Re: [ccp4bb] secondary structure assignment to PDB file

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

Re: [ccp4bb] rigid flexible analysis

KGS software can do this, as well as sampling based on rigidity (10.1016/j.jmps.2015.06.006 or 10.1021/acs.jctc.5b00995). The software is available from github: https://github.com/ExcitedStates/KGS. Henry From: CCP4 bulletin board

[ccp4bb] Abraham Szöke

Dear Colleagues: Is is with great sadness that I report the recent passing of Abraham Szöke, a friend, colleague, informal mentor, and an exceptionally intelligent and energetic source of boundless intellectual enthusiasm. Abraham was a physicist at Livermore who helped to design nuclear

Re: [ccp4bb] secondary structure assignment to PDB file

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

[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