Gerard Kleywegt's MOLEMAN and MOLEMAN2 from the Upsalla Structure Factory easily handles many of the described tasks and does MUCH MORE !
From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of David J. Schuller Sent: Thursday, September 8, 2022 4:01 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] PDBx-format utilities You don't often get email from schul...@cornell.edu<mailto:schul...@cornell.edu>. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> ALERT! Outside Org 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). ======================================================================= All Things Serve the Beam ======================================================================= David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu<mailto:schul...@cornell.edu> ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of Paul Emsley <pems...@mrc-lmb.cam.ac.uk<mailto:pems...@mrc-lmb.cam.ac.uk>> Sent: Thursday, September 8, 2022 3:28 PM To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> 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? 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