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: [log in to unmask]
> 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 /
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