Dear PyMol users!
I wounder to know about built-in PyMol option for electrostatic
potential visualisation.
For example I have pdb coordinates of my protein as well as its
electrostatic potential distribution (calculated by another software).
Using MolMol with both of that files I can visualize
I have a similar requirement, taking density and potential dstriutbutions from
jdftx which are written as plain binarry doubles. I use a script and
some code to create an xplor file which seems to work but I have
to adjust the position and scale to let it
overlay the ion positions that I read
As I understood the APBs plugin which already exist in PyMol is the
very efficient device for electrostatic potential calculations.
2 questions have been arisen:
1- How I could change cut-off distances for the electrostatic? E.g I'd
like to consider only interactions within 5 A between any
Greetings,
If you will be at the April ACS meeting in New Orleans, please feel free to
stop by the Schrödinger booth (#400). I will be there much of the time
answering questions, demoing new features, and generally discussing science
and visualization.
Specifically, we'll have a demo version of
Specifically, we'll have a demo version of PyMOL v1.6, PyMOL on the iPad,
and even a sneak peek of Leap Motion (https://www.leapmotion.com/)
controller integration with PyMOL.
Do you have it working under linux?
--
Hi Sabuj,
Do you have it working under linux?
Yes, I have demonstrated the same functionality on Ubuntu (12.10). Ubuntu
is the only Linux distro currently supported by Leap.
Cheers,
-- Jason
--
Jason Vertrees, PhD
Director of Core Modeling Products
Schrödinger, Inc.
(e)
by the way have someone had problems with the pdb2pqr usage with APBS in pymol?
I've tried to install pdb2pqr from source as well as via packages
then I've add usr/bin/pdb2pqr to the APBs plugin window
and when I've started APBS I obtained error like
Error: 5
type
