Understood. Thanks for your replies and for a great program.
Nicholas
From: Eric Martz
Sent: Sunday, April 23, 2017 11:18 AM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] Secondary structure does not match DSSP
Dear Nicholas,
Angel is correct. By default, Jmol shows the secondary structure that the
authors specified in the PDB file with HELIX, SHEET and TURN records. You will
notice that often, authors do not specify TURN records so there are no blue
turns initially. After you calculate structure, and color structure, turns are
colored blue, and the ends of strands and helices may be different than before.
Also, Jmol distinguishes three kinds of helices, and gives them distinct colors:
a.. Alpha 3.6(13)
b.. 3.0(10)
c.. Pi 4.4(16)
Each kind is illustrated here in JSmol:
http://proteopedia.org/w/Helices_in_Proteins
See also http://proteopedia.org/w/Secondary_structure
-Eric
On 4/23/17 4:56 AM, Angel Herráez wrote:
Hi Nicholas
However, if I issue the command $calculate structure and then redisplay, the
structure
is then shown with a ribbon consistent with DSSP, running from 365 to 373. Can
anyone
tell me why Jmol doesn't display this stretch according to DSSP in the first
place?
I am not certain, but it is likely that when you load a file Jmol will use the
secondary structure declared in the PDB file, and not the DSSP result unless
you invoke this later (using calculate).
As far as I can interpret, the pdb file says beta strands for
Tyr350---Trp356
Cys370---Pro373
so 365-368 are not a beta strand
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