Dear Pymol users!
Using below script I can load all pdbs from the work dir into 1 nmr-like
object. Could you suggest me how this script could be modified to make
alignment (or it's better structural alignment) of all pdbs against first
loaded pdb file
from pymol import cmd
import sys,glob
def
Yeping–
You have to make a new object with the desired atoms. Try 'help extract' or
'help create'.
Also, dropbox lets you share a link to any file. The file is visible at
https://www.dropbox.com/s/j2lkd2lvu0eb2l1/surface1.tif?dl=0. I would change
your password.
-Spencer
On Wed, Aug 27, 2014
also please tell me how is it possible to include ter record at the end of
each model.
James
2014-08-27 11:58 GMT+02:00 James Starlight jmsstarli...@gmail.com:
Dear Pymol users!
Using below script I can load all pdbs from the work dir into 1 nmr-like
object. Could you suggest me how this
Sometimes it is easier to see the overall structure when looking at a
single unit cell rather than the symmetry mates within a certain distance.
You might want to try the supercell
http://www.pymolwiki.org/index.php/Supercell script. Otherwise I tend to
generate symmetry mates multiple times and
split_states NMR-ensemble object name
alignto 1st NMR model name, method=cealign
On 27 August 2014 13:28, James Starlight jmsstarli...@gmail.com wrote:
also please tell me how is it possible to include ter record at the end of
each model.
James
2014-08-27 11:58 GMT+02:00 James Starlight
and than how to quick merged aligned conformers back to the NMR ensemble
including TER record between each model in it?
Actually I'm looking for the possibility to load this ensemble to the
http://biophysics.cs.vt.edu/uploadpdb.php to assign protonation states for
the titrable residues in case
On 27/08/14 07:43, James Starlight wrote:
and than how to quick merged aligned conformers back to the NMR ensemble
including TER record between each model in it?
Hi James,
in addition you need the MODEL # [1] - ENDMDL [2] entry.
Justin
1)
On 27/08/14 07:56, James Starlight wrote:
Hi
both of them are present in my ensemble. the problem is not here- if it
possible i could upload the ensemble.pdb to some server if someone could
check it.
James
Hi,
Go for some paste bins or do a gist on github.
Justin
--
Justin Lecher
is it working here?
https://www.sendspace.com/file/8i0aqo
James
2014-08-27 14:58 GMT+02:00 Justin Lecher j.lec...@fz-juelich.de:
On 27/08/14 07:56, James Starlight wrote:
Hi
both of them are present in my ensemble. the problem is not here- if it
possible i could upload the
*Q: My structure has multiple chains. Which one will be used for the
calculation? *
A: Generally, all of them. Be careful, though. While most chains are
legitimate chains corresponding to subunits of the whole multi-mer (as in
e.g. hemoglobin), some PDB files use chain identifier A, B, etc. to
Hi,
I ran into a bug with the find polar contacts function (distance with
mode=2) today. The problem arises when I was trying to find the hydrogen
bonds between a ligand and a receptor that had been processed with
reduce (http://kinemage.biochem.duke.edu/software/reduce.php). A
bug/feature of
Hi Matt,
this was a bug with the dynamic_measures setting. It was fixed in PyMOL 1.7.0.
So please upgrade PyMOL or read this old post for workarounds:
http://sourceforge.net/p/pymol/mailman/pymol-users/thread/501949e8.2080...@users.sourceforge.net/
Cheers,
Thomas
On 27 Aug 2014, at 10:30,
Hi,
I am running version 1.7.2.1 from the svn (revision 4088) and the bug
with dynamic_measures persists. Unsetting it as in that link corrects
that issue though.
I can send you my files that find the error if you would like.
Matt
On 08/27/2014 11:19 AM, Thomas Holder wrote:
Hi Matt,
this
Hi Matt,
I just double-checked, this was a major refactoring of the dynamic_measures
setting which didn't make it into Open-Source PyMOL yet. So if you don't have
access to Incentive PyMOL, then please use the workarounds.
Cheers,
Thomas
On 27 Aug 2014, at 11:25, Matthew Baumgartner
Dear PyMol Users,
I am a PyMol-Gromacs plugin (
http://www.pymolwiki.org/index.php/GROMACS_Plugin) user and find the plugin
great.
I used to use Ubuntu 10.04 OS and the plugin did not work on it. I could manage
to run the plugin only on Ubuntu 12.04 and higher.
The reason was not the kernel
Dear Pymol users,
I have encountered a problem while trying to install pymol from the source
code on Centos 7.
I am running the following script for installation:
*
#!/bin/bash -e
prefix=/home/christos/PROGRAMS/PYMOL/OPEN-SOURCE/pymol
modules=$prefix/modules
python setup.py build install
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