Thanks Manish. With the help of Paul and using JLigand, which is nicely connected to coot in version 0.7-pre1, I managed to create the bond and have the correct library CIF file.
Still, I can't manage to "regularize" the bond and residues close to it. It looks like I have to go through refcmac via "structure idealisation". Unlike in the case of "sphere refinement", when you have a density map, in my case I don't know how to "regularize" a zone which is comprised between two different chains. Thanks for the tip, ciao, s On Jul 26, 2012, at 2:19 PM, Manish Chandra Pathak wrote: > > > Just defining LINK in your pdb file should work. Try this format. > LINK NZ LYS A 233 C4A PLP A 400 > > > OR > > You need a dictionary file to tell the COOT that the two residues are > > connected. If an instance already exist in PDB, then you can download > > the refmac dictionary from http://xray.bmc.uu.se/hicup/ > Otherwise, use PRODRG Dundee server with coordinates of both > > residues (Cys-X) to create a new residue dictionary. > > all the best > Manish > > > > Manish Chandra Pathak, Ph.D. > Indian Institute of Science Education and Research > ITI (Gas Rahat) Building > Govindpura, Bhopal 462023 India > tel: +91-750-4092340 > > > > >> ________________________________ >> From: Sebastiano Pasqualato <sebastiano.pasqual...@gmail.com> >> To: CCP4BB@JISCMAIL.AC.UK >> Sent: Wednesday, July 25, 2012 9:48 PM >> Subject: [ccp4bb] modeling thioester bond >> >> >> >> >> No answers yet from the COOTbb (yet), so I'm cross posting this to the >> ccp4bb. >> Sorry for the double post. >> >> >> >> >> >> >> Hi there, >> I'd like to model a thioester bond, starting from protein A with an exposed >> Cys, and having juxtaposed the carboxyl group of a C-terminal residue of >> protein B. >> >> >> The way I would like to proceed is by: >> >> >> 1) telling coot that there's a bond between the S atom and the C atom of the >> two groups; >> 2) regularize that zone in order to have something that makes chemical sense. >> >> >> Could you advice me on how to proceed for the two steps? >> That is, how do I tell coot that the bond exists and it has to be taken into >> account? >> >> >> Thanks in advance, >> ciao, >> s >> >> >> >> >> >> -- >> Sebastiano Pasqualato, PhD >> >> Crystallography Unit >> Department of Experimental Oncology >> European Institute of OncologyIFOM-IEO Campusvia Adamello, 1620139 - Milano >> Italy >> >> tel +39 02 9437 5167 >> fax +39 02 9437 5990 >> >> please note the change in email address!sebastiano.pasqual...@ieo.eu >> >> >> >> >> >> >> >> >> -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990 please note the change in email address! sebastiano.pasqual...@ieo.eu
