[Xplor-nih] VMD-XPLOR

[Charles at Schwieters.org]

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Hello Marcela--

In the future, VMD-XPLOR questions should be directed to
vmd-xplor at nmr.cit.nih.gov 

> I started using VMD-XPLOR to visualize a molecule and its NMR 
> constrains. I would like to understand better what I am getting. I have 
> converted the AMBER restrain file to XPLOR format, and now I have a set 
> of three distances: d dlow dhigh. I understand the exact meaning of 
> these numbers depends on the restraining function used. So my question 
> is, what is the default for VMD-XPLOR? For example if I set
> 2.8, 0.5, 0.5
> does that mean the NOE distance is 2.8+-0.5 A?

correct.
> 
> Another question is what is the "cutoff" button that is in the NOE 
> window of VMD-XPLOR?

that is the threshold margin used to decide whether or not to count the
restraint as violated.

This information is available by clicking on the ``?'' button in the NOE
window. 

best regards--
Charles
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