English
 
User Manual Privacy Policy Disclaimer Contact us
  Advanced SearchBrowse

Item

ITEM ACTIONSEXPORT
  Real-space processing of helical filaments in SPARX

Behrmann, E., Tao, G., Stokes, D. L., Egelman, E. H., Raunser, S., & Penczek, P. A. (2012). Real-space processing of helical filaments in SPARX. Journal of structural biology, 177(2), 302-313. doi:10.1016/j.jsb.2011.12.020.

Item is

Basic

show hide
Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0028-63D7-3 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0028-63D8-1
Genre: Journal Article

Files

show Files
hide Files
:
Behrmann_Real_2012.pdf (Any fulltext), 2MB
 
File Permalink:
-
Name:
Behrmann_Real_2012.pdf
Description:
-
Visibility:
Private
MIME-Type / Checksum:
application/pdf
Technical Metadata:
Copyright Date:
-
Copyright Info:
-
License:
-

Creators

show
hide
 Creators:
Behrmann, E.1, Author
Tao, G., Author
Stokes, D. L., Author
Egelman, E. H., Author
Raunser, S., Author
Penczek, P. A., Author
Affiliations:
1External Organizations, ou_persistent22              

Content

show
hide
Free keywords: Actin Cytoskeleton/chemistry Actomyosin/*chemistry Algorithms Cryoelectron Microscopy/*methods Imaging, Three-Dimensional/*methods Models, Molecular Principal Component Analysis Protein Structure, Quaternary *Software
 Abstract: We present a major revision of the iterative helical real-space refinement (IHRSR) procedure and its implementation in the SPARX single particle image processing environment. We built on over a decade of experience with IHRSR helical structure determination and we took advantage of the flexible SPARX infrastructure to arrive at an implementation that offers ease of use, flexibility in designing helical structure determination strategy, and high computational efficiency. We introduced the 3D projection matching code which now is able to work with non-cubic volumes, the geometry better suited for long helical filaments, we enhanced procedures for establishing helical symmetry parameters, and we parallelized the code using distributed memory paradigm. Additional features include a graphical user interface that facilitates entering and editing of parameters controlling the structure determination strategy of the program. In addition, we present a novel approach to detect and evaluate structural heterogeneity due to conformer mixtures that takes advantage of helical structure redundancy.

Details

show
hide
Language(s):
 Dates: 2012
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Type: -
 Identifiers: Other: 22248449
DOI: 10.1016/j.jsb.2011.12.020
ISSN: 1095-8657 (Electronic)
ISSN: 1047-8477 (Linking)
 Degree: -

Event

show

Legal Case

show

Project information

show

Source 1

show
hide
Title: Journal of structural biology
  Alternative Title : J. Struct. Biol.
Source Genre: Journal
 Creator(s):
Affiliations:
Publ. Info: -
Pages: - Volume / Issue: 177 (2) Sequence Number: - Start / End Page: 302 - 313 Identifier: -