I recall using CME some time ago (within last couple of years) without problems. Also, an alternative approach is to incorporate BME as a separate residue instead - the disulfide bond will be correctly identified by refmac. I would think ideologically this is more appropriate - using a different residue type implies that this is the way your protein is, as if somehow the modified residue was incorporated during protein synthesis (as is the case with seleno-methionines). With post-translational modifications perhaps the better way is to represent additional entities as separate monomers that are bound to the protein via covalent bonds.
Cheers, Ed. On Fri, 2011-07-22 at 09:19 +0100, Garib N Murshudov wrote: > Dear Afshan > > > Make sure that group name for CME is peptide (or L-peptide). In the > new version CME is peptide. I am not sure it was the case in older > versions. I attach CME as a peptide. You can add this into your > dictionary. > > > > > Then CME can become part of a peptde. It would also be good to remove > all the link records in the beginning of refmac. > > > > > Regards > Garib > > > > > > > On 21 Jul 2011, at 16:13, Afshan Begum wrote: > > > Dear all, > > > > > > I have facing one problem during the refinement of my protein . > > Actually in my protein there are some modified amino acids are > > present like Cystein is modified into CME which i can get easily > > from monomer libraray in coot . but after refinement in Pdb text > > file indicated some gaps while in the structures there are no gap > > in between these amino acids so if any one suggest me what to do. I > > would appreciate your kind suggestions. > > > > > > > > LINKR GLU A 142 LEU A 144 > > gap > > LINKR SER A 328 GLY A 330 > > gap > > LINKR LEU A 138 GLU A 140 > > gap > > LINKR GLU A 126 ASP A 130 > > gap > > LINKR SER A 246 GLY A 248 > > gap > > > > > > Many thanks for your time > > > > Best regards > > > > Afshan > > > > > > > > > > Garib N Murshudov > Structural Studies Division > MRC Laboratory of Molecular Biology > Hills Road > Cambridge > CB2 0QH UK > Email: ga...@mrc-lmb.cam.ac.uk > Web http://www.mrc-lmb.cam.ac.uk > > > > > > -- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore ---------------------------------------------- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. ------------------------------ / Lao Tse /
