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: [email protected] www: http://schwieters.org/cds phone: (301) 402-4914 PGP key: http://schwieters.org/cds/pgp.txt
pgp93RNOEtWZr.pgp
Description: PGP signature
_______________________________________________ Xplor-nih mailing list [email protected] http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
