Software Updates

XDSAPP

a graphical user interface for processing diffraction data sets using XDS. It automates the data processing and generates graphical plots of various data set statistics provided by XDS and presenting new features of the dataset, such as radiation decay or the presence of pseudo-translational symmetry and/or twinning, using additional software. Generates intensity files suitable for CCP4, SHELX, and CNS.

PyTOM

a tool that unifies standard tomogram processing steps in a single python-based toolbox. For subtomogram averaging, we implemented an adaptive adjustment of scoring and sampling that clearly improves the resolution of averages compared to static strategies.

PLIP

Focus

an interface for cryo-transmission electron microscopy (cryo-EM) data collection with computer image processing. Focus creates a user-friendly environment to import and manage data recorded by direct electron detectors and perform elemental image processing tasks in a high-throughput manner, while new data is being acquired at the microscope.

PyMOL

a widely used molecular visualization package developed by Warren DeLano, now maintained by Schödinger, LLC. This installation includes official incentive builds of PyMOL.

BiopTools

a set of command line tools written in C and making use of the BiopLib library for manipulation of protein structure and sequence.

RNA Framework

a modular toolkit developed to deal with RNA structure probing and post-transcriptional modifications mapping high-throughput data. Toolkit will help with automatic reference transcriptome creation, automatic reads preprocessing (adapter clipping and trimming) and mapping, scoring and data normalization, and accurate RNA folding prediction by incorporating structural probing data.

OpenJDK

(Open Java Development Kit) a free and open source implementation of the Java Platform, Standard Edition (Java SE).

eiger2cbf

a simple program that converts diffraction images from EIGER in the HDF5 format to the miniCBF format.

Infernal

(INFERence of RNA ALignment) a program that searches DNA sequence databases for RNA structure and sequence similarities and uses a special case of profile stochastic context-free grammars called covariance models (CMs). In many cases It is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence.

MRC Cambridge Image Processing System

a system that determines the structure of macromolecular assemblies. The approach has been to study specimens with some form of symmetry, such as crystals or helical and icosahedral particles, using programs suitable for many kinds of 2-D and 3-D analysis.

XDSGUI

a GUI (graphical user interface) for XDS designed to help both novice and experienced users; it enables XDS data processing without the command line and supplies additional graphical information in a simple, user-modifiable and user-extensible way. It graphically displays the ASCII and cbf files that XDS writes and can run useful shell commands with a simple mouse click.

XDSCC12

a program for generating delta-CC1/2 values, for individual frames, or groups of frames, from a single dataset collected with the rotation method and processed by XDS.