Hi Anasuya
You must remember to also but in the name of the protein you. You were
almost there!
2013/8/8 Anasuya Dighe <anas...@mbu.iisc.ernet.in>
> Hello PyMOL users,
>
> Say, I have three pdb files loaded onto PyMOL. Lets assume that each of
> the pdb
> file has 3 chains, i.e A,B,C in them.
>
> If I want to select residues 1,5,6,7 in chain A of Protein_1, residues
> 4,8,9,12
> in chain B of Protein_2 and residues 1,5,12,43 in chain A of Protein_3.
>
> I know the command to select residues, i.e select name1, resi 1+5+6+7 and
> chain
> A , but when i execute this command, residues 1&5 of chainA of the
> Protein_1 and
> Protein_3, are selected.
>
> How do I specify that the selection has to be at the chain A in Protein_1 ?
> I tried loading the files one by one and doing this, but when I come to the
> third pdb file and execute the select command, I am running in to the same
> problem,i.e residues 1 and 5 of protein_1 are also getting selected.
>
>
You need to also specify the molecule:
select name1, Protein_1 and resi 1+5+6+7 and chain A
> How do i avoid this ? Some additional syntax required ?
> Also, once this is done, how to align these selections spanning 3 different
> chains among 3 separate proteins ?
> Will the align command suffice ?
>
>
I'm not sure, but I don't think the align command will work on just those
selections (too few atoms).
I think pair_fit is better to use
http://www.pymolwiki.org/index.php/Pair_fit
Hope this helps!
mvh
Folmer
> Please let me know.
>
> Thanks & Regards,
>
> Anasuya Dighe
> Molecular Biophysics Unit Annexe,
> Indian Institute of Science,
> Bangalore - 560012
> INDIA
>
>
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Folmer Fredslund
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