A variety of alternatives to DSSP are easily available here
http://2struc.cryst.bbk.ac.uk/
As has been pointed out, methods other than the well-known DSSP may be
particularly appropriate at lower-resolution or with model structures
where perfect geometry, H-bond formation etc are not to be expected.
Dan
On 29/01/17 17:11, Pavel Afonine wrote:
Tools like DSSP and such rely on model geometry to annotate SS
elements, so GIGO applies. For example, something that by eye looks
like an obvious helix but has enough distortions is unlikely to be
annotated correctly.
Pavel
On Sun, Jan 29, 2017 at 3:50 AM, Antonio Ariza
<[email protected] <mailto:[email protected]>> wrote:
I always use DSSP, which I believe has been the gold standard for
secondary structure assignment from pdb files for many years.
PYMOL also has a DSSP plugin that can be used to override its own
secondary structure assignment, which is nowhere near as good as DSSP.
Best
Tony
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Sir William Dunn School of Pathology
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------------------------------------------------------------------------
*From:* CCP4 bulletin board [[email protected]
<mailto:[email protected]>] on behalf of chemocev marker
[[email protected] <mailto:[email protected]>]
*Sent:* 29 January 2017 10:41
*To:* [email protected] <mailto:[email protected]>
*Subject:* [ccp4bb] secondary structure assignment to PDB file
Hi
Is there any tool that can assign secondary structure to the PDB
file. The problem is if I used different modelling tools, there
are regions in the protein which does not remain consistent and
looks different in different application.
best
J. Vitali
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