id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
14713	DSSP output in ChimeraX	r.joosten@…	Eric Pettersen	"{{{
Dear ChimeraX developers,

We are the current developers of DSSP and during a group meeting the 
DSSP implementation in ChimeraX came up.

 From the documentation I gather that you are using a reimplementation 
of the 1983 algorithm. There have been a number of updates to that 
algorithm. For instance there was an update for Alpha-bulges and more 
recently we added detection for poly-proline type II helices (a.k.a. 
kappa-helices).

To incorporate the latter, we have made backward compatible changes to 
the DSSP format (see https://pdb-redo.eu/dssp/about#DSSP). At the same 
time we also added direct annotation of mmCIF files (see 
https://github.com/PDB-REDO/dssp/blob/trunk/libdssp/mmcif_pdbx/dssp-extension.dic 
for the dictionary extension). The current version of DSSP is available 
as stand-alone executable, library code and an API (see 
https://pdb-redo.eu/dssp/download). The code is under a BSD 2-clause 
license.

Would you be interested in incorporating the current version of DSSP in 
ChimeraX, reading the mmCIF output and/or executing the algorthm? We 
would be happy to discuss by mail or in a short teleconference.


On a related note, we also develop the PDB-REDO databank and 
webserver/service. It would be great if PDB-REDO entries (i.e. rerefined 
and rebuilt versions of PDB entries, frequently better models than the 
original; see pdb-redo.eu) could be loaded directly into ChimeraX 
equivalent to how this is done for PDB and EMDB entries.

We host both models and map coefficients in MTZ format. For example, 
PDB(-REDO) entry '1cbs' is hosted as 
https://pdb-redo.eu/db/1cbs/1cbs_final.cif for the model and 
https://pdb-redo.eu/db/1cbs/1cbs_final.mtz for the electron density maps 
(normal, difference and, if availble, anomalous).

Similar options of fetching PDB-REDO data are available in Coot, 
Moorhen, YASARA and CCP4mg and we believe this could also be very useful 
for ChimeraX users.

Best wishes,
Robbie Joosten


}}}
"	defect	accepted	normal		Structure Analysis				Elaine Meng Tom Goddard m.hekkelman@… a.perrakis@… Greg Couch				all	ChimeraX