Dear Afshan,
I have been struggling with the same irrating "feature" (I would call it
a bug), which was for me one of the reasons to abandon refmac. For some
reason and against PDB standards, refmacs wants linked amino acids to be
consecutively numbered and otherwise decides that they are not linked
and creates a funny gap record. However, I do not know whether this
"feature" is still present in the latest refmac version.
My advice would be:
1) Make sure you have the most recent version of refmac.
2) check in coot that the affected residues have not been pushed away
from each other and delete the gap records from your pdb file.
3) run a round of refinement and see what happens. If the problem
persists you have two or three options:
a) try a different refinement program
b) renumber your pdb, so linked amino acids have consecutive residue
numbers
c) add explicit link records to link the affected residues. If I recall
correctly you have to specify the atoms (N and C). The link is probably
called "trans"
Good luck!
Herman
________________________________
From: CCP4 bulletin board [mailto:[email protected]] On
Behalf Of Afshan Begum
Sent: Thursday, July 21, 2011 5:13 PM
To: [email protected]
Subject: [ccp4bb] hello
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
