Hi Sebastiano,
In this case, having your own dictionary for both residues together will be useful. Same dictionary will be used in refmac refinement too, if you need precise refined positions. It will be easier, if you do the editing in text file. Get the CIF files for Cys-X together, rename residues and satisfy the valency - bond length etc. Let me know if you need help. all the best Manish >________________________________ > From: Sebastiano Pasqualato <[email protected]> >To: [email protected] >Sent: Thursday, July 26, 2012 6:06 PM >Subject: Re: [ccp4bb] modeling thioester bond > > > > >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 <[email protected]> >>> >>To: [email protected] >>> >>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 [email protected] >>> >> >>> >> >>> >> >>> >> >>> >> >>> >> >>> >> >>> >> >>> >> >>> > >-- >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 [email protected] > > > > > > > > >
