On 10/10/12 04:55, Nat Echols wrote:
On Tue, Oct 9, 2012 at 8:43 PM, Paul Emsley <[email protected]> wrote:
i am not sure if this is a coot or phenix problem, but i'll start here.
we work on large complexes and after refining in phenix
we try to open it in coot and get avalanched with
INFO:: found bad VAL chiral atom: B 14 CB
we get so many of the warnings that it can crash the session.
this is only in coot 0.7
the same file in coot 0.6.2 opens ok
Crash? Oh dear. I am surprised that phenix and coot don't agree about the
nomenclature of valines.
Just to clarify, does this particular error indicate that
a) the CG1 and CG2 atoms are reversed
Yes. It is a terrible console message. Sorry about that - I didn't
know anybody else looked at them :-/
or
b) the chirality is messed up in some other way
?
(b) could be caused by incorrect weighting of geometry restraints, but
(a) should be difficult to do by accident...
gigo or some such? coot won't swap atom names unless you ask it to.
Perhaps phenix.refine is the same.
Paul.
