Hi Michael,
if you haven't figured it out yet, this thread might help you:
https://sourceforge.net/p/pymol/mailman/pymol-users/thread/EAA6862A-4914-483F-A12F-92B5A1E81233%40schrodinger.com/
It can be done in the configuration file of the plugin.
Best regards!
Matic
On 1. 06. 22 05:26,
Dear all,
Can I save the "program locations" information in APBS plugin? Once I exit
the plugin and open it again, the previous input disappears.
I am using windows version pymol.
Thank you very much.
Michael
___
PyMOL-users
Hi Kamil,
The "Selection" field uses "polymer & ..." by default, which excludes
ions. You can use a selection which includes ions instead, for example
"all", "not solvent", or something like "(polymer | name CAL) & ...".
Here an example that works for me:
fetch 1rx1
alter elem Ca, resn="CAL"
Hi,
How to include Ca/Zn ions when using APBS built into Pymol? I'm switching
to CHARMM in command line options; CHARMM has CAL and ZN2 atoms already
defined in the DAT file. But there's still no difference in electrostatics
maps with and without ions in the structure. Also, the default
(if feasible, I am brainstorming!)
Thanks again for your help and for your help in advance,
Mario
-Original Message-
From: Thomas Holder
Sent: Monday, June 15, 2020 9:37 AM
To: Mario Garcia Urena
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] APBS plugin for Sugars
Hi
Hi Mario,
Incentive PyMOL 2.x includes regular APBS and PDB2QPR. You should be able to
manually edit the files there as well. For example with PyMOL 2.4.0 on Linux,
the AMBER force field data files can be found like this:
$ find . -name "AMBER.*"
Hi all,
I was trying to generate dipole moments with pymol using the APBS plugin. For
proteins I adapted a code and the dipole moments are correct and work just
fine, but for sugars it does not. I am well aware that the problem is that many
of the residues are not present in the AMBER force
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
Dear all,
I am trying to use APBS TOOLs 2.1 to calculate electrostatic potential of
proteins. After I finish "set grid", I press the "set grid" button, I get the
following error,
(, ImportError('No module named pdb2pqr',),
)
In show error 2
Could you tell what is the cause of the error and
Dear everyone,
I am trying to use the APBS plugin in pymol to calculate protein electrostatic
potentials. My system is centos 7. The pymol was installed with python 3.7
(~/software/build/anaconda3/bin/python). When I try to lauch the APBS Tool 2.1
from the plugin menu of pymol, a window jumps
Hello
I recently installed PyMOL version 1.5 no my MAC 10.9 using HomeBrew.
There were no problems with the installation at all however the APBS plugin
when loaded it gives me this error:
Error: 4
Exception in Tk callback
Function: at 0x106691758> (type: )
Args: ()
Traceback (innermost
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
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
Hi Albert,
I apologize that I take your email for a grumpy old man's rant, but I feel
this mailing list is getting washed out with poorly formulated questions.
What happened to specifying what OS you use, what version of PyMOL, what
version of the apbs plugin. Also, to give answers, it would
Hello:
I am trying to calculate the protein surface electstatic properities by
APBS plugin in pymol. But it always failed with messages:
Could not find/tmp/1.dx so searching for /tmp/1-PE0.dx
ObjectMapLoadDXFile-Error: Unable to open file!
ObjectMapLoadDXFile: Does '/tmp/1-PE0.dx' exist?
Does
thanks a lot for reply.
Problem solved after I specify the maloc library path explicitly in my
tcsh environment.
setenv FETK_LIBRARY /home/albert/install/apbs/apbs-1.4.0/lib
On 10/08/2015 05:02 PM, Andreas Forster wrote:
Hi Albert,
I apologize that I take your email for a grumpy old
Hi,
pdb2pqr.py doesn't exist in the pdb2pqr tar.gz file (for either 2.0.0 or
1.8 versions; in a previous question I was advised to use the 1.8
version) and consequently APBS tools doesn't work. I have tried turning
the pdb2pqr.py.in into pdb2pqr.py by removing the in extension, but
the APBS
Hello Brenton,
I used the pdd2pqr provided by Ubuntu repositories (version 1.8) and installed
it directly(with Synaptic) from there.
The path on my Xubuntu system is: /usr/share/pdb2pqr/pdb2pqr.py
I also tried setting something up on Windows but gave up eventually.
