*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.
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?
James
2014-08-27 15:05 GMT+02:00 Thomas Evangelidis <teva...@gmail.com>:
>
>
>
> On 27 August 2014 15:43, James Starlight <jmsstarli...@gmail.com> 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 <teva...@gmail.com>:
>>
>> 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 <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 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: tev...@pharm.uoa.gr
>>>
>>> teva...@gmail.com
>>>
>>>
>>> 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: tev...@pharm.uoa.gr
>
> teva...@gmail.com
>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
>
> ===============================================================
>
> *Physics is the only real science. The rest are just stamp collecting.*
>
> *- Ernest Rutherford*
>
>
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