VMD-L Mailing List

From: Bennion, Brian (bennion1_at_llnl.gov)
Date: Thu Aug 15 2024 - 00:33:18 CDT

Thank you Josh for your response.
That is a good suggestion if A and B where the only options in the pdb files I am working with.

In hundreds of pdb files, downloaded directly from rcsb, C and other letters exist in the altloc column
so for good or ill

altloc A or altloc \"\"

did work as far as my testing has shown

thanks
brian

________________________________
From: Josh Vermaas <vermaasj_at_msu.edu>
Sent: Wednesday, August 14, 2024 7:44 AM
To: Bennion, Brian <bennion1_at_llnl.gov>; vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: altloc pdb entries

Why not "not altloc B"? I know there is some shenanigans that can positively select for empty altloc fields (I think it was ""), but just excluding the "wrong" codes is probably easier to figure out quickly.

-Josh

On 8/13/24 8:47 PM, Bennion, Brian wrote:
Hello,

I would like to sort/clean up a set of pdb files and about 50% have altloc entries for many but not all the residues.

Initially i created a selection using altloc A but that removed the rest of the protein which had blank entries for altloc.

is there a proper selection syntax here
[atomselect top "atloc A and the rest of the protein without altlocB or empty"

Biosciences and Biotechnology Division|PLS|Lawrence Livermore National Laboratory|925-422-5722 

--
Josh Vermaas
vermaasj_at_msu.edu<mailto:vermaasj_at_msu.edu>
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
Michigan State University
vermaaslab.github.io