Hello Charles,
Thanks for the clarification. But I am confused from the 7 pseudo atoms.
>From the example gb1_rdc [from the tutorial]. I see that model.pdb has
ATOM 856 X ANI 500 322.383 -47.025 154.522 1.00 3.06
ATOM 857 Y ANI 500 322.080 -50.957 156.088 1.00 4.37
ATOM 858 Z ANI 500 323.128 -50.368 152.019 1.00 4.35
ATOM 859 OO ANI 500 324.205 -49.405 154.647 1.00 4.04
These 4 should define the tensor axis. And the RDC definition is done :
assign ( resid 500 and name OO )
( resid 500 and name Z )
( resid 500 and name X )
( resid 500 and name Y )
( resid 2 and name N )
( resid 2 and name HN ) -3.7330 0.2000
Out of which the first 4 lines are the axes and the remaning 2 are the
actual atoms.
Am I wrong ? And about the perpendicularity :
Do you mean that I need not manually maintain perpendicularity in the
model.pdb?
Sorry if I am overlooking something.
Thanks
Santhosh
On Sat, May 11, 2013 at 11:16 AM, Charles Schwieters <charles at schwieters.org
> wrote:
>
> 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
>
> --
> Charles Schwieters email: Charles at Schwieters.org
> www: http://schwieters.org/cds
> phone: (301) 402-4914 PGP key: http://schwieters.org/cds/pgp.txt
>
>
>
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