CCP4 bulletin board <[email protected]> wrote on 04/10/2008 04:12:23
PM:
> Sorry for re-posting --this time with subject
> Hi All,
> I am sure there are some experienced persons who can help me to
> check what’s wrong is going with my def file I used in anneal.inp
> I attached the def and out file.
> I am trying to restrain the dna (4 chains K, L, D, E) via Watson-
> Crick base pair and two long helices(A and B) via H-bond in my structure.
> Any suggestion is well appreciated.
>
> Regrards...
>
> Raja
>
>
Hi Raja -
You didn't say what problem you're experiencing. From looking at the
anneal.out file, it seems that the job finished without any errors, and
gave you a pdb file at the end. I suspect the problem you're asking about
is that the resulting structure looks terrible - the DNA is all messed up
and the base pair hydrogen bonds are broken. And I think I know why.
There are two problems that I can diagnose just from looking at the output.
First is this:
%NOESET-ERR: error in selection - no atoms spec.
%NOE-ERR: problem at 55 -999.000 -999.000
This error is during the assignment of the Watson-Crick hydrogen bonds. I
think you have a few bogus coordinates in your structure; perhaps at atom
55? There are other errors like this.
The second, more serious problem can be seen from the starting R factors:
============================================
R-value by resolution for test set
============================================
#bin | resolution range | #refl |
1 7.20 500.01 143 0.4725
2 5.71 7.20 125 0.5481
3 4.99 5.71 123 0.5232
4 4.54 4.99 123 0.5500
5 4.21 4.54 111 0.5524
6 3.96 4.21 114 0.5904
7 3.76 3.96 109 0.5589
8 3.60 3.76 84 0.5442
#bin | resolution range | #refl |
1 3.60 500.01 932 0.5166
>>>> Overall R-value for test set: 0.516556
============================================
R-value by resolution for working set
============================================
#bin | resolution range | #refl |
1 7.20 500.01 1434 0.4355
2 5.71 7.20 1444 0.5017
3 4.99 5.71 1410 0.4490
4 4.54 4.99 1388 0.4777
5 4.21 4.54 1387 0.4846
6 3.96 4.21 1175 0.5385
7 3.76 3.96 1140 0.6060
8 3.60 3.76 1043 0.5612
#bin | resolution range | #refl |
1 3.60 500.01 10421 0.4748
>>>> Overall R-value for working set: 0.474811
You're trying to perform simulated annealing with data that only go to 3.6
A, and that's being generous - based on your R factors, I'd say your model
and your data part company at more like 4 A. Annealing simply won't work
with such low resolution data. Your ending R factors (43.4 / 53.5) show
that all you did was over-refine your structure, causing the free R to
increase.
Assuming your experimental data only go to 3.6 A, I'm afraid you're going
to have a very hard time solving this protein-DNA complex. You definitely
can't rely on annealing to help you out - stick with energy minimization
and manual rebuilding. If you got your initial model from molecular
replacement, you need to be certain that your solution is correct.
Sorry for the bad news,
Matt
--
Matthew Franklin , Ph.D.
Senior Scientist, ImClone Systems
180 Varick Street, 6th floor
New York, NY 10014
phone:(917)606-4116 fax:(212)645-2054
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