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,
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"
(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 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
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
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
Hi,
I think this is a known bug:
http://sourceforge.net/p/pymolapbsplugin/bugs/1/
There is a fix mentioned but it involves patching the source code for the
plugin, which worked for me but is somewhat involved. However it might help you
find a solution or lead someone else to suggest something
.
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 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. within APBS itself or
within the plugin. If it is APBS, which is throwing the error you may want to
try to grab an updated version or the source code
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 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 that. You can either install an
upgraded version of APBS or switch to Pymol 1.8,
-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
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
Hi Chen.
If you are up for it, pdb2pqr exist in the Pymol-script repo.
http://pymolwiki.org/index.php/Git
I have made a automatic compile script.
See here:
http://pymolwiki.org/index.php/User:Tlinnet/Linux_Install#Install_script
That should fix it for you.
Try to look it through, and just write
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
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)
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
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
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
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
Hugo,
If building PyMOL from source, then please get APBS in source or binary form
from the APBS sourceforge project: http://apbs.sourceforge.net
Cheers,
Warren
-Original Message-
From: Hugo G. de Teran [mailto:hugo.te...@usc.es]
Sent: Thursday, August 27, 2009 10:06 AM
Cc:
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
, 2Z6W, 3AL1,
3B3R, 3C78, 3CNJ, 3D1P, 8A3H
Cheers!
-Tom
-Original Message-
From: Gilles Truan [mailto:gilles.tr...@cgm.cnrs-gif.fr]
Sent: Mon 9/22/2008 6:14 AM
To: Nathan Baker
Cc: David Gohara; apbs-us...@lists.sourceforge.net list;
pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL
I think I found the problem with reading externally generated pqr files...
When pymol generates by itself the pqr file, it puts it in the working
directory, hence the pymol-generated.in used for apbs and the pqr file
are in the same directory. In the pymol-generated.in the file name of
the
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 perfect!!),
and some of the problems were related to that.
When I tried running everything from the command line (ie pdb2pqr and
apbs) I did get the
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
I installed APBS 0.4.0 and my pymol version is the latest build for
windows, ie 1.1 r0, the apbs plugin is the latest also I believe.
The b factor error is only visible when calculating the grid. I already
use the b factor change (alter 1cjc, b=0), and the workaround works
perfectly when the
Hi Warren --
Strictly speaking, the issue may be with PDB2PQR itself, not APBS.
Furthermore, we don't yet know whether a combined development
version of all
three packages would still reproduce the problem.
This might be a good reason to start moving towards distribution of
APBS and
...@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
Nathan,
Strictly speaking, the issue may be with PDB2PQR itself, not APBS.
Furthermore, we don't yet know whether a combined development version of all
three packages would still reproduce the problem.
As an aside, a good reason for PyMOL to see PQR files is for diagnostic
visualization: to
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
Janet,
This is really a question for the electrostatics experts, but it sounds
reasonable to expect that a protein with a larger net charge would have more
regions showing a strong negative potential. Given the large difference in
net charge, a simple visual juxtaposition of potentials may not
It looks like quite a few people are actually still using the
electrostatics wizard, so I updated the code on my website
(http://www.umich.edu/~mlerner/PyMOL). For what it's worth, I just use
the visualization pane of the APBS plugin these days, but I understand
if the wizard is a little cleaner
Gianluigi,
The API changed in PyMOL 1.0 in order to accomodate multiple PyMOL instances
in a single Python interpreter -- your wizard needs to be updated so that
the init method takes a _self keyword argument:
def __init__(, _self=cmd):
...
--
DeLano Scientific LLC
Subscriber Support
-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
Hi,
Can you try installing the most recent version of my plugin from
http://www-personal.umich.edu/~mlerner/Pymol/index.html (you can use
the normal Install Plugin menu option .. there's no need to do things
by hand anymore)? It fixes some problems and gives better error
messages on others.
Caltabiano
Lab of Computational Medicine,
BioStatistic Dept.
