[Chimera-users] Sec structure loss

James Fethiere james.fethiere at umontreal.ca
Fri May 2 14:19:38 PDT 2008


I'm seing something strange with secondary structure assignments in 
peptides. Two examples: PDB 1axc has a peptide bound to PCNA with beta 
strand interactions and chimera doesn't pick it up as a strand. In the 
other example, 1rxz, it picks up the strand in a similar peptide but the 
strand disappear when I run matchmaker with 1ul1 (which also has a 
strand at the c-terminus that is not picked up. Is there any 
explanation? Are the criteria for secondary structure assignments to strict?

One more thing that may have been asked already!!  how does one keeps 
the NH and CO of the peptide bond displayed in the ribbons view?


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