| 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
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CME.cif
Description: Binary data
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
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