Good luck and all the best,
There is an INSTALL file that provides instructions. The first step,
calling ./configure , generates pdb2pqr.py from pdb2pqr.py.in
If you want to manually do it, it just changes the first line in the file
to point to your python installation. But, since there's a whole bunch of
other things
Dear Thomas,
thank you a lot for your quick reply.
Just to help the users that might find these posts in the future; the path in
my case was:
/usr/local/lib/python2.7/dist-packages/pmg_tk/startup/apbs_tools.py
and the plugin settings look like this:
...
# Global config variables
#
# To change
Dear Matic,
the only option to permanently store those paths is to edit the plugin file.
Look for apbs_tools.py in the PyMOL installation directory and there for
Global config variables.
Cheers,
Thomas
On 30 Jan 2015, at 00:33, Matic Kisovec matic.kiso...@ki.si wrote:
Dear Thomas,
Dear Thomas,
thank you for your quick reply.
I can confirm that now APBS tools2.1 plugin inside Pymol 1.7.4 works as
expected.
I do have one more issue. Every time I execute Pymol I get two lines saying:
Could not find default location for file: psize.py
Could not find default location for
Dear Pymol users,
I have recieved the same error as mentioned in the email ate bottom that was
sent by DE FALCO JR LOUIS in September 2014 to this list. There was one reply
that is a known bug and a link was provided. The bug was filed in March 2013.
The difference is this time this happened
Dear Matic,
this was fixed for 1.7.4: https://sourceforge.net/p/pymol/code/4099/
Please install the latest version.
Cheers,
Thomas
On 28 Jan 2015, at 10:04, Matic Kisovec matic.kiso...@ki.si wrote:
Dear Pymol users,
I have recieved the same error as mentioned in the email ate bottom
simpler that might
work.
Best wishes,
Jens
From: #DE FALCO JR LOUIS# [defa0...@e.ntu.edu.sg]
Sent: 01 September 2014 01:54
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] apbs error (Error in background function)
Hello,
I just updated
Hello,
I just updated PyMol Open Source to version 1.7.2.0-2 via the fink package
manager. Now, when I initiate the APBS Tools.1 plugin the following error
occurs:
Error in background function
Error: 1
class '_tkinter.TclError' Exception in Tk callback
Function: function lambda at
Dear PyMOL users,
I'm in trouble in using APBS plugin to display the molecular surface.
The calculations of set Grid and Run APBS were successfully finished,
but showing the surface by the button of show in the Visualization (1) tab
fails with the following message
ObjectMapLoadDXFile:
.
From: jp d yo...@yahoo.com
To: Thomas Holder thomas.hol...@schrodinger.com
Cc: Schubert, Carsten [JRDUS] cschu...@its.jnj.com;
pymol-users@lists.sourceforge.net pymol-users@lists.sourceforge.net
Sent: Wednesday, February 12, 2014 11:16 AM
Subject: Re: [PyMOL] apbs plugin
; pymol-users@lists.sourceforge.net
pymol-users@lists.sourceforge.net
Sent: Tuesday, February 11, 2014 12:14 PM
Subject: RE: [PyMOL] apbs plugin
Hi jpd,
try running APBS directly just using the .in file generated from a failed
run. That may provide a clue as to where the problem is, i.e
-users@lists.sourceforge.net
Sent: Wednesday, February 12, 2014 10:35 AM
Subject: Re: [PyMOL] apbs plugin
Hi jpd,
I can reproduce this, unfortunately. Thanks for reporting. It's indeed a
problem with the GUI toolkit and not apbs itself. We are looking into it.
Cheers,
Thomas
On 11 Feb 2014
hi,
anyone else having trouble with the apbs plugin?
i keep crashing as soon as i try to do anything.
if i select 'Choose externally generated PQR'
or 'run APBS' i get this
In show error 1
alloc: invalid block: 0x2c29fb78: 0 0
Abort
this is with pymol 1.7
ubuntu 12.04
using 1FAS fetched
to compile yourself.
