Hi Anasuya

You must remember to also but in the name of the protein you. You were almost there!

2013/8/8 Anasuya Dighe <anasuya@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

Hope this helps!


Please let me know.

Thanks & Regards,

Anasuya Dighe
Molecular Biophysics Unit Annexe,
Indian Institute of Science,
Bangalore - 560012

This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.

Get 100% visibility into Java/.NET code with AppDynamics Lite!
It's a free troubleshooting tool designed for production.
Get down to code-level detail for bottlenecks, with <2% overhead.
Download for free and get started troubleshooting in minutes.
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Folmer Fredslund