Eleanor Dodson wrote:
... Many of these are unlikely, and you may well correct them when
rebuilding.
However the pdb file output by COOT will retain the CISPEP records..
You need to check and edit these yourself..
For the record, I believe that this is no longer the case. Coot will
only write
One possibility is this:
By default, REFMAC decided something is a cis-peptide if the omega
angle is < 90.0 .
It also reads and believes any CISPEP records you have in your input pdb.
(You can turn this feature off by requesting REFMAC to only restrain to
a cis peptide if you have a CISPEP re
IT could be miscommunication between refmac and coot. Try to remove
cispep lines from your pdb and refine again. Then it may work. After
model building info about cispep and/or ssbridge should be removed
from the pdb file (unless you are confident about them)
regards
Garib
On 25 Jan 2009,
Dear All,
I am refining a structure (resolution 2.4A) using Refmac and am getting a lot
of cis-peptides (about 16 for prolines as well as other amino acids). There are
some side chain swaps as well leading to high differences Rfactor: 20.6 and
Rfree: 27.6. Although I tried to convert them
