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 <antonio.ar...@path.ox.ac.uk> 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 > > > ------------------------------------------------------ > > > > > > > * Dr. Antonio Ariza University of Oxford Sir William Dunn School of > Pathology South Parks Road Oxford OX1 3RE* > > *Links to my public profiles:* > ResearchGate <https://www.researchgate.net/profile/Antonio_Ariza> > LinkedIn <https://www.linkedin.com/in/antonioariza1> > GoogleScholar > <https://scholar.google.co.uk/citations?user=9pAIKV0AAAAJ&hl=en> > ORCID <https://orcid.org/0000-0003-4364-823X> > ------------------------------ > *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of chemocev > marker [jirivit...@gmail.com] > *Sent:* 29 January 2017 10:41 > *To:* CCP4BB@JISCMAIL.AC.UK > *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 >
