Hello András--
>
> 1. The old user guide contains a sperate refinement (refine.inp) and
> analysis (accept.inp) section. Am I right that the refine.py
> includes both?
There is some analysis performed in standard refine.py scripts. Of
course, additional analysis can always be performed.
> 2. How does the XPLOR-NIH handle the distance restraints of those methyl (HG2*
> etc.), methylene (HB* etc) as well as aromatic protons (HE* etc) where there
> is
> only one observed chemical shift? Does it create a pseudoatom with averaged
> coordinates? If so, should I increase the upper bound of these restraints to
> make sure that the distances will be valid for the real atoms as
> well?
There is usually no pseudo-atom when dealing with methyls- usually
1/r^6 sum averaging is used, but the upper bounds may be increased by
0.5 Angstrom for methyls only.
> 3. I noticed that the violation threshold for NOE restraints is 0.5A. Is it
> worth to try to do the refinement with lower (e.g. 0.2 or 0.3A) threshold
> value? If not, is there any option to print out all distances which violate
> the
> NOE upper distance bounds, even if the differences are between
> 0.0-0.5A?
All distances are printed in the .viols files if showAllRestraints is
set to True, i.e.:
pot = create_NOEPot(name,file)
pot.setShowAllRestraints(True)
> 4. I have done the structure calculation by Cyana, thus, I had to convert my
> data to XPLOR-NIH format. For this purpose, I used the PdbStat. I have read
> two
> guides about the conversion of the NOE distance restraints, which contradict
> with each other. One suggested to use the same upper bound as it was present
> in
> Cyana, the other advised to add further 10-15%. What do you think about it,
> which method would yield the better result?
This I do not have experience with.
> 5. During my first test I got a low number (2-4) hb violations. How
> important are they and how can I improve my structure? My
> experimental input data are the following: structure file (pdb),
> distance and backbone dihedral restraints.
>
I can't really give advice on your specific case, but there likely
shouldn't be this sort of violation. Certainly, if the same restraints
are consistently violated (as listed in the .stats file), it indicates
some sort of inconsistency.
Charles
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