Dear Ngo,
What do you mean by "no positive map"? If you mean the green difference
map density, this should go away if the refinement program did its job
properly. The residual green density at the Tyr is probably due to the
fact that when the Tyr is not at this position, something else (e.g.
water) is present what is not modeled. If you scroll down the contour
level of the blue 2FOFCWT map to say 0.6 sigma and see reasonable
density, I would keep the alternate positions. Because of the low
occupancy, you cannot expect great density at a higher contour level.
Best,
Herman
________________________________
From: CCP4 bulletin board [mailto:[email protected]] On
Behalf Of Tri Ngo
Sent: Friday, July 27, 2012 10:01 AM
To: [email protected]
Subject: [ccp4bb] Alternative conformation of Phe and Tyr?
Dear ccp4bb,
I am working on refinement of an enzyme structure. I notice an
alternative conformation (gauche+ and gauche-) on both residues Phe and
Tyr.
Here is the image of electron density before refinement. Based
on the different map intensity, I am quite sure there is an alternative
conformation on both positions.
http://i50.tinypic.com/29zaoap.jpg
However, after running occupancy refinement by Phenix, I don't
see the density map at the gauche- conformation of Tyr residue. Please
take a look at the image 2.
http://i50.tinypic.com/anzfrn.png
So do you think the gauche- conformation of Tyr exists in this
structure. Should I keep it in the final model because there is no
positive map there?
Thank you very much for your input.
--
Ngo Duc Tri
PhD Student
Structural Biology Lab
School of Medicine - Sungkyunkwan University - Korea
Phone: 031-299-6150 - Cell: 010-7774-8210
