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,
michael
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 mailing
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"
alt
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 'prepared01
(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.*"
./lib/python3.7/site-packages/src/dat/AMBER.name
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 fie
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 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 h
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 o
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 last
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
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 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 hel
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 a
Hello all,
I'm running incentive pymol 1.7.4 on Windoze 7 64bit professional. The APBS
plugin fails with; below is the output.
Temp file locations are standard:
Temp PQR: C:\Users\mheller\AppData\Local\Temp\pymol-generated.pqr
Temp PDB: C:\Users\mheller\AppData\Local\Temp\pymol-generated.pdb
T
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 ./co
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,
M
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
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 the
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 wrote:
> Dear Thomas,
>
> thank you for you
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 file:
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 wrote:
> Dear Pymol users,
>
> I have recieved the same error as mentioned in the email ate bottom that was
> sent by
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 on
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
Exception in Tk callback
Function: at 0x10cc75230> (type: )
Args: ()
Traceback
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: L
.
From: jp d
To: Thomas Holder
Cc: "Schubert, Carsten [JRDUS]" ;
"pymol-users@lists.sourceforge.net"
Sent: Wednesday, February 12, 2014 11:16 AM
Subject: Re: [PyMOL] apbs plugin
hi,
if i enable debugging i get a little more info
get_default_loca
16:21, jp d wrote:
> hi,
> good idea, it runs from the command line after adding
> /pymol/ext/lib to my library path
>
> but the plugin still crashes.
> something is odd about my APBS plugin setup.
> if i even just click to change the file locations
> it crashes.
>
>
t;Schubert, Carsten [JRDUS]"
> To: jp d ; "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 pro
From: "Schubert, Carsten [JRDUS]"
To: jp d ; "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
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
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 from
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 men
pymol-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
, 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 versi
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
/var/folders/ZV/ZV5Pv67hjYmI8-m0PQU0
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 t
Hi Vaheh,
regarding psize.py: There is indeed a problem, I'm sorry. The simple
hotfix is to replace
C:\Program Files\PyMOL\PyMOL\modules\freemol\apbs.py
with
http://pymol.org/tmp/apbs.py
Regarding the "program stopped working" error: This doesn't happen for
me with 64bit Windows 7 or XP. Is t
Hi PyMOLers,
It looks like v1.6.0.0 treats APBS plugin differently, at least on my 64 bit
Windows laptop. After setting grid and few seconds after clicking "Run APBS"
button message appears in new window stating that program stopped working and
needs to close the window. Also, it looks like I
if you have problems.
Troels Emtekær Linnet
2013/6/18 Chen Zhao
> 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.
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
> Thank you so much Troels,
>
> This solves my problem. But based on this, it seems that APBS In pymol
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 wrote:
> Have a look on the earlier message on this.
>
> http://www.mail-archive.com/pymol-users@lists.sourceforg
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
> Dear Pymol Users,
>
> I have been trying to configure APBS-1.4 plugin of pymol 1.6 on a Debian
> Wheezy machine. The initializa
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
Exception in Tk callback
Function: at 0x33a6938> (type: )
Args: ()
Traceback (inne
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
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 comput
Dear all,
we have with our system Ubuntu a problem with APBS in the new pymol 1.5.
We use exactyl this version:
This Executable Build integrates and extends Open-Source PyMOL 1.5.0.4.
The following error occurs:
PDB2PQR - a Python-based structural conversion utility
--
Pl
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)
http://www.pymolwiki.org/index.php/Alter_S
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 happenin
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
wrote:
> 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 porti
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
recaulc
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 anticipatio
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 protein
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, d
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: Un
Hi Nick,
Could you send me a specific example of this happening? Feel free to email
it to me off-list if you'd like.
One thing I can think of off-hand is that the most recent version of the
plugin defaults to using more memory for the electrostatics calculation,
which can certainly make a differe
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 re
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 accessi
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 all
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 th
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 wrote:
> Can you go to the "Program Locations" tab and find out which version of APBS
> you're using? Th
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 ne
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 po
6 AM
> Cc: apbs-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
>
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
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 this
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'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
generated pqr (error
with alt conformations) or using the pqr file 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 alterna
e
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
was and added a few commands after line 1491:
using the pymol generated pqr (error with alt
conformations) or using the pqr file 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 an
Nathan Baker
Cc: 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 enviro
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
or using the pqr file 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!!!
oun...@lists.sourceforge.net [mailto:pymol-users-
boun...@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] [Ap
may have issues
reading
non-PDB-like PQR files. I would generally agree that use of
PDB2PQR to
convert PDBs to PQRs is the preferred route, since PyMOL doesn't do
any
checking or optimization.
Anyway, based on reported symptoms alone, the problem appears to be
that
some component in t
ed 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 the space
between
preferred route, since PyMOL doesn't do any
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 o
oesn't do any
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
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 bu
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 space-delimi
users-boun...@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 wi
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
Hi,
One of our researchers is trying to build an electrostatic map of his model
using the APBS plugin and is generating the following error. This is
Pymol 1.0r2 on Linux with APBS 0.5.1.
Any suggestions on how to fix it would be appreciated.
Error: 11
CmdException Exception in Tk callback
Fu
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
Functi
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 PyM
> 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
Hey all,
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. Am I blind or daft? But the question I'd
really l
ource endeavor!" -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
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 th
.net
> [mailto:pymol-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 "
ge.net
[mailto:pymol-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
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