VMD-L Mailing List
From: Bennion, Brian (bennion1_at_llnl.gov)
Date: Thu Aug 15 2024 - 00:33:18 CDT
- Next message: Vardan Vardanyan: "Re: fftk, ORCA, Bond and Angle Optimization, error As a subsequent Frequencies calculation has been requested"
- Previous message: Josh Vermaas: "Re: altloc pdb entries"
- In reply to: Josh Vermaas: "Re: altloc pdb entries"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
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
- Next message: Vardan Vardanyan: "Re: fftk, ORCA, Bond and Angle Optimization, error As a subsequent Frequencies calculation has been requested"
- Previous message: Josh Vermaas: "Re: altloc pdb entries"
- In reply to: Josh Vermaas: "Re: altloc pdb entries"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]