Re: Individual Distance restraint weightings in dist geometry and anneal ?
2011-01-07 13:09:00 GMT
Thanks so much for your message a few weeks ago - I only just got back to the problem.
I wonder if you could explain to me what you mean by "classes" ?
in your reply to my question. I * think* you mean that I cannot enter force constants for individual restraints in the 'anneal.inp' files but can somehow use different NOE objects to achieve this
Apols for the ignorant question , I am very new to these programs.
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Hello Debora--This is done on the level of the script. You may have different NOE
> I am using distance restraints with both upper and lower bounds, starting
> from extended conformations of proteins ( 100-300 aas) and want to know
> 1. Can we also WEIGHT the distance restraints INDIVIDUALLY as well as set
> the bounds ? ( or can we 'only' do this in the anneal program)
objects (Python interface) or classes (old XPLOR interface) which have
different force constants. A force constant is not specified in the
restraint file.repulsive restraints are achieved by setting long lower bounds.
> 2. Can we set negative restraints? ( Or do we simply~ do this by setting
> long range lower bounds)
Please try anneal.py with the soft NOE potential. This should allow for
> 3. Is it better to use the anneal program to determine structures from
> restraints rather than DG ? (we do have false positives ( not many ) and
> the restraints are sparse, if that helps)
a small number bad restraints.
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