X-ray Crystallography

SBGrid supports 47 x-ray crystallography software titles. The following software packages are supported by SBGrid; availability of a specific software package may be limited based on license requirements.

Software Title Description Linux 32-bit Linux 64-bit OS X Intel Links

3DNA

- a package for analyzing, visualizing and rebuilding 3-dimensional nucleic acid structures. 3DNA was created by Dr. Xiang-Jun Lu in the laboratory of Professor Wilma K. Olson at the Department of Chemistry and Chemical Biology, Rutgers-the State University of New Jersey.

yes yes yes

adxv

- displays protein crystallography X-ray diffraction data. The data may be displayed as a 2-D image, 3-D wire mesh or as integer pixel values. Data files may be saved in tiff or postscript format. adxv was written by Andrew Arvai.

yes yes yes

ARP/wARP

An interpretation of crystallographic electron density maps and automatic construction and refinement of macromolecular models. At the request of the developer, this software is licensed on a per-user basis. To obtain an ARP/wARP license and enable use in the SBGrid environment, each user should: - visit the [ARP/wARP website](http://www.embl-hamburg.de/ARP/) to request a license. - download any of the current versions via your web browser. - in the shell run 'sbgrid-register -r path/to/the/arp_warp-file-you-downloaded'. - open a new terminal to utilize the newly registered software title. Please cite the applications of ARP/ wARP that you have used. Please consult the ARP/ wARP log file for the most relevant citation. The complete citation list is in the [ARP/wARP manual][arpman] . [arpman]:http://www.embl-hamburg.de/ARP/Manual/UserGuide7.4.html#x1-530005

yes yes yes

autoPROC

autoPROC combines third-party processing programs with new tools and an automated workflow script for automated treatment of multi-sweep X-ray diffraction data. <br><br> autoPROC is freely available to academic labs, but each lab must register with Global Phasing before this software can be used. To include this software in your installation, please submit a license request to <a href = "http://www.globalphasing.com/autoproc/licence/request.html">http://www.globalphasing.com/autoproc/licence/request.html</a>, then copy your license file to /programs/local/autoproc/autoproc_licence, and the software will start working.

yes yes

BALBES

- aims to integrate into one system all the components necessary for finding a solution structure by MR. It consists of a database, scientific programs and a python pipeline. The system is automated and needs no user intervention when running a complicated combination of jobs, such as model searching, molecular replacement and refinement.

yes yes yes

BEST

- a program for optimal planning of X-ray data collection from protein crystals. <br><br> BEST is freely available to non-profit labs, but each lab must register with EMBL before we can install the software. To include this software in your installation, please register here <a href = "http://www.embl-hamburg.de/BEST/download_request3.1.html">http://www.embl-hamburg.de/BEST/download_request3.1.html</a>, then send a copy of your registration confirmation to us at <a href = "mailto:licensing@sbgrid.org">licensing@sbgrid.org</a>. <br><br>

yes yes yes

BnP

- Buffalo and Pittsburgh) an interface for complete protein phasing suite includes SnB and Phases.

yes yes

BUSTER

BUSTER is a software system for crystallographic structure determination by Bayesian statistical methods <br><br> BUSTER is freely available to academic labs, but each lab must register with Global Phasing before this software can be used. To enable this software in your installation, please submit a license request to <a href = "http://www.globalphasing.com/autoproc/licence/request.html">http://www.globalphasing.com/autoproc/licence/request.html</a>, then copy your license file to /programs/local/buster/buster_licence, and the software will start working.

yes

CCP4

- (Collaborative Computational Project, Number 4) a collection of programs and associated data and software libraries which can be used for macromolecular structure determination by X-ray crystallography. <br><br> CCP4 is freely available to non-profit labs, but each lab must complete the CCP4 <a href= "http://www.ccp4.ac.uk/ccp4license.php">license</a> and return the executed document directly to the STFC Daresbury Laboratory, as specified on the CCP4 webpage.

yes yes yes

CNS

- an X-ray crystallography suite used for refinement, phasing, and molecular replacement

yes yes yes

Coot

- (Crystallographic Object-Oriented Toolkit) supports model building and real space refinement. The application interfaces with refmac, Phenix, and several other applications. Coot was recognized as the best structural biology application in 2008 by SBGrid.

yes yes yes

DPS

- (Data Processing Suite) a suite of programs for processing of single crystal X-ray diffraction data of proteins, viruses, nucleic acids and other large biological complexes with an emphasis on data collected at synchrotron sources. The software website has not been updated since 2000, but software updates are posted on a regular basis.

