Direct access Research units

Software and websites

Image of S2S
Assemble2 – Designed by Fabrice Jossinet
Logo RNA society
RNA Society – Designed by Fabrice Jossinet

Myelotracker – Designed by Agnès Gaudry
MicroOMix – Designed by Agnès Gaudry
CAES Alsace – Designed by Agnès Gaudry
Phusion curve
Processing of fusion curves – Designed by François Disdier et Philippe Dumas
thaumatin crystals
BioCrystalloGraphica – Designed by Julien Vanwinsberghe & Philippe Dumas

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

Made by Fabrice Jossinet

Made by Ludmila Urzhumtseva and Alexandre Urzhumtsev

Urzhumtseva, L., Urzhumtsev, A. (2016) “COMPaRS : a stand-alone program for map comparison using quantile rank scaling”. J Appl Cryst., 49(6), 2270-2275

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

Computer requirements for the software

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

No installation is required after downloading COMPaRS.py.


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Made by Ludmila Urzhumtseva and Alexandre Urzhumtsev

The purpose of the program

The suite dec3D has been developed to decompose spherically symmetric functions in three-dimensional space into a sum of terms of a special form, each reproducing a shell solitary wave (Urzhumtsev & Lunin; BioRxiv, https://doi.org/10.1101/2022.03.28.486044 ). An example of such functions is atomic images at a limited resolution, with a peak in the origin surrounded by Fourier ripples. The terms are expressed through a specially designed function W(r;m,n). One of its properties is that, once decomposed, an atomic image can be then calculated with any value of the displacement parameter (ADP) and at any resolution by a simple modification of the parameter values m and n. Algorithms and programs are described in Urzhumtseva et al., http://arxiv.org/abs/2206.08935

Computer requirements for the software

The software has been developed under Windows.

The fortran version (4 programs) has been compilied with g77. The python version (4 programs + GUI script) was developed in Python3 (Python 3.7.4 and higher) using numpy (1.18.4 and higher) and scipy (1.6.3 or higher).

The GUI version requires additionally wxPython (4.0.6 or higher) and matplotlib (3.4.3 or higher) ; it is independent of other individual programs of the package.

The programs may be compatible with some earlier versions of python and its libraries.

For the fortran version, simply compile dec3D-atom and dec3D-sum and run respective make-files to generate exe files of dec3D and dec3D-sumr.

The commands to run the command line versions are:

  • dec3D***.exe
  • dec3D***.py

where *** is ignored for the main program and is -atom, -sum, -sumr for other programs.

Each *.dat file contains the full list of parameters, many of them being optional and can be removed.


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Made by Ludmila Urzhumtseva and 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

The crystallographic calculator works with various 3D objects (or lists of theis) expressed in Cartesian or crystallographic coordinates (fractions) or defined in the reciprocal space.

Logo Cryc3D

System requirements

The program requires that your computer has the standard Tcl/tk libraries (Windows, Linux, MacOSX). If not, they are available for free on 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, place the cryc3D_v4.tcl file in any directory on your computer.

IMPORTANT: The first line of the cryc3D_v4.tcl file should show the correct path to the “wish” command in the Tcl/tk libraries – please correct if this is not the case.


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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

Computer requirements for the software

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.


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Made by Ludmila Urzhumtseva and Alexandre Urzhumtsev

Urzhumtseva, L., Urzhumtsev, A. (2011) “A program to analyze the distributions of unmeasured reflections”. J Appl Cryst., 44(4), 865-872

The purpose of the program :

to study the distribution of unmeasured diffraction data. Differently from usual statistics of overall data completeness, the program shows how these reflections are distributed in reciprocal space. The program identifies continuous regions of unmeasured (absent) data and displays the sphere of reciprocal space at a given resolution indicating the measured and unmeasured reflections. Unmeasured reflections can be shown all together or by the continuous regions to which they belong.

logo FORBSCOM

System requirements

The basic version of the program was developed for Windows while it runs also under Linux and Mac OS.

For Python 2: Python versions starting from 2.6 + wxPython library.
For Python 3: Python versions starting from 3.7 + wxPython library.
To install the program, copy the files fobscom2_1.py (version Python 2) or fobscom3_1.py (Python 3 version) et fam.itc and fam.itc in any directory.

Download:

Made by Ludmila Urzhumtseva and 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 program requires that your computer has the standard Tcl/tk libraries installed (Windows, Linux, MacOSX).

To install the program, place the files polygon0612.tcl and pdb_2009-04-29_ord in the same directory.

IMPORTANT: The first line of the polygon0612.tcl file must show the correct path to the “wish” command in the Tcl/tk libraries – please correct if this is not the case.


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pym_convrot was created by Ludmila Urzhumtseva and Alexander Urzhumtsev

Urzhumtseva, L., Urzhumtsev, A. (2019) “py_convrot: rotation conventions, to understand and to apply”. J Appl Cryst., 52, 869-881

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: pym2_convrot_270820.py or pym3_convrot_270820.py.

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