[PyMOL] problem installing on CENTOS 7

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

[PyMOL] PyMol_Gromacs plugin

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 s

Re: [PyMOL] Problem with finding polar contacts

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 wrote:

Re: [PyMOL] Problem with finding polar contacts

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, > > thi

Re: [PyMOL] Problem with finding polar contacts

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, Ma

[PyMOL] Problem with finding polar contacts

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 r

Re: [PyMOL] Making nmr-like ensemble from several pdbs

On 27 August 2014 16:10, James Starlight wrote: > *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. hemog

Re: [PyMOL] Making nmr-like ensemble from several pdbs

*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. t

Re: [PyMOL] Making nmr-like ensemble from several pdbs

is it working here? https://www.sendspace.com/file/8i0aqo James 2014-08-27 14:58 GMT+02:00 Justin Lecher : > 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 serv

Re: [PyMOL] Making nmr-like ensemble from several pdbs

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

Re: [PyMOL] Making nmr-like ensemble from several pdbs

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 2014-08-27 14:52 GMT+02:00 Justin Lecher : > On 27/08/14 07:43, James Starlight wrote: > > and than how to quick merged aligned co

Re: [PyMOL] Making nmr-like ensemble from several pdbs

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) http://wwpdb.org/documentation/format33/sec

Re: [PyMOL] Making nmr-like ensemble from several pdbs

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 of

Re: [PyMOL] Making nmr-like ensemble from several pdbs

split_states alignto <1st NMR model name>, method=cealign On 27 August 2014 13:28, James Starlight 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 : > > Dear Pymol users! >> >> Using be

Re: [PyMOL] symmetry mates

Hi, If the linear arrangement is defined as 'biological assembly' in the PDB file, you can use "Biological Unit" script in http://www.pymolwiki.org/index.php/BiologicalUnit to quickly generate it. Best regards, Takanori Nakane On 2014-08-27 11:57, Spencer Bliven wrote: > Sometimes it is easier

Re: [PyMOL] symmetry mates

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 script. Otherwise I tend to generate symmetry mates multiple times and

Re: [PyMOL] Making nmr-like ensemble from several pdbs

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 : > 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 modi

Re: [PyMOL] how to get the surface representation look better?

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 at

[PyMOL] Making nmr-like ensemble from several pdbs

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 ge