Hello Charles, I think I know the answer for these questions but just want to confirm with you.
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 : 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. 2). In case of multiple RDC constraints, would there be a problem if I overlap many such pseudo-atoms on top of each other? eg : 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 ATOM 860 X ANI 600 322.383 -47.025 154.522 1.00 3.06 ATOM 861 Y ANI 600 322.080 -50.957 156.088 1.00 4.37 ATOM 862 Z ANI 600 323.128 -50.368 152.019 1.00 4.35 ATOM 863 OO ANI 600 324.205 -49.405 154.647 1.00 4.04 Would this be fine as per VDW calculations or anything. I am hoping that they could overlap as I have many RDC datasets and it would be tricky to create many such random points. Thanks a lot, Santhosh -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/20130510/32f36ea9/attachment.html>
