Hi Tommi, This can be done in cns with the following script I wrote. You will need to make the cns-formatted molecular topology and coordinate files with the generate_easy.inp script, which can be found in the input files section of http://cns-online.org/v1.3/.
Best Regards, Jack Tanner ----------------------- John J. Tanner Professor of Biochemistry and Chemistry Department of Biochemistry University of Missouri 117 Schweitzer Hall 503 S College Avenue Columbia, MO 65211 Phone: 573-884-1280 Email: [email protected]<mailto:[email protected]> https://cafnrfaculty.missouri.edu/tannerlab/ Lab: Schlundt Annex rooms 3,6,9, 203B, 203C Office: Schlundt Annex 203A ------------------- start bridgingwaters.inp ------------ !read cns-formatted molecular topology and coordinate files struc @5kf6.pdb.cns.mtf end coord @5kf6.pdb.cns.pdb !store chain A protein iden (store1)(segid A and (byres name CA)) !store chain B protein iden (store2)(segid B and (byres name CA)) !select waters within 3.2 Angstrom of chain A iden (store3)(resname HOH and (store1 around 3.2)) !select waters within 3.2 Angstrom of chain B iden (store4)(resname HOH and (store2 around 3.2)) !select intersection to get bridging waters iden (store5)(store3 and store4) !write results to pdb file write coor output=bridgingwater.pdb form=pdbo sele=(store5) end stop ------------------- end bridgingwaters.inp ------------ Dear all, Is there a something available to automatically analyse/identifiy/quantify bound (“bridging”) water molecules at protein-protein interfaces? Could not find anyting right away. Thanks in advance, Best, Tommi ######################################################################## 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/