HTH
Carsten
From: jp d [mailto:yo...@yahoo.com]
Sent: Tuesday, February 11, 2014 2:52 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] apbs plugin
hi,
anyone else having trouble with the apbs plugin?
i keep crashing as soon as i try to do anything.
if i select
From: Schubert, Carsten [JRDUS] cschu...@its.jnj.com
To: jp d yo...@yahoo.com; pymol-users@lists.sourceforge.net
pymol-users@lists.sourceforge.net
Sent: Tuesday, February 11, 2014 12:14 PM
Subject: RE: [PyMOL] apbs plugin
Hi jpd,
try running APBS directly just using the .in file
Hi all,
I was trying to use the APBS plug in with PyMOL version 1.7 and I'm getting
this error with pymol generated files not being found in the tmp directory:
Could not find
/var/folders/ZV/ZV5Pv67hjYmI8-m0PQU0ElL-r0o/-Tmp-/pymol-generated.dx so
searching for
, which has a working APBS
version.
HTH
Carsten
From: Seth Harris [mailto:set...@gmail.com]
Sent: Wednesday, January 22, 2014 4:16 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] APBS plug in (2.1) with PyMOL v1.7
Hi all,
I was trying to use the APBS plug in with PyMOL version 1.7
-users@lists.sourceforge.net
Subject: Re: [PyMOL] APBS plug in (2.1) with PyMOL v1.7
Hi Seth,
I had problems with the underlying APBS version (1.4 I believe) under Windows
in Pymol 1.7. It croaked with an memory allocation error, which I only found
after I ran the .in file manually in APBS. Try
Hi Seth,
ObjectMapLoadDXFile-Error: Unable to open file!
ObjectMapLoadDXFile: Does
'/var/folders/ZV/ZV5Pv67hjYmI8-m0PQU0ElL-r0o/-Tmp-/pymol-generated-PE0.dx'
exist?
It is true that neither of these files exist there, though
pymol-generated.pqr, .in and .pdb are there.
You didn't mention
Dear PyMOLers,
I can set the grid in the apbs_tools gui using the default file locations
(they are correct; I checked), but I get kernel dump when I try to run apbs.
A gui pops up with the message that MacPyMOL crashed although the PyMOL guis
are still open and functional. The pop-u gui gives
Thank you so much Troels,
This solves my problem. But based on this, it seems that APBS In pymol
failed to find PDB2PQR.
Chen
On Tue, Jun 18, 2013 at 1:40 AM, Troels Emtekær Linnet tlin...@gmail.comwrote:
Have a look on the earlier message on this.
Do you have linux or windows?
Do you have PDB2PQR on your system?
http://pymolwiki.org/index.php/Apbsplugin
http://www.poissonboltzmann.org/pdb2pqr
Troels Emtekær Linnet
2013/6/18 Chen Zhao chenzhaoh...@gmail.com
Thank you so much Troels,
This solves my problem. But based on this, it
if you have problems.
Troels Emtekær Linnet
2013/6/18 Chen Zhao chenzhaoh...@gmail.com
I am using Debian linux and I installed PDB2PQR with path specified in
pymol APBS GUI. However, it seems that there are some problems in python,
although I don't understand because I am not a programmer
Dear Pymol Users,
I have been trying to configure APBS-1.4 plugin of pymol 1.6 on a Debian
Wheezy machine. The initialization is successful, but when I hit set
grid, I got the error message below:
*error: 1
type 'exceptions.UnboundLocalError' Exception in Tk callback
Function: function lambda
Have a look on the earlier message on this.
http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg11148.html
Troels Emtekær Linnet
2013/6/18 Chen Zhao chenzhaoh...@gmail.com
Dear Pymol Users,
I have been trying to configure APBS-1.4 plugin of pymol 1.6 on a Debian
Wheezy
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
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
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
Hi Christian.
I had a similar problem on my windows machine, but with .
Try to set the temp path.
*reinitialize*
*fetch 4ins, async=0*
*
*
*import os*
*print os.environ['temp']*
*print os.getcwd()*
*os.environ['temp']=os.getcwd()*
and then run the apbs plugin.
My own problem on my windows
Hi Warren,
run pdb2pqr with the --whitespace argument to make sure the columns
are separated with whitespace.
If you still want to adjust the coordinates, you can use the
alter_state command in PyMOL.
alter_state 1, all, (x,y,z)=(x+100,y+100,z+100)
Hi,
I am having trouble running APBS on a structure, and it appears to be
because some of the coordinates are -100 or more negative. This leads to APBS
reading numbers from adjacent columns as concatenated strings because there is
no space between the columns.
