Hi Jacob
In Pymol, have you tried adding in a direct light source? e.g.
set direct, 0.5
It worked nicely in a similar situation for me
Daniel
On Wed, 2005-11-23 at 11:42 +0100, Jacob Poehlsgaard wrote:
> Hi folks
>
>
>
> I’m trying to visualize a section of the inner workings of the
> rib
Dear Pete
Thanks for the help. The one that didn't work was the standard 0.99,
not a beta version - pymol-0_99rc1-bin-win32.zip. As you suggested, the
earlier 0.98 - pymol-0_98rc5-bin-win32.zip *does* work so I'm up and
running. I guess others will know the ins and outs of the error.
Daniel
Dear all
I've used PyMol with the APBS plugin successfully with other structures
but now it's giving problems with a model structure (made with Rosetta
then SCWRL).
I set up the grid and then press run and the plug-in zips around the
structure making a pqr file. However, I get an error message s
Hi Pete
Thanks for the idea. In fact adding a chain ID doesn't make any
difference in this case.
Based on a mail from Kostas Tripsianes I successfully used the pdb2pqr
server to get a pqr file independently to feed to the plug-in. I got a
good looking pqr file but when I try to run apbs, after
Dear all
After following the suggestion to try apbs at the command line and some
googling, I found that the problem was that new-ish apbs 0.4 was
expecting a new keyword 'sdens' that my slightly old apbs plugin for
PyMol was not outputting.
http://sourceforge.net/mailarchive/forum.php?thread_id=9
Hi Clara
Try
set ribbon_trace_atoms, 1
or
set cartoon_trace_atoms, 1
Daniel
On Wed, 2007-02-28 at 10:10 +0100, Clara Marco wrote:
> Hi!
> I'm trying to build a morphing movie to show the transition between
> two conformational states of a protein. I've run morphing with
> program LSQMAN, wh
Dear all
First let me confess that my problem does not just involved pymol.
However, it is hampering my use of pymol amongst other things and there
must be many python experts who read this list.
My problem, on a completely fresh Ubuntu 8.04 install, is that python
can find modules when asked to
aniel
On Tue, 2008-07-22 at 16:54 +0200, Michael Banck wrote:
> On Tue, Jul 22, 2008 at 03:38:53PM +0100, Daniel Rigden wrote:
> > First let me confess that my problem does not just involved pymol.
> > However, it is hampering my use of pymol amongst other things and there
> > m
py
>
> Cheers,
> Warren
> --
> DeLano Scientific LLC
> Subscriber Support Services
> mailto:supp...@delsci.com
>
>
> -Original Message-
> From: pymol-users-boun...@lists.sourceforge.net
> [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of
rors, there is little chance of PyMOL
> building or running correctly.
>
> Cheers,
> Warren
>
> -Original Message-
> From: pymol-users-boun...@lists.sourceforge.net
> [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Daniel Rigden
> Sent: Tuesda
Dear all
I've just extracted a region of B sheet from a structure to produce a
session for teaching purposes. To my surprise, when I created an object
from the four distinct stretches making up the sheet, PyMOL redrew the
previously complete strands in a very incomplete way (attached). When I
co
heers,
> Warren
>
> --
> DeLano Scientific LLC
> Subscriber Support Services
> mailto:supp...@delsci.com
>
>
> -Original Message-
> From: Daniel Rigden [mailto:drig...@liverpool.ac.uk]
> Sent: Thursday, October 09, 2008 3:20 AM
> To: pymol-users@lists.source
Hi Alan
Thanks for the tip! Taking the tar route rather than the rpm one makes
installation trivial on Mandrake 9.1. I'm even more impressed to see
that PYMOL automatically detects both processors so rendering is just
phenomenally fast.
Cheers
Dan
On Tue, 2003-09-09 at 20:48, a...@lac.inpe.br
Hi Camille
The Espript server is the easiest way I know. Go here
http://prodes.toulouse.inra.fr/ESPript/cgi-bin/ESPript.cgi
choose Execute then Expert mode. SUpply an alignment and a
supplementary pdb file then execute. You get back an annotated
alignment + the pdb file with a conservation sc
Hi all
I've been trying to install apbs to use this new plugin, as I imagine a
lot of people will want to. I run into a problem in the compilation
which I wonder if anyone can help with. [I know this is not strictly a
Pymol question but given the general interest perhaps I can be excused.
There
Hi all
When I visualise sequences, all Glu residues (as well as all Asp
residues) are shown as D!
Has anyone else seen this?
Daniel
--
Dr Daniel John Rigden Tel:(+44) 151 795 4467
School of Biological Sciences FAX:(+44) 151 795 4414
Room 101, Biosciences Buildi
Hi
It looks to me as if there is a glitch in the sequence viewer for some
PDB files like 4PFK. The symptom is that waters get mixed up among the
protein sequences as in the snapshot here
http://pcwww.liv.ac.uk/~drigden/dross.png
If you write the structure out again you get things like this
ATO
This strategy seems to work for Mandrake 9.1 too, BTW.
Daniel
On Thu, 2004-07-15 at 11:26, Marc Saric wrote:
> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
>
> | Hi all,
> |
> | APBS (http://agave.wustl.edu/apbs/) is a package that allows you to
> | perform very fast, accurate electrostatics
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