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

On 27 August 2014 16:10, James Starlight <jms...@gm...> 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. hemoglobin), some PDB files use chain identifier "A", "B", etc. to
> denote different models of the same monomer (as in e.g. 2TRX). Make sure
> you supply only the one you want. For NMR structures, *you get a window
> where you can choose which model to use*.
>
>
But still it says you can use only one at a time.


> i guess it indicate that in principle some ensembles are possible as the
> input :) Alternatively do you know any other tools (software) for the
> processing of the ensembles with such options for the analysis?
>
>
No.


> James
>
>
> 2014-08-27 15:05 GMT+02:00 Thomas Evangelidis <te...@gm...>:
>
>
>>
>>
>> On 27 August 2014 15:43, James Starlight <jms...@gm...> wrote:
>>
>>> 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.
>>>
>>> I think H++ server processes one structure per job. Where did you find
>> that you can upload an ensemble?
>>
>>
>>>
>>> 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*
>>>>
>>>>
>>>
>>
>>
>> --
>>
>> ======================================================================
>>
>> 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*
>>
>>
>


-- 

======================================================================

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*