yes yes

d*TREK

- a software suite and toolkit that processes single crystal X-ray diffraction images from two-dimensional position sensitive detectors. <br><br> d*TREK is a commercial software application that we can include in your installation for ease of use, but that requires you or your institute to have a current license in place. To enable the SBGrid installation for d*TREK please send an email to <a href = "mailto:licensing@sbrid.org">licensing@sbgrid.org</a> with information confirming that your license is active. <br><br>

yes yes yes

Eden

- a crystallographic real-space electron-density refinement and optimization program that produces electron density maps with minimal model bias in a robust manner.

yes yes yes

Elves

- automates most of the repetitive and mindless procedures used in solving macromolecular crystal structures, and is capable of autonomously carrying out all the steps needed to convert raw X-ray diffraction image data to a phased electron density map.

yes yes yes

EPMR

- a program that finds crystallographic molecular replacement solutions using an evolutionary search algorithm. The program directly optimizes three rotational and three positional parameters for the search model with respect to the correlation coefficient between Fo and Fc.

yes yes yes

HKL2000

- A data processing suite for X-ray crystallography that provides a sleek interface for devising a data collection strategy and processing data. HKL is based on the extended versions of Denzo, Xdisplayf and Scalepack.HKL was developed and is maintained by Wladek Minor (University of Virginia). <br><br> HKL2000 is a commercial software application that we can include in your installation for ease of use, but that requires you or your institute to have a current license in place. To enable the SBGrid installation for HKL2000, copy the license file to the directory /usr/local/lib on each machine and HKL2000 will work.

yes yes yes

HKL2MAP

A graphical user-interface for macromolecular phasing. HKL2MAP is freely available to non-profit labs, but each lab must register with EMBL before we can install the software. To include this software in your installation, please register [here][1], then send a copy of your registration confirmation to us at <licensing@sbgrid.org>. [1]: http://webapps.embl-hamburg.de/bundle/download.php?hkl2mp=true&sitcom=false

yes yes yes

iMosflm

- a data processing application for macromolecular crystallography. iMosflm (Graphical User Interface) and Mosflm (data processing application) are distributed with this package. iMosflm is maintained by Harry Powell and distributed under a CCP4 license.

yes yes yes

LAFIRE

- (Local-correlation-coefficient-based Automatic FItting for REfinement) is an automatic refinement system for protein crystallography. The system starts with an initial model (approximate or partial model) and finishes with the final structure including water molecules. LAFIRE uses the refinement programs CNS or Refmac5.

yes yes yes

MAIN

- a model building application for X-ray crystallography.

yes yes yes

MIExpert

- an expert system for running molecular replacement and refinement applications, and analyzing the data obtained from high-throughput co-crystallography and fragment screening projects. MIExpert is a module of MIFit.

yes

MIFit

- an interactive graphics application for molecular modeling, fitting, and refinement of protein structures from X-ray crystallography developed by Bradley Smith as an Open Source project while working for Rigaku/MSC Inc. A particular focus of the MIFit software is the efficient solution and analysis of protein:ligand complexes.

yes yes

MOSFLM

- a package for processing film and image plate data.

yes yes yes

O

- a model building application for X-ray crystallography.

yes yes yes

PHENIX

- (Python-based Hierarchical Environment for INtegrated Xtallography) provides tools for automated structure solution by X-ray crystallography. The PHENIX software provides algorithms to proceed from reduced intensity data to a refined molecular model, and facilitate structure solution for both the novice and expert crystallographer. We also maintain a recent PHENIX nightly build in the software suite.

yes yes yes

PROFphd

- a new package added as part of the pipeline to create fragments for Rosetta. For commercial users, Biosof LLC (www.bio-sof.com) offers additional customization and data analysis of PROFphd.

yes yes yes

RCrane

- allows for semi-automated building of RNA structure within Coot.

yes yes yes

Reduce

- a program for adding hydrogens to a Protein DataBank (PDB) molecular structure file. Hydrogens are added in standardized geometry with optimization of the orientations of OH, SH, NH3+, Met methyls, Asn and Gln sidechain amides, and His rings. Both proteins and nucleic acids can be processed. HET groups can also be processed as long as the atom connectivity is provided.

