Re: [PyMOL] missing residues

[Tsjerk W. <ts...@gm...>]

Selam Ahmet,

I cordially suggest to have a look at
http://catb.org/~esr/faqs/smart-questions.html to phrase your question
more effectively, such that we can provide more tailored help. It
would have been nice to have an example that we could try ourselves.

I find that as preparation for MD simulations you can often get away
with more casual modeling, using pymol for copy-paste. That is,
provided you have a structure with the missing parts resolved, which
is the case. Here is a working example, where the chains are from
different models, but the principle is the same.

# Get a structure with a missing loop
fetch 1d0g, async=0

# Get the structure which has that loop resolved
fetch 1d4v, async=0

# Extract  the chain you want to fit; not really (necessary)
create chainb, 1d4v and chainb

# Fit the chain onto the one with the missing loop
align chainb, 1d0g and chain a

# Alter the chain identifier to match the target:
alter chainb, chain="A"

# Write the residues that are missing
save missing.pdb, chainb and resi 132-144

# Now you can take the coordinates from 'missing.pdb' and insert them
in the target pdb file in the right place

# Remove the rubbish
delete 1d4v
delete chainb

# Load the loop
load missing.pdb

# Et voila...


Hope it helps,

;)

Tsjerk

2011/10/14 ahmet yıldırım <ahm...@gm...>:
> Thanks Michael,
>
> How can I overcome using Pymol?
>
> 14 Ekim 2011 23:05 tarihinde Michael Zimmermann <mic...@ia...>
> yazdı:
>>
>> The easiest way to model in the missing loops is to make a homology model
>> of the full sequence using the incomplete structure as a template.
>> (http://swissmodel.expasy.org or I-TASSER)
>>
>> Alternatively, you can use Modeller to model in the loop and refine it.
>>
>>
>>
>> 2011/10/14 ahmet yıldırım <ahm...@gm...>
>>>
>>> Dear users,
>>>
>>> There are 7 missing residues in xxx.pdb file. xxx.pdb consist of chain a
>>> and chain b. In chain b there are only 7 missing residues. chain a is
>>> complete.
>>> I fitted the complete chain onto the one with missing residues, wrote the
>>> new coordinates for the fitted chain and put them in the broken chain using
>>> a text editor.
>>> I think the chain a and chain b do not fit/overlap
>>> As result, in chain b alpha is incomplete (see result image). what should
>>> I do?
>>>
>>> 1.way:
>>> pymol-file-open-protein.pdb
>>> PyMOL>create chaina, chain a
>>> PyMOL>align chaina and resi 2-230, chain b and resi 2-230
>>> PyMOL>save chaina.pdb, chaina
>>>
>>> 2.way:
>>> pymol-file-open-protein.pdb
>>> PyMOL>create chaina, chain a
>>> PyMOL>create chainb, chain b
>>> PyMOL>align chaina and resi 2-230, chainb and resi 2-230
>>> PyMOL>save chaina.pdb, chaina
>>>
>>>
>>> Again the result didnt change :(
>>> --
>>> Ahmet YILDIRIM
>>>
>>>
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>>
>>
>>
>> --
>> Michael Zimmermann
>> Ph.D. student in Bioinformatics and Computational Biology
>> Department of Biochemistry, Biophysics and Molecular Biology
>> Iowa State University
>
>
>
> --
> Ahmet YILDIRIM
>
> ------------------------------------------------------------------------------
> All the data continuously generated in your IT infrastructure contains a
> definitive record of customers, application performance, security
> threats, fraudulent activity and more. Splunk takes this data and makes
> sense of it. Business sense. IT sense. Common sense.
> http://p.sf.net/sfu/splunk-d2d-oct
> _______________________________________________
> PyMOL-users mailing list (PyM...@li...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands