Dear Yogesh
Could you please try the version from York
www.ysbl.york.ac.uk/refmac/latest_refmac.html
You need to take appropriate refmac 5.4 (it is current stable
version) and dictionary. I remember that in older version there was a
problem in one of RNA bases and it has now
been corrected.
If the problem persists with this version also please let me know.
regards
Garb
On 25 Dec 2007, at 06:47, Yogesh Gupta PhD wrote:
Dear CCP4 users,
I refined my final model (protein-RNA complex) using TLS refinement
in Refmac but when i am validating the coordinates I am having an
issue with Bond Distances and Bond Angles of some of the bases of
RNA, these values for some of the bases are higher ( >6 times) then
the standard values. I figured that it happened only after REFMAC
refinement. The coordinates before the REFMAC (the last CNS refined
coordinates) were found to be acceptable by the same validation
program. So my guess is something wierd is happening with RNAs only
during REFMAC refinement. Although, Rfree improved by almost 1.5%
with REFMAC.
In an attempt to fix this, I ommitted both chains of the RNAs
during the REFMAC (.tls file contains only protein monomers) but
that did not resolve the isssue either.
Is there any way to fix this problem or a way to restrain
particular RNA bases/chains during TLS refinement?
Thanks for your time and help.
Happy Holidays
Yogesh
--
Yogesh K. Gupta, Ph.D.
Post Doctoral Fellow
Molecular Physiology & Biophysics
Mount Sinai School of Medicine
1425, Madison Av. (East Bldg. 16-26)
Box 1677, New York, NY 10029-6574
Tel:+1 212-659-8639
Fax:+1 212-849-2456
E-mail: [EMAIL PROTECTED]
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