yes yes yes

REFMAC

- carries out rigid body, tls, restrained or unrestrained refinement against Xray data, or idealisation of a macromolecular structure. It minimises the coordinate parameters to satisfy either a Maximum Likelihood or Least Squares residual. There are options to use different minimization methods. (At the moment only CGMAT is active.) REFMAC also produces an MTZ output file containing weighted coefficients for SigmaA weighted mFo-DFcalc and 2mFo-DFcalc maps, where missing data have been restored.

yes yes yes

REPLACE (GLRF and TF)

- a suite of programs for molecular replacement calculations. It currently consists of two major programs, GLRF for rotation function calculations and TF for translation function calculations. In addition, a small program (ANGCAL) is a convenient tool for conversions between angles and matrices.

yes yes yes

Ringer

- a program to detect molecular motions by automatic electron density sampling.

yes yes yes

RSRef2000

- supports real-space simulated annealing refinement with X-ray data. RSRef uses an electron density function that is resolution dependent, so that it accurately models a medium resolution map. When combined with TNT’s Geometry, or CNS, full stereochemical refinement is possible. RSRef can be used to quickly pre-refine a protein structure during or after model building, or to completely refine structures with high non-crystallographic symmetry, that have good electron density. Application developed by Michael Chapman at Florida State University.

yes yes

SHARP/autoSHARP

- an automated structure solution pipeline built around the heavy-atom refinement and phasing program SHARP, the density modification program SOLOMON, and the ARP/wARP package for automated model building and refinement (using REFMAC). It allows fully automated structure solution, from merged reflection data to an initial model, without any user intervention.

yes yes yes

SHELX-2013

A set of programs for macromolecular phasing. SHELXC is designed to provide a simple and fast way of setting up the files for the programs SHELXD (heavy atom location) and SHELXE (phasing and density modification) for macromolecular phasing by the MAD, SAD, SIR and SIRAS methods. hkl2map provides a simple user interface to SHELX and is installed separately. SHELX was written and is actively maintained by George Sheldrick and his group at the University of Gottingen. SHELX-2013 is freely available to non-profit labs, but each lab must register with George Sheldrick before we can install the software. To include this software in your installation, please register [here][1] then send a copy of your registration confirmation to us at <licensing@sbgrid.org>. [1]: http://shelx.uni-ac.gwdg.de/SHELX/register.php

yes yes yes

SHELX-97

- a set of programs for macromolecular phasing. SHELXC is designed to provide a simple and fast way of setting up the files for the programs SHELXD (heavy atom location) and SHELXE (phasing and density modification) for macromolecular phasing by the MAD, SAD, SIR and SIRAS methods. hkl2map provides a simple user interface to SHELX and is installed separately. SHELX was written and is actively maintained by George Sheldrick and his group at the University of Gottingen. <br><br> This version of SHELX-97 is now obsolete and has been replaced by SHELX-2013. If you would like SHELX-2013 included in your installation, please see details on how to register <a href = "http://www.sbgrid.org/software/title/SHELX-2013">here</a>.

yes yes yes

SnB

- determination of the anomalously scattering substructures of selenomethionyl-substituted proteins containing as many as 160 Se sites. SnB is based on Shake-and-Bake, a dual-space direct-methods procedure.

yes yes yes

SOLVE/RESOLVE

- a program that can automatically search for heavy atom sites, calculate initial phases and perform density modification.

yes yes yes

SOMoRe

- 6D global search and multi-start optimization molecular replacement package.

yes yes yes

Untangle

- a program designed to separate overlapping diffraction patterns from a set of crystals with slightly different orientations. The program can read x files from the HKL Package and CCP4 MTZ files. It can output data files from which the offending reflections have been removed. A case study for a dataset from an aggregate with three dominant subcrystals can be found here.

yes yes

USF Gerard Utilities

- the Swiss Army knife of crystallography tools. The installation includes the packages from RAVE, SBIN, X-UTIL, VOIDOO, DEJAVU and SPASM.

yes yes yes

WASP

- searches PDB files for misidentified water molecules that should be modeled as cations.

yes yes yes

XDS

- X-ray Detector Software for processing single-crystal monochromatic diffraction data recorded by the rotation method. Written by Wolfgang Kabsch (see Tales about Developers section on SBGrid website).

yes yes yes

XDSi

- allows processing of datasets in a given directory with minimum effort when you supply it with a result directory and the directory where your frames are stored. All datasets consisting of more than 100 frames within the given directory and all its subdirectories will be processed. For each dataset a space group assignment is done using POINTLESS from the CCP4 software package. