Dear Sun:
Starting the refinement again, with a molecular replacement structure
in which the residues in question are deleted, shouldn't take that
much time. However, I would be really surprised to see much model
bias in a sigma-A weighted 2Fo-Fc map generated after an omit
simulated annealing procedure, especially if you crank the temperature
up to 6000K.
Another possible approach is to use EDEN. I put it on googlecode:
http://code.google.com/p/edencrystallography/
I recently solved an RNA structure just with molecular replacement of
random A-helix fragments. With this sort of psychotic approach to
molecular replacement, model bias is a major problem. One trick that
helped was to blur the HL coefficients (there is a script to do so in
CNS) and then solvent-flatten/flip.
But if the first approach isn't working, this is telling you something
I think. Is it possible the result you are getting is correct after
all?
William G. Scott
Contact info:
http://chemistry.ucsc.edu/~wgscott/
On Jul 27, 2008, at 6:19 PM, Sun Tang wrote:
Hello Charlie,
Thank you very much for your comments. I mostly agree with you.
However, as far as I know most of the complexes structures are
solved with MR with the their apo-enzyme as search model and refined
the structures with CCP4 or CNS. I tried the simulated annealing
omitting the residue and 4 neighboring residues on each side and I
found the conformation are essentially the same. I also tried to use
composite omit-map calculation in CSN but I gave it because it took
several days of computer time but only finished only 1/4 of the
calculation.
I understand the starting from the beginning is one choice. I wonder
whether there are other easier ways in CCP4 to deal with this
situation because this problem is quite common in refinement.
I appreciate all the replies to my questions and I say "Thank you
very much" here.
Best,
Sun
--- On Sat, 7/26/08, Charles W. Carter Jr. <[EMAIL PROTECTED]> wrote:
From: Charles W. Carter Jr. <[EMAIL PROTECTED]>
Subject: Re: [ccp4bb] question about getting rid of model bias in
refinement
To: CCP4BB@JISCMAIL.AC.UK
Date: Saturday, July 26, 2008, 3:15 PM
Sun,
I'm most of the way to one side of this debate: I believe that it
is not possible to emerge fully from model bias without avoiding it
in the first place with experimental phases. I may be overly
pessimistic, but have considerable experience supporting at least
skepticism.
My interpretation of the experimental result you describe is that
the covariances among the parts of the structure you left in place
and those side chains you omitted is so strong and extensive that
you'll never see the correct density coming back upon refinement,
because other parts of the structure are ever so slightly off their
true mean positions to compensate for the (evidently false)
positions of the residues you omitted. Bill's suggestion that you
actually refine the structure using simulated annealing without the
omitted residues is an improvement over what you did, but it will
require many cycles to get a much better approximation, and there is
really no way to be sure when you can be confident. Starting the
entire refinement over is a more aggressive strategy. If you decide
to try this, you should examine the projection of the residue by
residue real-space correlation coefficients across the entire
sequence to ensure that you have only one
population of values and delete all residues that comprise any
population that has a distinctly different real-space correlation
coefficient, building them back into the structure as it refines.
That is, you should ensure that you don't begin refining any
residues at the very beginning for which there is evidence that they
might be different from their positions in your molecular
replacement model.
Charlie
On Jul 26, 2008, at 2:12 PM, William G. Scott wrote:
Hi Sun:
It might be worth doing a simulated annealing omit refinement in
phenix or CNS, with the residues in question omitted. CNS also
allows you to make a composite-omit map. I haven't seen that in
phenix yet but presumably it is doable.
Bill
William G. Scott
Contact info:
http://chemistry.ucsc.edu/~wgscott/
On Jul 25, 2008, at 10:53 PM, Sun Tang wrote:
Hello Everyone,
I have a question about getting rid of model bias in refinement with
refmac. I solved the structure with molecular replacement. After
final refinement of the structure, I found out some key amino acids
in the structure and wanted to make sure their conformations are
correct. I omitted these amino acids (by setting occupancy to zero)
and refined the structure. I manually fit the amino acids into the
density and refined the structure again. I found these amino acids
return to the precious conformations even though the conformations I
fit were different. Should I omit these amino acids from the
beginning of the refinement? What is the best way to get rid of the
model bias? Your suggestions are greatly appreciated!
Best,
Sun
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