This is
Dear users,
there's a particular case where I'm using the APBS plugin and the resultant
grid
leaves a portion of the protein out of it. This portion is show in full white
because no potential is calculated there.
Why isnt the grid centered as usual? Changing the values by hand and them
Can you send me the files (off list) so that I can take a look?
Thanks,
-Michael
On Thu, May 5, 2011 at 5:11 PM, Ricardo O. S. Soares
ross_...@yahoo.com.brwrote:
Dear users,
there's a particular case where I'm using the APBS plugin and the resultant
grid leaves a portion of the protein out
I am replying since your question did not get addressed in the past, but
know that I am not intimately familiar with PyMOL code or python. I do have
a thought, though, if using a grid approximation would work. I have done
some work with using MRC density map format in pymol, partly in
I posed this question some while back and thought I'd submit it again as my
question wasn't answered completely.
Is it possible to have APBS spit out a list of values for points on the
surface? I'd like to be able to quantitatively compare surface
electrostatics of volumetrically identical
Hi Matt,
PyMOL does not currently allow you to export the data mapped to the surface.
However, the dx format is very straightforward. It follows a subset of the
OpenDX standard, as described on the APBS site (
http://www.poissonboltzmann.org/file-formats/mesh-and-data-formats/opendx-scalar-data
Greetings,
I'm looking to use an electrostatic surface map for downstream calculations
and was wondering whether it's currently possible (after using APBSv2 to
calculate a surface potential map) to export a mesh of data points in a list
format with each data point's associated potential? If not,
Dear PyMOL users,
I want to compute electrostatic with APBS plugin, and I create PQR file in
http://pdb2pqr-1.wustl.edu/pdb2pqr/ .
When I run APBS in PyMOL, it displays the errors as followed:
Could not find pymol-generated.dx so searching for pymol-generated-PE0.dx
ObjectMapLoadDXFile-Error:
Hi,
I have noticed an 'odd' behavior when calculating electrostatic surface
potential representations between the APBS Tools (v1.2r3) and APBS Tools2
(v1.3) where the results are significantly different depending on which version
of Pymol I use (recently upgraded to 1.3 and noticed this when
Hi all,
I've been working with Jason Vertrees on a new version of the PyMOL-APBS
plugin and it's now ready for pre-release. There are three big advantages of
the new version:
* It's been tested modern OS X, Windows and Linux systems and fixes several
long-standing bugs.
* It allows you to call
On 28/01/10 21:31, Michael Lerner wrote:
Hi all,
I've been working with Jason Vertrees on a new version of the PyMOL-APBS
plugin and it's now ready for pre-release.
Hi,
that's really good news, that you are going to develop the plugin in a
more public accessible manner!
For all gentoo user
We solved the problem this afternoon. The version of APBS that comes with
PyMOL does not work on Tiger (10.4). Neither does the universal binary of
apbs-1.2.1b available on sourceforge.
An older version of apbs (0.5) worked. We are in the middle of installing
APBS via MacPorts, as it seems like
I download and install macpymol-1_2r2.tgz.
I make a copy of MacPyMOL.app and rename it PyMOLX11Hybrid.app and fire it up.
Load a pdb file after removing HETATM lines.
Open APBS Tools and set grid:
Log:
Maximum number of grid points exceeded. Old grid dimensions were
[129, 97, 129]
Fine grid
Can you go to the Program Locations tab and find out which version of APBS
you're using? There's a problem with the one in
/Applications/PyMOLX11Hybrid.app/pymol/freemol/bin.
I've added instructions for fixing this problem to
http://pymolwiki.org/index.php/User:Mglerner . The instructions are
FYI, that worked for me. I just copied the binary to /usr/local/lib.
-- Jason
--
Jason Vertrees, PhD
PyMOLWiki -- http://www.pymolwiki.org
On Mon, Nov 30, 2009 at 2:56 PM, Michael Lerner mgler...@gmail.com wrote:
Can you go to the Program Locations tab and find out which version of APBS
Hi,
I am trying to use APBS in pymol v1.2 (x86_64 linux compilation). I have
compiled with no problem APBS, but when I try to start a calculation I
get the following error:
File
/usr/local/lib64/python2.6/site-packages/pmg_tk/startup/apbs_tools.py,
line 998, in __init__
from freemol import
-us...@lists.sourceforge.net; pymol-users@lists.sourceforge.net
Subject: [PyMOL] APBS in pymol1.2
Hi,
I am trying to use APBS in pymol v1.2 (x86_64 linux compilation). I have
compiled with no problem APBS, but when I try to start a calculation I
get the following error:
File
/usr/local
Hi,
I just installed pymol-py25 and APBS via fink.
