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
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
