Re: [Jmol-users] Bug? Secondary structure in PDB/CIF ignored.

[Angel H. <ang...@ua...>]

Hello

It is indeed normal that the result of "calculate structure" is different from the original.
By default, Jmol should use what is wriitten in the PDB file SHEET and HELIX records. As Eric said, this case looks like some failure of Jmol in recognizing one of the beta strand stretches.
When you issue "calculate structure", Jmol's own algorithm is used to detect (judge) what are helices and sheets; the result is likely slightly different. There is also another method "calculate structure DSSP"  It is normal that they may all differ a little.


 Dr. Angel Herráez
 Biochemistry and Molecular Biology,
 Dept. of Systems Biology, University of Alcalá
 E-28805 Alcalá de Henares  (Madrid), Spain