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. <[log in to unmask]> wrote:
>
> From: Charles W. Carter Jr. <[log in to unmask]>
> Subject: Re: [ccp4bb] question about getting rid of model bias in
> refinement
> To: [log in to unmask]
> 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
>
>
>
>
>
>
>
>
> **********UNCrystallographers NOTE new website url******************
> [log in to unmask]
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> Department of Biochemistry and Biophysics CB 7260
> UNC Chapel Hill, Chapel Hill, NC 27599-7260
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>
>
>
>
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