Literature DB >> 10222271

XtalView/Xfit--A versatile program for manipulating atomic coordinates and electron density.

D E McRee1.   

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.

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Year:  1999        PMID: 10222271     DOI: 10.1006/jsbi.1999.4094

Source DB:  PubMed          Journal:  J Struct Biol        ISSN: 1047-8477            Impact factor:   2.867


  692 in total

1.  Crystal structure of a Staphylococcus aureus protein A domain complexed with the Fab fragment of a human IgM antibody: structural basis for recognition of B-cell receptors and superantigen activity.

Authors:  M Graille; E A Stura; A L Corper; B J Sutton; M J Taussig; J B Charbonnier; G J Silverman
Journal:  Proc Natl Acad Sci U S A       Date:  2000-05-09       Impact factor: 11.205

2.  The mechanism of aconitase: 1.8 A resolution crystal structure of the S642a:citrate complex.

Authors:  S J Lloyd; H Lauble; G S Prasad; C D Stout
Journal:  Protein Sci       Date:  1999-12       Impact factor: 6.725

3.  Functional role of internal water molecules in rhodopsin revealed by X-ray crystallography.

Authors:  Tetsuji Okada; Yoshinori Fujiyoshi; Maria Silow; Javier Navarro; Ehud M Landau; Yoshinori Shichida
Journal:  Proc Natl Acad Sci U S A       Date:  2002-04-23       Impact factor: 11.205

Review 4.  Advances in determination of a high-resolution three-dimensional structure of rhodopsin, a model of G-protein-coupled receptors (GPCRs).

Authors:  D C Teller; T Okada; C A Behnke; K Palczewski; R E Stenkamp
Journal:  Biochemistry       Date:  2001-07-03       Impact factor: 3.162

5.  Excision of a proposed electron transfer pathway in cytochrome c peroxidase and its replacement by a ligand-binding channel.

Authors:  Robin J Rosenfeld; Anna-Maria A Hays; Rabi A Musah; David B Goodin
Journal:  Protein Sci       Date:  2002-05       Impact factor: 6.725

6.  The 1.6-A crystal structure of the class of chaperones represented by Escherichia coli Hsp31 reveals a putative catalytic triad.

Authors:  Paulene M Quigley; Konstantin Korotkov; Francois Baneyx; Wim G J Hol
Journal:  Proc Natl Acad Sci U S A       Date:  2003-03-05       Impact factor: 11.205

7.  Three-dimensional structure of the Neisseria meningitidis secretin PilQ determined from negative-stain transmission electron microscopy.

Authors:  Richard F Collins; Robert C Ford; Ashraf Kitmitto; Ranveig O Olsen; Tone Tønjum; Jeremy P Derrick
Journal:  J Bacteriol       Date:  2003-04       Impact factor: 3.490

8.  Structural view of a fungal toxin acting on a 14-3-3 regulatory complex.

Authors:  Martin Würtele; Christian Jelich-Ottmann; Alfred Wittinghofer; Claudia Oecking
Journal:  EMBO J       Date:  2003-03-03       Impact factor: 11.598

9.  The mechanism of topoisomerase I poisoning by a camptothecin analog.

Authors:  Bart L Staker; Kathryn Hjerrild; Michael D Feese; Craig A Behnke; Alex B Burgin; Lance Stewart
Journal:  Proc Natl Acad Sci U S A       Date:  2002-11-08       Impact factor: 11.205

10.  A Hoogsteen base pair embedded in undistorted B-DNA.

Authors:  Jun Aishima; Rossitza K Gitti; Joyce E Noah; Hin Hark Gan; Tamar Schlick; Cynthia Wolberger
Journal:  Nucleic Acids Res       Date:  2002-12-01       Impact factor: 16.971

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