Hello Santhosh--
>
> In refinement of structures using RDC's, we use 4 pseudo-atoms to define an
> axis and these are part of the PDB also. For more than one RDC dataset, we
> should have more than such 4 pseudo-atoms. Now the questions are :
If you use the Python interface (suggested) then there are 7 pseudo
atoms per alignment tensor.
>
> 1). Should the four atoms be created as a axis? I mean should O-XX be
> perpendicular to O-YY and so on? Or could it be any four atoms far away from
> the protein? In the examples, they are mostly perpendicular.?
The axes must be perpendicular, or you will get nonphysical
results. In a proper Xplor-NIH Python script, you don't have to
manually configure any pseudo atoms, and the axes will remain
perpendicular irrespective of force constants.
>
> 2). In case of multiple RDC constraints, would there be a problem if I
> overlap many such pseudo-atoms on top of each other?
No- overlap of pseudo atoms corresponding to different alignment
tensors is no problem, and with standard parameters there should be no
VDW energy calculated.
best regards--
Charles
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Charles Schwieters email: Charles at Schwieters.org
www: http://schwieters.org/cds
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