[Chimera-users] I need SSEBuilder and SSEHunter plug in

Baker, Matthew L mbaker at bcm.edu
Mon Nov 7 11:35:34 PST 2016


Unfortunately, the GUIs for SSEHunter and SSEBuilder in Chimera are no longer supported, though I do have a version of the old AIRS plugins that is compatible with EMAN2 and the latest stable release of Chimera (a bit buggy, however). A few years ago, we transitioned our SSE detection into Gorgon, our own toolkit for modeling and analysis of intermediate resolution density maps. You can access step-by-step tutorials and videos on our Gorgon webpage (http://gorgon.wustl.edu/) or from the EMAN 2015 workshop page (http://ncmi.bcm.edu/ncmi/events/workshops/workshops_145). Additionally, we have a new version of Gorgon that should be released by the end of 2016, which in addition to the Gorgon UI, also has command-line utilities and a new Chimera plugin for a subset of the Gorgon utilities (including SSE detection with SSEHunter).

Currently, SSE detection in Gorgon is divided up into 2 parts. The first part consists of several steps that generate a set of pseudoatoms, which are scored depending on their likelihood of being part of a helix or part of a sheet. In Gorgon, these pseudoatoms are colored from red (helix) to white (no SSE assignment) to blue (sheet), with the intensity of the color reflecting the confidence of the prediction. While the first step is mostly automated, save for parameter selection, the second step is manual. In this phase of  SSE detection, you need to group pseudoatoms and annotate them as either a helix or a sheet. This selection can be performed by multiply selecting pseudoatoms (of the same color) - you will see the selected atom numbers and scores appear in the bottom half of the Identify SSEHunter widget- and then "building them" with the Add Sheet or Add Helix button. You iterate through this entire procedure until you have selected all SSEs. Once you are done, you can save the helix or sheet annotations in the file menu; we offer two output files for SSEs (dejavu and vrml), both of which are human readable and parseable for the information you need.

NCMI Workshop on Single Particle Reconstruction ...<http://ncmi.bcm.edu/ncmi/events/workshops/workshops_145>
NCMI Workshop on Single Particle Reconstruction, Structural Variability and Modeling: DATE: Oct. 30, 2015 ...

The Gorgon Project<http://gorgon.wustl.edu/>
Gorgon is an interactive molecular modeling system specifically geared towards cryo-EM and other low resolution structures of macromolecular complexes.

Matthew Baker, Ph.D.
Assistant Professor
Department of Biochemistry and Molecular Biology
Baylor College of Medicine
Houston, TX
(713) 798-7319
From: chimera-users-bounces at cgl.ucsf.edu <chimera-users-bounces at cgl.ucsf.edu> on behalf of b.behkamal at mail.um.ac.ir <b.behkamal at mail.um.ac.ir>
Sent: Saturday, November 5, 2016 2:17:38 PM
To: Chimera-users at cgl.ucsf.edu
Subject: [Chimera-users] I need SSEBuilder and SSEHunter plug in


I am a Ph.D. candidate of computer engineering in structural bioinformatic from Ferdowsi University of Mashhad, Iran. I'm working on cryo-em modeling. I necessary need the "SSEBuilder and SSEHunter plug in" in chimera to build the SSEs and continue my work. Would you mind please help me about this matter.

Thank you very much in advanced.


Bahareh Behkamal
Ph. D. Candidate of Computer Engineering
Researcher in Structural Bioinformatics
Dept. of Computer Engineering
Ferdowsi University of Mashhad, Mashhad, Iran

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