Dear Henrike, I use the pymol plugin show_bumps: https://pymolwiki.org/index.php/Show_bumps Best, Daniel
------------------------------------------------------------------ Daniel Lietha, PhD Group Leader Cell Signalling and Adhesion Group Structural and Chemical Biology Margarita Salas Center for Biological Research Spanish National Research Council (CSIC) Calle Ramiro de Maeztu 9, E-28040 Madrid, Spain Tel: +34 91 109 8016 Email: daniel.lie...@cib.csic.es http://cib.csic.es/research/structural-and-chemical-biology/cell-signalling-and-adhesion#sec1 On Thu, Jul 14, 2022 at 7:30 PM Eleanor Dodson < 0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > 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 < > kay.diederi...@uni-konstanz.de> 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 < >> henrike.wag...@studium.uni-hamburg.de> 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 > > > ######################################################################## 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/
