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Interactive model building in neutron macromolecular crystallography

Logan, Derek T. LU (2020) In Methods in Enzymology 634. p.201-224
Abstract

This chapter aims to give an overview of the process of interactive model building in macromolecular neutron crystallography for the researcher transitioning from X-ray crystallography alone. The two most popular programs for refinement and model building, phenix.refine and Coot, respectively, are used as examples, and familiarity with the programs is assumed. Some work-arounds currently required for proper communication between the programs are described. We also discuss the appearance of nuclear density maps and how this differs from that of electron density maps. Advice is given to facilitate deposition of jointly refined neutron/X-ray structures in the Protein Data Bank.

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author
organization
publishing date
type
Chapter in Book/Report/Conference proceeding
publication status
published
subject
keywords
Model building, Model refinement, Neutron macromolecular crystallography, Nuclear density maps, Perdeuterated proteins, Protein Data Bank
host publication
Methods in Enzymology
series title
Methods in Enzymology
editor
Moody, Peter C.E.
volume
634
pages
24 pages
publisher
Academic Press
external identifiers
  • scopus:85076852480
  • pmid:32093833
ISSN
0076-6879
1557-7988
ISBN
978-0-12-819214-6
DOI
10.1016/bs.mie.2019.11.017
language
English
LU publication?
yes
id
0b28888d-aa69-4dff-bf8e-b82e26056702
date added to LUP
2020-01-14 13:23:47
date last changed
2021-01-19 02:09:52
@inbook{0b28888d-aa69-4dff-bf8e-b82e26056702,
  abstract     = {<p>This chapter aims to give an overview of the process of interactive model building in macromolecular neutron crystallography for the researcher transitioning from X-ray crystallography alone. The two most popular programs for refinement and model building, phenix.refine and Coot, respectively, are used as examples, and familiarity with the programs is assumed. Some work-arounds currently required for proper communication between the programs are described. We also discuss the appearance of nuclear density maps and how this differs from that of electron density maps. Advice is given to facilitate deposition of jointly refined neutron/X-ray structures in the Protein Data Bank.</p>},
  author       = {Logan, Derek T.},
  booktitle    = {Methods in Enzymology},
  editor       = {Moody, Peter C.E.},
  isbn         = {978-0-12-819214-6},
  issn         = {0076-6879},
  language     = {eng},
  pages        = {201--224},
  publisher    = {Academic Press},
  series       = {Methods in Enzymology},
  title        = {Interactive model building in neutron macromolecular crystallography},
  url          = {http://dx.doi.org/10.1016/bs.mie.2019.11.017},
  doi          = {10.1016/bs.mie.2019.11.017},
  volume       = {634},
  year         = {2020},
}