Sorry to go back in time but distang is useful. You set radii Example: distang xyzin CCP4_JOBS/job_100/100_adam_xyzout_coot_rebuild_1.pdb
RADI CA 1 end will give all CA withion 2A of each other distang xyzin CCP4_JOBS/job_100/100_adam_xyzout_coot_rebuild_1.pdb end Will give all C N O S within VDW contact. - On Thu, 14 Jul 2022 at 17:28, Kay Diederichs <[email protected]> wrote: > Hi Henrike, > > I use CCP4's "contact" program: > > #!/bin/bash > # find bad contacts: list all CA-CA distances < 3.8A between non-adjacent > residues > # in a well-folded protein, these should be very rare (1 contact in 1000 > residues) > # KD 20.12.21 > grep CA $1 > /tmp/temp.pdb > contact xyzin /tmp/temp.pdb <<EOF | awk '/LIST OF CONTACTS/,/FONT > COLOR/{print}' | grep -v FONT > MODE IRES > LIMIT 0 3.8 > EOF > rm /tmp/temp.pdb > > If you are interested in non-CA atoms, modify accordingly. But this should > give you the idea. > > HTH, > Kay > > > On Thu, 14 Jul 2022 17:52:40 +0200, Henrike Wagler < > [email protected]> wrote: > > >Dear all, > > > > > >We are looking into a way to find clashes / bumps between protein chains > >(closer than van der Waals contacts). > > > >Ideally, we would like to that with a script, for example, reading in a > >pdb file, and giving back the number of clashes. > >Of course, this is possible within Coot or PyMol, but maybe there is a > >software as part of CCP4 that we can directly use with a script. > > > >Apologies if there an obvious solution that we are currently not aware of. > > > >Many thanks > > > >Best, > >Henrike Wagler > > > >######################################################################## > > > >To unsubscribe from the CCP4BB list, click the following link: > >https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > >This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
