Display Settings:

Format

Send to:

Choose Destination
See comment in PubMed Commons below
J Struct Biol. 2012 Feb;177(2):302-13. doi: 10.1016/j.jsb.2011.12.020. Epub 2012 Jan 11.

Real-space processing of helical filaments in SPARX.

Author information

  • 1Max Planck Institute for Molecular Physiology, Department of Physical Biochemistry, Otto-Hahn-Straße 11, 44227 Dortmund, Germany.

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.

Copyright © 2012 Elsevier Inc. All rights reserved.

PMID:
22248449
[PubMed - indexed for MEDLINE]
PMCID:
PMC3288516
Free PMC Article

Images from this publication.See all images (8)Free text

Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7
Figure 8
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for Elsevier Science Icon for PubMed Central
    Loading ...
    Write to the Help Desk