Hello Afshan,
Maybe the programm that you use for refinement need specific entry with
restraint for your modified amino acids.
More precisely, i think about the *.cif file for exemple.
HTH.
Nicolas
Le 21/07/11 17:13, Afshan Begum a écrit :
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
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