Is there NCS? (How's the self rotation look? How about the native
patterson?)
Does your search model have flexible loops? You may have the right
solution, but the flexible loops may be in a different conformation
and cause clashes. Trim the search model to the conserved / structured
domains.
Do you have *any* anomalous signal? (whether you collected Sulfur-SAD,
you have a metalloprotein, etc). These can be useful in verifying the
correctness of the MR solution.
I use only one chain of the monomer model
Why?
F
On Mar 15, 2011, at 12:41 AM, Careina Edgooms wrote:
Dear CCP4 members
I have a confusion with molecular replacement. I wish to solve a
monomeric protein in P21 where there are 2 monomers in asymmetric
unit. I have a search model that also has 2 monomers in asymmetric
unit.
First I try using Phaser. I use only one chain of the monomer model
and search for 2 copies. This gives a good solution that refines
with low R-factor but it shows many clashes. In other words, the 2
monomers are too close together and there are clashes where they
meet. Then I try using Phaser and both chains of the model and
search for 1 copy. This does not give a solution and says asymmetric
unit is too full. Then I try using MolRep with the 2 chain search
model. It gives solution that looks better because you can see that
the 2 monomers do not physically clash but it refines very badly
giving R factors of about 50%
So I am confused. What am I doing wrong? Please help me with
suggestions
Many thanks
Careina
---------------------------------------------
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder
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8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
