If resolution is around 2.0 or better, ARP/wARP is particularly
powerful for such cases when model bias needs to be reduced.
For more info:
http://www.ncbi.nlm.nih.gov/pubmed/18094467?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum
http://www.ncbi.nlm.nih.gov/pubmed/11567158?ordinalpos=4&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum
Tassos
On Jul 28, 2008, at 3:19, 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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