If there is a covalent link between CYS and UNK then it is better to create that using jligand from ccp4. There are nice tutorials designed by Andrey Lebedev. Tutorials are on this site: http://www.ysbl.york.ac.uk/mxstat/JLigand/
Regards Garib On 5 Feb 2014, at 15:59, Ronnie <ronnie...@yahoo.com> wrote: > I am asking this question on behalf of a friend: -Thanks! > > Hi All - I am working at small biotech. We have minimal budget for software, > only CCP4 and Coot. We have a ligand that binds covalently to cysteine. I > define the parameter file using Prodrg in CCP4 to get drug.cif file and then > make a link in Coot between the Cys and the Drug. The problem is Refmac > keeps complaining that there is no link_id for this bond: > > I am reading library. Please wait. > mon_lib.cif > WARNING : link: CYS<-->UNK is without link_id > link will be created with covalent bond only. Bond= 1.610 > WARNING : description of link:CYS-UNK is not in the dictionary > link will be created with bond_length = 1.610 > > Where do I specify this link_id, and where can I find an example for the > correct syntax? Is this done in mon_lib.cif or the drug.cif file?? The bond > length, if I'm not mistaken should be ~1.82 A for distance between carbon and > sulfur. > > Thanks for any help. Dr Garib N Murshudov MRC-LMB Francis Crick Avenue Cambridge CB2 0QH UK Web http://www.mrc-lmb.cam.ac.uk, http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/
