[phenixbb] Add restraints between base-pairs in GUI & structures comparison

Xiang Li li338 at purdue.edu
Sun Jan 13 11:12:50 PST 2013

Hi everyone,

I am a new user of Phenix and have a few questions asking for help.

1 I worked on a DNA structure and wanted to add restraints during the refinement. I used GUI version and chose "secondary structure restraints"->"restraint base pairs". However, there were some distortion of the base pairing after refinement. Is there a way to assign the base pairing between specific base pairs and force the base pairings in the GUI version? 

2 I want to compare two DNA structures to see the RMSD. Each of them were composed of 4 strands. Seems "structure comparison" software can not work with such multiple strands DNA structures. Do you have any suggestions on how to do the comparison please?

Thank you very much for your reply!


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