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Sequences & structures, software and websites

The research unit “RNA Architecture and Reactivity” gives you access to free scientific software:

Made by Fabrice Jossinet

pym_convrot was created by Ludmila Urzhumtseva and Alexander Urzhumtsev

The purpose of the program

The programme has a double purpose:

  • Conversion of rotation parameters from one convention to another
  • Teaching of various conventions of rotation parameters

The program is a natural methodologic suite of the program ‘convrot’ while technically it is fully original and written in python. All possible conventions of Euler and polar angles can be used, as well as those in terms of direction cosines and in terms of rotation matrices. Interactive demos for input / output conventions help to understand features of these conventions, their differences and common aspects. The presence of symmetry operations and different choice of the unit cell orthogonalisation can be taken into account. For a list of atoms, defined as a PDB or PDBx/mmCIF file, the program can directly recalculate their coordinates accordingly to the transformation obtained (rotation + translation).

System requirements

The basic version of the programme has been developed for Windows, but it also works under Linux and Mac OS.

The program can be run using independently installed Python (versions 2.6 – 2.7 and 3.7 – 3.8), with the wxPython library. When GUI PHENIX is installed, one can also run the program typing a command: ym2_convrot_270820.py or pym3_convrot_270820.py.

Download (source file in wxPython + help files in .pdf: pym2_convrot.zip or pym3_convrot.zip )

The purpose of the program

The program defines the effective resolution of a set of reflections whatever its completeness is.
By definition, the effective resolution d_effective coincides with the highest resolution, d_high, for any complete data set and is different (usually lower) for an incomplete data set.
For anisotropic data sets both the highest and the lowest resolutions, depending on the direction, are determined. The corresponding directions are also identified.
The program defines also the minimum and maximum optical resolution with the values of the amplitudes / intensities of these reflections

Pré-requis informatiques nécessaires au logiciel

The basic version of the program was developed for Windows while it runs also under Linux and Mac OS.
The program can be run using independently installed Python ( starting from version 2.6), wxPython and Numpy libraries.
When GUI PHENIX is installed, one can also run the program typing a command: efresol_3_1.py

No installation is required after efresol_3_1.py is downloaded.


Download

Made by Ludmila Urzhumtseva et Alexandre Urzhumtsev

The purpose of the program

The program compares two crystallographic or cryoEM maps (Fourier syntheses) calculated in the same set of the grid nodes. The metrics used by the program are inspired by a visual comparison of two such maps. For comparison, each grid node is characterized by its quantile rank which is an intrinsic characteristic of an isosurface and which does not change with any monotonous scaling, linear or not. The calculated discrepancy function shows the normalized difference between the regions chosen in these maps applying the same quantile rank cut-off. The peak correlations show the similarity of the peaks, also scaled in the quantile ranks, inside these selected regions.

Logo Compars

Pré-requis informatiques nécessaires au logiciel

The basic version of the program was developed for Windows while it runs also under Linux and Mac OS.
The program can be run using independently installed Python ( starting from version 2.6), wxPython and Numpy libraries.
When GUI PHENIX is installed, one can also run the program typing a command: COMPaRS.py

No installation is required after COMPaRS.py is downloaded.


Download

Made by Ludmila Urzhumtseva et Alexandre Urzhumtsev

Urzhumtseva, L., Afonine, P.V., Adams, P.D., Urzhumtsev, A. (2009) “Crystallographic model quality at a glance”. Acta Cryst., D65, 297-300

The purpose of the program

Shows qualitatively if some models parameters are over- or under-refined compares the model characteristics with those for previously refined models.

The program requires that your computer has the standard Tcl/tk libraries installed (Windows, Linux, MacOSX).

To install the program, put the file polygon0612.tcl in any directory, unzip pdb_2009-04-29_ord.zip files and then look the polygon_readme_2 file.

The third file, polygon_pdb-mvd-examples.zip , contains examples of files that POLYGON can process complementary to the database

Logo Polygon

System requirements

The basic version of the program was developed for Windows while it runs also under Linux and Mac OS.
Python versions starting from 2.6 are required.
The program can be run using independently installed Python and wxPython libraries.
When GUI PHENIX is installed, one can also run the program typing a command
fobscom2_1.py

To install the program, copy the files fobscom2_1.py and fam.itc in any directory.


Download

Made by Ludmila Urzhumtseva et Alexandre Urzhumtsev

Urzhumtseva, L., Urzhumtsev, A. (2008) “Program CRYC3D for geometric computing in crystallography : teaching and applications”. J. Appl.Cryst., 41, 479-480

The purpose of the program

Crystallographic Calculator operates with various 3D objects (or theis lists) expressed in Cartesian or crystallographic (fractions) coordinates or defined in reciprocal space.

Logo Cryc3D

System requirements

The program requires that your computer has the standard Tcl/tk libraries installed (Windows, Linux, MacOSX). If it is not the case, they are free available from a number of sites, for example

  • http://www.tcl.tk/software/tcltk/
  • http://ankif.free.fr/info

or others and automatically installed.

To install the program put the file cryc3D_v4.tcl in any directory at your computer.

IMPORTANT: THE FIRST LINE of cryc3D_v4.tcl should indicate the correct PATH to the command ’wish’ of the Tcl/tk libraries – please correct if it is not the case.


Download

Made by Ludmila Urzhumtseva et Alexandre Urzhumtsev

Urzhumtseva, L.M., Urzhumtsev, A.G. (1997) “Tcl/Tk based programs. II. CONVROT : program to recalculate different rotation descriptions”. J.Appl. Cryst., 30, 402-410

Logo Convrot
Picture of S2S
Assemble – Made by Fabrice Jossinet
Logo RNA society
RNA Society – Made by Fabrice Jossinet

Phusion curve
Traitement des courbes de fusion – Made by François Disdier et Philippe Dumas
thaumatin crystals
BioCrystalloGraphica – Made by Julien Vanwinsberghe et Philippe Dumas