[MMTK] Re: Correct Hydrogens

Stuart Murdock s.e.murdock at soton.ac.uk
Thu May 27 14:22:08 CEST 2004


Thanks Eric, - thats the right track but my problem is a little more general.  


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Message: 1
Date: Wed, 26 May 2004 21:35:21 +0000
From: Stuart Murdock <s.e.murdock at soton.ac.uk>
Subject: [MMTK] Correct Hydrogens
To: mmtk at python.net
Message-ID: <40B50D99.4020002 at soton.ac.uk>
Content-Type: text/plain; charset=ISO-8859-15; format=flowed

Hi

I have PDB formatted files (for proteins) which have some missing 
hydrogen atoms. I would like
 to be able to read them into MMTK from the PDB file without the correct 
additional hydrogens being
introduced by MMTK. I would like to analyse sub-sections of proteins 
with MMTK, which are not the
complete molecule.

I can currently do this by simply not performing the

chain.findHydrogenPositions()

statement in the file PDB.py when creating peptide chains and deleting 
any undefined atoms, but was
wondering if there was a cleaner way of doing this without editing any 
files.

Any suggestions would be great.

Thanks,

Stuart
  
------------------------------

Message: 2
Date: Wed, 26 May 2004 15:56:24 -0700
From: Eric Zollars <zollars at caltech.edu>
Subject: Re: [MMTK] Correct Hydrogens
Cc: mmtk at python.net
Message-ID: <40B52098.1060606 at caltech.edu>
Content-Type: text/plain; charset=ISO-8859-15; format=flowed

Stuart-
    My first thought on this would be:

from MMTK import *
from MMTK.PDB import PDBConfiguration
conf = PDBConfiguration('blah.pdb')
chains = conf.createPeptideChains('no_hydrogens')


>> This is great if the pdb file contains no hydrogens and MMTK is great if 
>> the pdb file contains all of them as well.
>> The problem is that I have 'some' hydrogens, which will be like an intermediate 
>> between 'no_hydrogens' and 'all' of them. So, when I try to create the peptide chains 
>> I will get problems 
>> 1. (with 'no_hydrogens') as there are some hydrogens present
>> 2. (with 'all') as MMTK will put in the missing hydrogens. 
>> In general I will have complete residues its just that sometimes the chains will 
>> be terminated and sometimes they wont - but I need it kept that way.

But I may be missing something?
Z

>>Thanks Again,

>>Stuart



-- Stuart Murdock Ph.D, Research Fellow, Dept. of Chemistry / E-Science, 
University of Southampton, Highfield, Southampton, SO17 1BJ, United 
Kingdom http://www.biosimgrid.org ------------------------------ 
Message: 2 Date: Wed, 26 May 2004 15:56:24 -0700 From: Eric Zollars 
<zollars at caltech.edu> Subject: Re: [MMTK] Correct Hydrogens Cc: 
mmtk at python.net Message-ID: <40B52098.1060606 at caltech.edu> Content-Type: 
text/plain; charset=ISO-8859-15; format=flowed Stuart- My first thought 
on this would be: from MMTK import * from MMTK.PDB import 
PDBConfiguration conf = PDBConfiguration('blah.pdb') chains = 
conf.createPeptideChains('no_hydrogens') This But I may be missing 
something? Z Stuart Murdock wrote:

>> Hi
>>
>> I have PDB formatted files (for proteins) which have some missing 
>> hydrogen atoms. I would like
>> to be able to read them into MMTK from the PDB file without the 
>> correct additional hydrogens being
>> introduced by MMTK. I would like to analyse sub-sections of proteins 
>> with MMTK, which are not the
>> complete molecule.
>>
>> I can currently do this by simply not performing the
>>
>> chain.findHydrogenPositions()
>>
>> statement in the file PDB.py when creating peptide chains and deleting 
>> any undefined atoms, but was
>> wondering if there was a cleaner way of doing this without editing any 
>> files.
>>
>> Any suggestions would be great.
>>
>> Thanks,
>>
>> Stuart
>>  
>>
>  
>






-- 

Stuart Murdock Ph.D,
Research Fellow,
Dept. of Chemistry / E-Science,
University of Southampton,
Highfield, Southampton,
SO17 1BJ, United Kingdom
 
http://www.biosimgrid.org





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