Dear Changyi,
If refmac distorts the ring to fit INTO the density, the first question
I would ask myself is whether the sugar ring has been fitted correctly.
Sugars can be a pain in the neck with different puckers, chair/boat
conformations, different anomers etc. If the sugar is somewhat
disordered, or the resolution of your data is low, it is even possible
that the sugar ring needs to be rotated 180 degrees. Also make sure that
you use the right anomer.
Only after you are sure the ring has been fitted correctly and you
merely need cosmetic corrections because of low resolution data and/or a
disordered binding mode, I would try to restrain the ring more tightly.
For this, you need to locate the cif file with the parameters of your
ligand and increase the weight on the angle restraints.
Good luck!
Herman
________________________________
From: CCP4 bulletin board [mailto:[email protected]] On
Behalf Of Changyi Xue
Sent: Wednesday, August 04, 2010 10:16 PM
To: [email protected]
Subject: [ccp4bb]
Dear all,
In my structure, there is a ligand, which contains a sugar
ring. In the process of refinement, refmac always tried to distort the
sugar ring to fit into the density. Is there any way to fix or restrain
the ring conformation more tightly? I know CNS has such function, just
wandering if refmac could do it also.
all suggestions are welcome.
changyi
