(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
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,
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
.
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
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
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
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
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
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
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
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
On Wed, 21 Dec 2005, William Scott wrote:
Dear Michael:
Thanks.
It works great. Sorry that I stupidly didn't think to check it.
No problem. I'm glad it works. Almost everything should be the same.
APBS has a new required parameter, sdens (Vacc sphere density) that I've
added to the
I'm not getting very far...
parsePBE: Warning -- parsed deprecated calcforce 0 statement.
parsePBE: Please use calcforce no instead.
PBEparm_check: SDENS not set!
NOsh: MG parameters not set correctly!
Error while parsing input file.
There's a new version on my website
(http://www.umich.edu/~mlerner/PyMOL/). Please feel free to try it out
and let me know if it works. I've tested it on a few systems that I work
with, and it seems fine. One person has reported some difficulties, but
these may not be related to my plugin.
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