If this is happening something is wrong!
REFMAC can certainly use multiple NCSR requests..
I usually check the agreement with the Superpose molecules task
(Coordinate utilities) matching all atoms just to make sure that AC does
match A'C' and B matches B'. If the RMS difference is greater than 1A
say you probably shouldnt try to impose NCS.
One problem is that there may already be differences in nomenclature p-
ie one PHE has CD1 CG1 matching CD2 CG2 in the other partner.
You will see this in your list of outliers after superposition.
So I usually start NCS refinement by fiitting A over A' and replacing
the A' with the rotated coordinates, and so on. That way you are sure
the initial models are going to match..
Eleanor
Kevin Cowtan wrote:
Or download the latest refmac 6.6, and it will do NCS fully
automatically, and handle conformational flexibility too.
David Schuller wrote:
I think you should be able to specify two different "NCSR" lines, one
to cover chains A&A' and C&C', and another to cover chains B&B'.
On 06/23/10 18:51, Oganesyan, Vaheh wrote:
Dear bb contributors,
I would like to refer to your expertise and get advice regarding
multiple NCS relations between two macromolecular complexes in asu.
Resolution 2.5A, s.g. C2221, R-merge 6%, synchrotron data, 2 complexes
per a.s.u. Each complex consist of three polypeptide chains, let's say
A, B, C and A', B' and C'. A and A' have one NCS operator and B and B'
have another. C molecule follows A.
When I impose ncs in refinement my R-factors jump to ~30(35)% while
without they are around 21(27)%.
Does this mean that I can not use two different NCS operators or it
means I'm not applying ncs correctly?
I'm using refmac5 with TLS through GUI.
Thank you.
Vaheh
P.S. I don't remember if such question have ever been discussed on bb.
To the extent this electronic communication or any of its attachments
contain information that is not in the public domain, such
information is considered by MedImmune to be confidential and
proprietary. This communication is expected to be read and/or used
only by the individual(s) for whom it is intended. If you have
received this electronic communication in error, please reply to the
sender advising of the error in transmission and delete the original
message and any accompanying documents from your system immediately,
without copying, reviewing or otherwise using them for any purpose.
Thank you for your cooperation.
