Software for handling macromolecular envelopes

1999 ◽  
Vol 55 (4) ◽  
pp. 941-944 ◽  
Author(s):  
G. Jacob Kleywegt ◽  
Thomas A. Jones
Keyword(s):  
Electron Density ◽  
Local Density ◽  
Computer Programs ◽  
Real Space ◽  
Atomic Model ◽  
Density Correlation ◽  
Phase Extension ◽  
Crystallographic Symmetry ◽  
Averaging Techniques ◽  
Electron Density Averaging

Macromolecular phase-refinement and phase-extension calculations using real-space electron-density averaging techniques require accurate envelopes (or masks) to define the boundaries of each domain or molecule whose density is to be averaged. An extensive set of tools, implemented in four computer programs (O, MAMA, COMA and MASKIT) are described which can be used to generate such envelopes (either from an atomic model or based on local density-correlation maps), to improve them, to remove overlap owing to crystallographic or non-crystallographic symmetry, to display them and to manipulate them in a variety of manners.

IL MILIONE: a suite of computer programs for crystal structure solution of proteins

2007 ◽  
Vol 40 (3) ◽  
pp. 609-613 ◽  
Author(s):  
Maria C. Burla ◽  
Rocco Caliandro ◽  
Mercedes Camalli ◽  
Benedetta Carrozzini ◽  
Giovanni L. Cascarano ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Electron Density ◽  
Heavy Atom ◽  
Direct Methods ◽  
Computer Programs ◽  
Atomic Resolution ◽  
Protein Crystal ◽  
Anomalous Scattering ◽  
Isomorphous Replacement ◽  
Phase Extension

IL MILIONEis a suite of computer programs devoted to protein crystal structure determination by X-ray crystallography. It may be used in the following key activities. (a)Ab initiophasing,viaPatterson or direct methods. The program may succeed even with structures with up to 6000 non-H atoms in the asymmetric unit, provided that atomic resolution is available, and with data at quasi-atomic resolution (1.4–1.5 Å). (b) Single or multiple isomorphous replacement, single- or multiple-wavelength anomalous diffraction, and single or multiple isomorphous replacement with anomalous scattering techniques. In the first step the program finds the heavy-atom/anomalous scatterer substructure, then automatically uses the above information to phase protein reflections. Phase extension and refinement are performed by electron density modification techniques. (c) Molecular replacement. The orientation and the location of the protein molecules are foundviareciprocal space methods. Phase extension and refinement are performed by electron density modification techniques. All the programs integrated intoIL MILIONEare controlled by means of a user-friendly graphical user interface, which is used to input data and to monitor intermediate and final results by means of real-time updated messages, diagrams and histograms.

Experimental assessment of differences between related protein crystal structures

1999 ◽  
Vol 55 (11) ◽  
pp. 1878-1884 ◽  
Author(s):  
Gerard J. Kleywegt
Keyword(s):  
Crystal Structures ◽  
Electron Density ◽  
Local Density ◽  
Structure Refinement ◽  
Protein Structures ◽  
Biological Significance ◽  
Protein Crystal ◽  
Related Protein ◽  
Density Correlation ◽  
Experimental Electron Density

Prior to attaching any biological significance to differences between two related protein crystal structures, it must be established that such differences are genuine, rather than artefacts of the structure-determination protocol. This will be all the more important as more and more related protein structures are solved and comparative structural biology attempts to correlate structural differences with variations in biological function, activity or affinity. A method has been developed which enables unbiased assessment of differences between the structures of related biomacromolecules using experimental crystallographic information alone. It is based on the use of local density-correlation maps, which contain information regarding the similarity of the experimental electron density for corresponding parts of different copies of a molecule. The method can be used to assess a priori which parts of two or more molecules are likely to be structurally similar; this information can then be employed during structure refinement. Alternatively, the method can be used a posteriori to verify that differences observed in two or more models are supported by the experimental information. Several examples are discussed which validate the notion that local conformational variability is highly correlated to differences in the local experimental electron density.

Combination of methods used in the structure solution of pyruvate:ferredoxin oxidoreductase from two crystal forms

1999 ◽  
Vol 55 (9) ◽  
pp. 1546-1554 ◽  
Author(s):  
E. Chabrière ◽  
A. Volbeda ◽  
J. C. Fontecilla-Camps ◽  
M. Roth ◽  
M.-H. Charon
Keyword(s):  
Electron Density ◽  
Real Space ◽  
Molecular Replacement ◽  
Crystal Forms ◽  
Isomorphous Replacement ◽  
Resolution Electron ◽  
Structure Solution ◽  
Phase Extension ◽  
Pyruvate:Ferredoxin Oxidoreductase ◽  
Combination Of Methods

The structure of the homodimeric 267 kDa pyruvate:ferredoxin oxidoreductase (PFOR) of Desulfovibrio africanus was solved with data from two crystals forms, both containing two monomers per asymmetric unit. Phases were obtained from multiwavelength anomalous dispersion (MAD), solvent flattening (SF), molecular replacement (MR) using a 5 Å resolution electron-density search model, multiple isomorphous replacement (MIR) and, finally, electron-density averaging (DA) procedures. It is shown how the combination of all these techniques was used to overcome problems arising from incompleteness of MAD data and weak phasing power of MIR data. A real-space refinement (RSR) procedure is described to improve MR solutions and obtain very accurate protein envelopes and non-crystallographic symmetry (NCS) transformations from 5 Å resolution phase information. These were crucial for the phase extension to high resolution by DA methods.

scholarly journals Imaging electron-density fluctuations by multidimensional X-ray photon-coincidence diffraction

2018 ◽  
Vol 116 (2) ◽  
pp. 395-400 ◽  
Author(s):  
Lyuzhou Ye ◽  
Jérémy R. Rouxel ◽  
Daeheum Cho ◽  
Shaul Mukamel
Keyword(s):  
Charge Density ◽  
Electron Density ◽  
Real Space ◽  
Density Fluctuations ◽  
X Ray ◽  
Density Correlation ◽  
Ab Initio Simulations ◽  
Electron Density Fluctuation ◽  
Point Correlation ◽  
Electron Density Fluctuations

The ultrafast spontaneous electron-density fluctuation dynamics in molecules is studied theoretically by off-resonant multiple X-ray diffraction events. The time- and wavevector-resolved photon-coincidence signals give an image of electron-density fluctuations expressed through the four-point correlation function of the charge density in momentum space. A Fourier transform of the signal provides a real-space image of the multipoint charge-density correlation functions, which reveal snapshots of the evolving electron density in between the diffraction events. The proposed technique is illustrated by ab initio simulations of the momentum- and real-space inelastic scattering signals from a linear cyanotetracetylene molecule.

A Comparison of Two Algorithms for Electron-Density Map Improvement by Introduction of Atomicity: Skeletonization, and Map Sorting Followed by Refinement

1998 ◽  
Vol 54 (1) ◽  
pp. 81-85 ◽  
Author(s):  
F. M. D. Vellieux
Keyword(s):  
Electron Density ◽  
Initial Density ◽  
Acta Cryst ◽  
Density Maps ◽  
Resolution Electron ◽  
Crystallographic Symmetry ◽  
Density Map ◽  
Ornithine Transcarbamoylase ◽  
Electron Density Map ◽  
Pseudo Atom

A comparison has been made of two methods for electron-density map improvement by the introduction of atomicity, namely the iterative skeletonization procedure of the CCP4 program DM [Cowtan & Main (1993). Acta Cryst. D49, 148–157] and the pseudo-atom introduction followed by the refinement protocol in the program suite DEMON/ANGEL [Vellieux, Hunt, Roy & Read (1995). J. Appl. Cryst. 28, 347–351]. Tests carried out using the 3.0 Å resolution electron density resulting from iterative 12-fold non-crystallographic symmetry averaging and solvent flattening for the Pseudomonas aeruginosa ornithine transcarbamoylase [Villeret, Tricot, Stalon & Dideberg (1995). Proc. Natl Acad. Sci. USA, 92, 10762–10766] indicate that pseudo-atom introduction followed by refinement performs much better than iterative skeletonization: with the former method, a phase improvement of 15.3° is obtained with respect to the initial density modification phases. With iterative skeletonization a phase degradation of 0.4° is obtained. Consequently, the electron-density maps obtained using pseudo-atom phases or pseudo-atom phases combined with density-modification phases are much easier to interpret. These tests also show that for ornithine transcarbamoylase, where 12-fold non-crystallographic symmetry is present in the P1 crystals, G-function coupling leads to the simultaneous decrease of the conventional R factor and of the free R factor, a phenomenon which is not observed when non-crystallographic symmetry is absent from the crystal. The method is far less effective in such a case, and the results obtained suggest that the map sorting followed by refinement stage should be by-passed to obtain interpretable electron-density distributions.

scholarly journals CRYO-EM Atomic Model of Brome Mosaic Virus Derived from Direct Electron Detection Images and a Real-Space Model Optimization Protocol

2014 ◽  
Vol 106 (2) ◽  
pp. 600a ◽  
Author(s):  
Zhao Wang ◽  
Corey Hryc ◽  
Benjamin Bammes ◽  
Pavel Afonine ◽  
Joanita Jakana ◽  
...  
Keyword(s):  
Mosaic Virus ◽  
Real Space ◽  
Brome Mosaic Virus ◽  
Atomic Model ◽  
Model Optimization ◽  
Space Model ◽  
Electron Detection

FINDNCS: a program to detect non-crystallographic symmetries in protein crystals from heavy-atom sites

1999 ◽  
Vol 32 (2) ◽  
pp. 365-368 ◽  
Author(s):  
Guoguang Lu
Keyword(s):  
Protein Data Bank ◽  
Root Mean Square ◽  
Heavy Atom ◽  
Data Bank ◽  
Protein Crystals ◽  
Translation Vector ◽  
Mean Square ◽  
Acta Cryst ◽  
Crystallographic Symmetry ◽  
Averaging Techniques

In order to facilitate applications of averaging techniques in the MIR/MAD procedure, a program,FINDNCS, which automatically identifies non-crystallographic symmetry (NCS) from heavy-atom sites, has been developed. The program outputs the NCS operations (a rotation matrix and a translation vector), the corresponding root-mean-square (r.m.s.) deviations of heavy-atom sites, polar angles and screw translations, and writes coordinates of matching sites in Protein Data Bank (PDB) format. The program has an interface with the graphics programO[Joneset al. (1991).Acta Cryst.A47, 110–119] so that the NCS operations can be displayed automatically. In the test examples, all the correct NCS operations were identified and were above the noise solutions.

An Ab-Initio Multicenter Tight-Binding Model for Molecular Dynamics Simulations

1988 ◽  
Vol 141 ◽  
Author(s):  
Otto F. Sankey ◽  
David J. Niklewski
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Local Density ◽  
Tight Binding ◽  
Real Space ◽  
Hamiltonian Matrix ◽  
Binding Model ◽  
Annealing Study ◽  
Total Energies ◽  
Dynamics Simulations

AbstractA new, approximate method has been developed for computing total energies and forces for a variety of applications including molecular dynamics simulations of covalent materials. The method is tight-binding-like and is based on the local density approximation within the pseudopotential scheme. Slightly excited pseudo-atomic-orbitals are used, and the tight-binding Hamiltonian matrix is obtained in real space. The method is used to find the total energies for five crystalline phases of Si and the Si 2 molecule. Excellent agreement is found with experiment. A molecular dynamics simulated annealing study has been performed on the Si 3 molecule to determine the ground state configuration.

First-Principles Calculation of Force Constants and Full Phonon Dispersions

1992 ◽  
Vol 291 ◽  
Author(s):  
Siqing Wei ◽  
M. Y. Chou
Keyword(s):  
First Principles ◽  
Phonon Dispersion ◽  
Local Density ◽  
Real Space ◽  
Force Constants ◽  
First Principles Calculation ◽  
Dynamical Matrix ◽  
Phonon Dispersion Curves ◽  
Super Cell ◽  
Silicon And Germanium

ABSTRACTWe calculated the real-space force constants and full phonon dispersion curves for elemental semiconductors (silicon and germanium) under the local-density approximation with the Hellmann-Feynman forces. The force constants are obtained through super- cell calculations for planar displacements in three different symmetry directions. From these real-space force constants the dynamical matrix for an arbitrary wave vector in the Brillouin zone can be constructed. The procedure is simple in concept and requires no complicated computer programing. It is also possible in principle to handle the anharmonic effects.

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