UAB, Universitat Autonoma de Barcelona
Spain
- Messaggio originale -
Da: Mike Summers summ...@hhmi.umbc.edu
A: Gianluigi Caltabiano chimic...@yahoo.it
Inviato: Martedì 27 marzo 2007, 20:14:37
Oggetto: Re: [PyMOL] APBS
, Universitat Autonoma de Barcelona
Spain
- Messaggio originale -
Da: Mike Summers summ...@hhmi.umbc.edu
A: Gianluigi Caltabiano chimic...@yahoo.it
Inviato: Martedì 27 marzo 2007, 20:14:37
Oggetto: Re: [PyMOL] APBS surface
You need to create individual proteins and then create maps
: Michael Lerner mgler...@gmail.com
A: Gianluigi Caltabiano chimic...@yahoo.it
Cc: pymol-users@lists.sourceforge.net
Inviato: Lunedì 2 aprile 2007, 15:40:24
Oggetto: Re: [PyMOL] APBS surface
PyMOL doesn't know where the electrostatic potential map comes from.
If you load up a map and a structure
Hi Georgios --
I am a newcomer in this field and the use of APBS. I am trying to
produce
an electrostatic potential map for a protein surface and I am using
Windows XP. Although I have installed succesfully Pymol v0.99, APBS
v0.4.0
and the M.Lerner's plug-in,following Lerner's
Hi Anastassis,
I got the same error with a few pdb files.
The problem is the following. The B-factor in the pymol-generated pdb
file is somtimes set to values larger than 100 (119.63 in your case)
thus occupying all its columns of the lovely PDB-format and not leaving
any space to the
Hi,
parseInput
self.parseLines(file.readlines())
File /usr/local/apbs-0.4.0/tools/manip/psize.py, line 116, in
parseLines
self.q = self.q + float(words[3])
ValueError: invalid literal for float(): 1.00119.63
Any clues ?
It looks like it's reading from a pdb file when it's
Florian,
I had the same problem and I couldnt get everything to work internally
in pymol. I never got pymol to write the *.pqr files. I couldn't
figure it out. However, you can give your pdb to the PDB2PQR server:
http://agave.wustl.edu/pdb2pqr/server.html
Strip the waters/ligands and load in
Hi,
at this purpose, what kind of range (positive - negative) should be
used in order to visualize correctly the potential surface on a
protein? Normally I used -10 to +10 but I am wondering how you behaves
with this issue too.
Thanks in advance
andrea
2006/11/23, D. Eric Dollins
This is using the binary distributions of APBS?
Becker, Joseph W wrote:
I'm trying to install APBS on a LINUX (IBM T43P) box running SuSE 9.3
Professional. I've successfully installed maloc, but the apbs install
gives:
error: Failed dependencies
libreadline.so.4 is needed by
I have the same problem on a mac G5 dual processor with newly compiled pymol
0.98 and apbs 3.2, installed by fink. Also occurs with the standalone
mac/xll hybrid executable, calling apbs 3.2 using the plug in menu.
Interestingly, the programs work fine together on my mac G4 laptop, with
single
Hi,
I just checked the apbs download page and I couldn't find apbs binaries
available for windows. The only way I've seen (through previous mailing
lists posts) is to compile it using cygwin, but the performance is less
than optimal.
So if you or someone else has compiled apbs for windows, the
I have stumbled across the parameter causing the difference.
In all of the examples distributed with APBS, the pdie (solute dielectric)
value is set to 2.0 whereas ABPS-tools.py defaults this to 20.0. I find
that if I use 2.0 instead of 20.0 for pdie, the resulting electrostatic
potential map
Hi Jack,
In all of the examples distributed with APBS, the pdie (solute dielectric)
The pdie must be the protein dielectric constant though the comment for
pdie in the pymol generated .in-file reads # Solute dielectric ...
that is probably a mistake. The APBS-plugin says Protein Dielectric.
The
Richard,
Actually I don't have a copy of Delphi available (hence the use
of APBS). I did notice that I see more positive surface area on a
molecule with a -13 net charge when the run is done with pdie of 2.0
compared to 20.0 even in the presence of 0.150 mM NaCl ions. I also
noticed an oddity
Hi,
I've been meaning to update APBS tools so that some of the warnings are
larger and better explained.
WARNING: 53 atoms did not have properties assigned
means that PyMOL couldn't automatically assign properties for 53 atoms in
yoru molecule. This is usually because you have
Hi,
On Mon, 7 Feb 2005, Sabuj Pattanayek wrote:
Dear Mr. Lerner,
Thanks for letting me know about the PDB2PQR server. I was able to generate a
pqr from the NBCR website that then works with APBS to generate the dx map.
I'm not sure how to get the same electrostatic gradient effect on the
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