the data from all the example folders comes with
Delphi. The calculation all went well. When we tried to read the ph
There has been some talk on the list regarding failure of PyMOL in
reading Delphi generated potential maps that I missed. I have generated
phimap using a modified version of Delphi in the GRASP format that
PyMOL reads and displays without any problem. So I am not sure what the
problem is. C
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