[Chimera-users] question about Chimera

吴雪 wuxue at nankai.edu.cn
Tue Sep 22 04:18:56 PDT 2009

Dear colleague:
    I have  a question about the "find hydrongen bond" in Chimera. The dumb relax constraints in Chimera are "0.04 nm" and "20 degree".
   I don't understand the meaning of the parameter. 20 degree may means the angle bias the line,but I can't figure out what is the 0.04nm. 
The cutoff of the hydrogen is 0.4nm, and the angle is about 90 degree or some other parameters depending on the strength of the hydrogen bond.
  If we set the constraint as 0.02nm or0.03nm , few hydrogen bonds are found. I don't know the criteria. Can you give me some advice so that I can follow your instruction?
   Sincerly Yours
   WU Xue
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