Re: [PyMOL] missing residues

[ahmet y. <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
>>
>>
>> ------------------------------------------------------------------------------
>> 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
>> Archives: http://www.mail-archive.com/pym...@li...
>>
>
>
>
> --
> Michael Zimmermann
> Ph.D. student in Bioinformatics and Computational Biology
> Department of Biochemistry, Biophysics and Molecular Biology
> Iowa State University
>



-- 
Ahmet YILDIRIM