I can use APBS to generate some beautiful electrostatic potential maps but
when I exit APBS the pymol command line is frozen. I can move molecules
around in the Pymol viewer but I cannot save the images or files.
Can anyone suggest a fix for
I've installed apbs and used it from the command line. Now I'd like
to run it (more conveniently)
as a MacPyMOL plugin.
Anybody know how I can set this up?
Thanks!
- Paul
Paul Shannon schrieb:
I've installed apbs and used it from the command line. Now I'd like
to run it (more conveniently)
as a MacPyMOL plugin.
Anybody know how I can set this up?
Thanks!
- Paul
-
This SF.Net email is
generated independantly (PATH error
with spaces in path names). It is all sorted out now. I can use the
pdb2pqr web site to generate the pqr and apbs input files or directly
pymol APBS plugin with the b factor and alternate conformation blanked
out before use!!!
I finally looked at the apbs.py file
or
directly pymol APBS plugin with the b factor and alternate
conformation blanked out before use!!!
I finally looked at the apbs.py file to see where the pqr calculation
was and added a few commands after line 1491: here they are:
pymol.cmd.remove('%s and alt b' %sel)
pymol.cmd.alter ('%s' %sel,'b
in path names). It is all sorted out now. I can use the
pdb2pqr web site to generate the pqr and apbs input files or directly
pymol APBS plugin with the b factor and alternate conformation blanked
out before use!!!
I finally looked at the apbs.py file to see where the pqr calculation
Hello Gilles,
The ObjectMapLoadDXFile-Error you are still having may sound familiar to us.
Could you send us the following screenshots from your PyMOL APBS Tools?
1. A screenshot of the Main tab.
2. A screenshot of the APBS Location tab.
3. A screenshot of the Temporary File Locations tab
: David Gohara; apbs-us...@lists.sourceforge.net list;
pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] [Apbs-users] Strange behaviour with APBS
Dear all,
Sorry for the late answer but I finally managed to find what the error is...
First thing, I work on a Windows XP environment (nobody's
or optimization.
Anyway, based on reported symptoms alone, the problem appears to be that
some component in the PyMOL-APBS pipeline assumes that the input PDBs are
space-delimited rather than column-delimited. This guess is based on the
observation that a B-factor of 100 or greater eliminates
symptoms alone, the problem appears to be
that
some component in the PyMOL-APBS pipeline assumes that the input
PDBs are
space-delimited rather than column-delimited. This guess is based
on the
observation that a B-factor of 100 or greater eliminates the space
between
the occupany
...@lists.sourceforge.net] On Behalf Of Nathan Baker
Sent: Thursday, September 18, 2008 11:54 AM
To: DeLano Scientific
Cc: apbs-us...@lists.sourceforge.net; gilles.tr...@cgm.cnrs-gif.fr;
pymol-
us...@lists.sourceforge.net
Subject: Re: [PyMOL] [Apbs-users] Strange behaviour with APBS
Hi Warren
Hi,
I noticed the latest version of the PDB file format description was
posted today.
http://www.wwpdb.org/docs.html
Chris
On 17 Sep 2008, at 20:21, DeLano Scientific wrote:
The PyMOL and APBS programs have differing views as to whether PDB
PQR
files are column-based or
Hi Warren --
The PQR format (which doesn't really have a standard) is basically
just whitespace delimited. I'm curious, though -- why would a PyMOL
APBS invocation ever see the PDB file? Wouldn't a user first convert
it to PQR with PDB2PQR (ideally) or with PyMOL's built-in functionality
checking or optimization.
Anyway, based on reported symptoms alone, the problem appears to be that
some component in the PyMOL-APBS pipeline assumes that the input PDBs are
space-delimited rather than column-delimited. This guess is based on the
observation that a B-factor of 100 or greater
Hi All,
I am having some problems with surface display of the output from the
APBS plugin distributed with PyMOL (version 1.1r0) using the color by
potential on sol. acc. surf. option. Steps to reproduce the problem:
1. Load in a structure.
2. Perform the APBS calculation (execute Set
...@lists.sourceforge.net
[mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Douglas
Kojetin
Sent: Tuesday, July 22, 2008 9:33 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] distorted electrostatic surface color with PyMOL/APBS
Hi All,
I am having some problems with surface display
Dear all,
when trying to use the APBS plugin I experience the following problem
The first time I tried to run it it the error message was simply
ObjectMapLoadDXFile-Error: Unable to open file!
Now the second time it pops up an error log:
Error: 1
WindowsError Exception in Tk callback
I would like to use apbs from within PyMOL. I have downloaded and
installed the latest version of apbs, and apbs_tools.py exists in
$PYMOL_PATH/modules/pmg_tk/startup/. However, I find no plugins entry
in any of the PyMOL menus.
I think that you need to rename the application bundle to
Thanks to Michael and Warren for a quick and correct but somewhat
baffling solution. In OSX, one renames an application and it starts up
looking quite dissimilar from before. I'm still new to the Gospel
according to Steve, and I wouldn't mind enlightenment.
In any case, using MacPyMOL as
Dear all,
I have posted this message also to the APBS list but have not yet had
a response so if anyone here can help I'd be most grateful.
We are using APBS tools in Pymol to compare the electrostatic surfaces
of two related proteins. We are concerned about the correct way to
display these so
! -WLD
-Original Message-
From: pymol-users-boun...@lists.sourceforge.net
[mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf
Of Janet Deane
Sent: Friday, October 19, 2007 2:59 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] APBS - Net charge and contour level
, October 04, 2007 7:55 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] APBS-electrostatics
Hi everybody,
I am trying to use the electrostatic wizard to read some .dx file I made.
It always worked..since I up-graded to pymol 1.0.
Now it doesn't work ( I have already checked
Hi everybody,
I am trying to use the electrostatic wizard to read some .dx file I made.
It always worked..since I up-graded to pymol 1.0.
Now it doesn't work ( I have already checked the modification in
__init__.py file, it's fine).
The message it give to me is:
Traceback (most
-users-boun...@lists.sourceforge.net] On Behalf Of Gianluigi
Caltabiano
Sent: Thursday, October 04, 2007 7:55 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] APBS-electrostatics
Hi everybody,
I am trying to use the electrostatic wizard to read some .dx file I made.
It always worked..since I
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: function lambda at 0x182892b0 (type: type 'function')
Args: ()
Traceback (innermost last):
File
_
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
,
Warren
_
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
Hi,
I'm working on an update to the PyMOL-APBS plugin. Are there any
features that you would like to see included? As an example, I'm
including the ability to use PDB2PQR to generate PQR files in the next
version. Please request anything you'd like, no matter how
trivial/difficult you think
-boun...@lists.sourceforge.net]on Behalf Of Robert
Campbell
Sent: Wednesday, May 30, 2007 11:06 AM
To: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] APBS
Hi Vaheh,
* Oganesyan, Vaheh oganesy...@medimmune.com [2007-05-30 09:45] wrote:
I did not get much luck with those recommendations
==
Comments and solutions are appreciated.
VO
-Original Message-
From: Todd M. Link [mailto:toddml...@gmail.com]
Sent: Tue 5/29/2007 3:44 PM
To: Michael Lerner
Cc: Oganesyan, Vaheh; pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] APBS
I also
@lists.sourceforge.net
Subject: Re: [PyMOL] APBS
I also continually had this problem unless I got pqr coordinates
(with hydrogens)
below is the instructions I wrote for myself and group so that I
would be able to do it again next time (getting old and the memory
isn't what it used to be)
pqr corrdinates - Can
Hi Vaheh,
* Oganesyan, Vaheh oganesy...@medimmune.com [2007-05-30 09:45] wrote:
I did not get much luck with those recommendations either. I was doing
exactly the same. Something is phishy with my pymol and/or APBS installation.
I did check for different pdb files, so it is not pdb related.
I also continually had this problem unless I got pqr coordinates
(with hydrogens)
below is the instructions I wrote for myself and group so that I
would be able to do it again next time (getting old and the memory
isn't what it used to be)
pqr corrdinates - Can do it on the web at
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