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
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
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
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
Yeah that's perfect. Just what I was looking for!
One other thing, anyone know how to turn the stereo visual off
completely so that pymol doesn't load into an opengl stereo visual even
if pymol detects that you have stereo capable hardware? Even when stereo
is turned off the screen flickers li
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
m
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
molecule surface generated using APBS tools using t
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 non-standar
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