XtalView/Xfit--A versatile program for manipulating atomic coordinates and electron density
- PMID: 10222271
- DOI: 10.1006/jsbi.1999.4094
XtalView/Xfit--A versatile program for manipulating atomic coordinates and electron density
Abstract
Xfit is a model-building and map viewing program in XtalView that is used by the structural biology community including researchers in the fields of crystallography, molecular modeling, and electron microscopy. Among its distinguishing features are built-in fast Fourier transforms that allow users flexibility in map calculations including the creation of OMIT maps and the updating of structure factors to reflect model changes from within the program. Written in C and using the freely available XView toolkit, it is highly portable to almost any X-windows based workstation including Intel-based LINUX systems. Its user interface is designed to aid in facile model-building and contains a semiautomated fitting system that allows the user to interactively and rapidly build chain de novo into an electron density map. The program is highly optimized to allow such features as interactive contour levels and map calculations to be completed within a few seconds. Features in the latest version including phase-combination, solvent-flattening, automated water addition, and small-probe dot contact surfaces, as well as basic design features, are discussed.
Copyright 1999 Academic Press.
Similar articles
-
Ximdisp--A visualization tool to aid structure determination from electron microscope images.J Struct Biol. 1999 Apr-May;125(2-3):223-8. doi: 10.1006/jsbi.1998.4073. J Struct Biol. 1999. PMID: 10222278
-
NORMA: a tool for flexible fitting of high-resolution protein structures into low-resolution electron-microscopy-derived density maps.Acta Crystallogr D Biol Crystallogr. 2006 Sep;62(Pt 9):1098-100. doi: 10.1107/S090744490602244X. Epub 2006 Aug 19. Acta Crystallogr D Biol Crystallogr. 2006. PMID: 16929111
-
Windows .NET Network Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST).BMC Bioinformatics. 2005 Apr 8;6:93. doi: 10.1186/1471-2105-6-93. BMC Bioinformatics. 2005. PMID: 15819992 Free PMC article.
-
Web-based telemicroscopy.J Struct Biol. 1999 Apr-May;125(2-3):235-45. doi: 10.1006/jsbi.1999.4095. J Struct Biol. 1999. PMID: 10222280 Review.
-
Combining electron microscopy and comparative protein structure modeling.Curr Opin Struct Biol. 2005 Oct;15(5):578-85. doi: 10.1016/j.sbi.2005.08.001. Curr Opin Struct Biol. 2005. PMID: 16118050 Review.
Cited by
-
Relationship of structure and function of DNA-binding domain in vitamin D receptor.Molecules. 2015 Jul 7;20(7):12389-99. doi: 10.3390/molecules200712389. Molecules. 2015. PMID: 26198224 Free PMC article. Review.
-
Crystal structure of the protein At3g01520, a eukaryotic universal stress protein-like protein from Arabidopsis thaliana in complex with AMP.Proteins. 2015 Jul;83(7):1368-73. doi: 10.1002/prot.24821. Epub 2015 May 14. Proteins. 2015. PMID: 25921306 Free PMC article.
-
Structure-function relationship of assimilatory nitrite reductases from the leaf and root of tobacco based on high-resolution structures.Protein Sci. 2012 Mar;21(3):383-95. doi: 10.1002/pro.2025. Epub 2012 Jan 31. Protein Sci. 2012. PMID: 22238192 Free PMC article.
-
Volume-conserving trans-cis isomerization pathways in photoactive yellow protein visualized by picosecond X-ray crystallography.Nat Chem. 2013 Mar;5(3):212-20. doi: 10.1038/nchem.1565. Epub 2013 Feb 3. Nat Chem. 2013. PMID: 23422563 Free PMC article.
-
Molecular basis for RNA polymerization by Qβ replicase.Nat Struct Mol Biol. 2012 Jan 15;19(2):229-37. doi: 10.1038/nsmb.2204. Nat Struct Mol Biol. 2012. PMID: 22245970
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources
