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MATTHEWS PROBABILITIES

 

A new resolution dependent extension to the basic Matthews Coefficient, introduced by Brian Matthews in the early 70's. Published in Protein Science 12:1865-1871 (2003) 

 

ELBOW ANGLE OF ANTIBODY Fabs

 

Calualtion of elbow angle by the standardized Stanfield method. Needs 2 PDB files, preferrably Kabat-numbered. Published in J. Mol. Biology, 357(5):1566-1574 (2006).

 

SPACE GROUP DECODING

 

A old time favorite. Hammer in a valid space group, and get back transformation matrices, symbolic operators, reciprocal space unit cell, and more....

 

DCC CV-VALUE CALCULATOR

 

This is useful if you have a model railroad and some legacy DCC decoders that do not have direct long address entry of 4-digit decoder addresses. It calculates the register representation (bytes) for CV 17 and CV 18 for the extended 4-digit address.

 

CRYSPRED CRYSTALLIZATION pH PREDICTOR

 

A predictive tool that computes the crystallization success probabilities for a given protein pI based on the empirical pH distribution in the PDB. The pI is generally not the most likely pH for a protein to crystallize! Published in Bioinformatics 20(14): 2171-2174 (2004)

 

ATOMIC SCATTERING FACTORS

 

A little calculator that returns the nine Cromer-Mann coefficients, and a corresponding scattering factor curve for a given B-factor. Also computes the mean displacement equivalent for the given B-factor. See tutorial page for associated exercises.

 

1-D STRUCTURE FACTOR CALCULATION

 

Calculates the structure factors and a 1-d diffraction pattern for a one-dimensional structure with two atoms in the asymmetric unit. Atom positions, atom type, cell dimension, resolution, X-ray wavelength and use of anomalous scattering factors can be selected. See tutorial page for associated exercises.

 

1-D FOURIER AND PATTERSON MAPS

 

From 1-d structure factors (calculated from program above) this applet generates a Forurier map and a Patterson map. Effects of grid spacing, resolution, and Fourier truncation effects can be investigated. See tutorial page for associated exercises.

 

ANOMALOUS DISPERSION RATIOS, WAVELENGTH-ENERGY

 

Very useful tool for MAD experiments, estimating the anomalous (Bijvoet) and dispersive rations at 4 selectable wavelength and a fixed anode around an absorption edge, depending on protein size and number of anomalous scatterers. Also has a wavelength<>energy converter. See tutorial for associated exercises.

 

RECIPROCAL CELL (d-SPACING)and N(ref)

 

Simple calculator for d-spacing from cell constants for any given hkl plane. Also calculates number of total and unique reflections for a given resolution cutoff. 

 

MOLECULAR WEIGHT FROM SEQUENCE

 

Molecular weight, F(000), residue statistics, isoelectric point, and PDB SEQRES residue from sequence.

 

XLAT CELL CONSTANT REFINEMENT

 

Refines cell constants for uniaxial or higher systems using internal standards for different diffraction techniques, wavelengths and standard materials. Please reference XLAT - Least Squares Refinement of Cell Constants, B.Rupp, Scripta Metall. 22, I (1988) when using the program in published work.


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