I have a set of utilities for handling PDB files, known as "PDB Pipeline". Each
one does a single distinct thing: manipulate the spatial coordinates, reset the
B, pull out a particular subset of residue numbers, fix particular known
problems, etc. There are several dozen. They work very nicely with Linux
command line utilities such as grep and sed. They are so old that they were
written in Fortran-77 (with VMS FORTRAN extensions).
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All Things Serve the Beam
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David J. Schuller
modern man in a post-modern world
MacCHESS, Cornell University
[email protected]
________________________________
From: CCP4 bulletin board <[email protected]> on behalf of Paul Emsley
<[email protected]>
Sent: Thursday, September 8, 2022 3:28 PM
To: [email protected] <[email protected]>
Subject: [ccp4bb] PDBx-format utilities
A spectre is haunting structural biology - it is the spectre of the PDBx
format.
We at CCP4 are interested in providing tools that are equivalents of
those that one might have trivially made with utilities such as grep or sed.
For example:
delete the hydrogen atoms
extract the hydrogen atoms
extract the SD of MET
find the atoms with B-factors greater than 100.0
So, what useful tool have you made can that works because it based on
the PDB format - that (of course) doesn't work with PDBx?
Thanks,
Paul.
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