Also, keep in mind that pdb2pqr isn't python3 friendly so you will have to
use an externally generated pqr file. The current mechanism for calling
pdb2pqr from within the APBS Tool results in pdb2pqr running under the same
python as pymol.
Jack
On Mon, Dec 2, 2019 at 5:58 PM Jack Howarth
You need more patches in your installed Pmw 2.0.0. On MacPorts, we use...
https://github.com/macports/macports-ports/blob/master/python/py-pmw/files/patch-pmw2-py36.diff
and
https://github.com/macports/macports-ports/blob/master/python/py-pmw/files/patch-pmw2.diff
applied over Pmw_2_0_0.
Jack
Dear all,
I get the following errors when trying to launch the APBS plugin from the
plugins menu
Traceback (most recent call last):
File "/home/quyen/Pymol/install/lib64/python/pmg_tk/startup/apbs_tools.py",
line 322, in
command = lambda s=self: APBSTools2(s))
File "/home/quyen/Pymol/i
Dear Thomas,
thank you for these short and perfect answers.
1. All fine now.
2. Updated the plugin and the GUI bug is gone. One more thing though.
Whenever I click the button to either set temporary file locations or to set
program locations in APBS GUI window I immediately get a Segmenta
Hi Matic,
1. If you have conflicting (non-unique) file names, you have two options:
a) Specify an object name with the "load" command (load foo_1.dx, foo_1_map)
b) Set the "auto_rename_duplicate_objects" setting
2. The APBS GUI update bug has been fixed in the PyMOL SVN repository two days
a
Dear all,
I wish to report two issues (numbered 1. and 2.) with APBS plugin in Pymol. I
use Xubuntu 14.04 (Xubuntu is a flavour of Ubuntu) and opensource Pymol 1.8.0.0.
1. First I tried to perform a couple of APBS calculations through the APBS
plugin window and all went great. Then I did a
Hi Troels,
Many thanks for your email!
I found a work around for my problem this morning: I copied the pdb2pqr
directory from my Mac and now the plugin works. I guess for the Ubuntu
pymol package, the pdb2pqr is not installed by default?
>svn co svn://svn.code.sf.net/p/pymol/code/trunk/pymol
>sv
Hej Tobias.
Some time ago, a year+?, I played around fixing some small things in APBS,
to make it easier to work. (Most fixing small path things)
Orginal version:
http://pymolwiki.org/index.php/APBS
Small modified version:
http://pymolwiki.org/index.php/Apbsplugin
The modified version, is packe
Dear all,
I am trying to run the ABPS plugin with PyMOL Version 1.6.0.0 on Ubuntu
12.10. I have compiled pymol from source (
http://www.pymolwiki.org/index.php/Linux_Install).
When running the plugin, I can set the grid, but after clicking on Run
APBS, I get the following error:
Unexpected error
z)=(int(x*1000)/1000.0, int(y*1000)/1000.0,
int(z*1000)/1000.0)
Cheers,
Warren
_
From: pymol-users-boun...@lists.sourceforge.net
[mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Evan
Kantrowitz
Sent: Friday, September
_
From: pymol-users-boun...@lists.sourceforge.net
[mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Evan
Kantrowitz
Sent: Friday, September 21, 2007 7:28 AM
To: PyMOL-users@lists.sourceforge.net
Subject: [PyMOL] Pymol apbs problem
With a certain file 1za1 from pdb when I try to run
With a certain file 1za1 from pdb when I try to run apbs I get the
errors below. Other files are OK. Any suggestions?
error: 1
ValueError Exception in Tk callback
Function: at 0x182892b0> (type: )
Args: ()
Traceback (innermost last):
File "/Applications/MacPyMol/PyMOLX11Hybrid.app/pymo
Hi, I just want to use pymol+apbs and do some calculation on protein
(PDB 1cse ).
Unfortunately, I got the error msg in the following.
This PyMOL(TM) Incentive Product is Copyright (C) 2005 DeLano
Scientific LLC.
A current PyMOL Maintenance and/or Support Subscription may be requi
Has anyone noticed major differences between the results obtained in
GRASP when using the method...
1) Read| PDB file
2) Read|Radius Charge File(+Assign)
Input AMBER.crg
3) Build|Molecular Surface|All atoms
4) Calculate|New Potentail Map
5) Calculate|Pot. via Map at Surfaces/Atoms|All atoms
Douglas Kojetin asked the following question on February 9, 2005:
>For example, the molecular surface "numbers" default to
>-1, 0 and 1. If they are changed to -5, 0 and 5, the displayed surface
>looks "less charged" than that displayed with the default numbers.
>What do the numbers mean?
I'm no
I just download & compiled apbs on a G4 using the instructions found
here:
http://www.chemistry.ucsc.edu/~wgscott/xtal/programs.html
(although I had to modify the fink files slightly, it was a relatively
painless installation)
Many thanks for the apbs_tools plugin -- very cool! Is there any
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
On Thursday 15 July 2004 13:30, Daniel Rigden wrote:
> -- begin configuring for MALOC linkage
> checking for FETK_INCLUDE... yes
> checking for FETK_LIBRARY... yes
> checking maloc/maloc.h usability... yes
> checking maloc/maloc.h presence... yes
> checking for maloc/maloc.h...
-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 calculations. I've written a
| PyMOL plugin that allows you to run APBS and visualize the results very
| easily from within
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,
APBS (http://agave.wustl.edu/apbs/) is a package that allows you to
perform very fast, accurate electrostatics calculations. I've written a
PyMOL plugin that allows you to run APBS and visualize the results very
easily from within PyMOL (version 0.96 or higher).
The plugin lets you confi
Hi,
Those of you interested in APBS-based electrostatics in PyMOL via
Michael Lerner's plugins may be interested in an RPM available at
"http://mccammon.ucsd.edu/~cmura/PYMOL_examples/pymol-0.96apbs-2rh90.i386.rpm";.
It is basically a CVS snapshot of a recent version of PyMOL (v0.96beta5;
05/
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