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 each model and obtained back ensemble with
the processed conformers.


At this time using such nmr ensemble I've faced with the below error

FAILURE: Sequence discontinuity occurred between residues 289 and 1 at the
line ATOM 1 N ASP 1 62.482 8.961 22.846 1.00103.76 N

I don't why this error occurs (I have not this in case of ONE model from
the ensemble)

James


2014-08-27 13:10 GMT+02:00 Thomas Evangelidis <te...@gm...>:

> split_states <NMR-ensemble object name>
> alignto <1st NMR model name>, method=cealign
>
>
> On 27 August 2014 13:28, James Starlight <jms...@gm...> 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 <jms...@gm...>:
>>
>> 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 get_file_list(files):
>>>   file_list = glob.glob(files)
>>>   return file_list
>>>
>>> def load_models(files,obj,discrete=0):
>>>   """
>>>   load_models <files>, <object>, <discrete=0>
>>>
>>>   loads multiple files (using filename globbing)
>>>   into a single object (e.g. from modelling or NMR).
>>>
>>>   use discrete=1 if you want to color individual states separately
>>>
>>>   e.g. load_models prot_*.pdb, prot
>>>   """
>>>   if type(files) == type('string'):
>>>     file_list = get_file_list(files)
>>>   else:
>>>     file_list = files
>>>
>>>   if file_list:
>>>     file_list.sort()
>>>     for name in file_list:
>>>       cmd.load(name,obj,discrete=discrete)
>>>   else:
>>>     print "No files found for pattern %s" % files
>>>
>>> cmd.extend('load_models',load_models)
>>>
>>>
>>> Many thanks for help,
>>>
>>> James
>>>
>>
>>
>>
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>
>
>
> --
>
> ======================================================================
>
> Thomas Evangelidis
>
> PhD student
> University of Athens
> Faculty of Pharmacy
> Department of Pharmaceutical Chemistry
> Panepistimioupoli-Zografou
> 157 71 Athens
> GREECE
>
> email: te...@ph...
>
>           te...@gm...
>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
>
> ===============================================================
>
> *Physics is the only real science. The rest are just stamp collecting.*
>
> *- Ernest Rutherford*
>
>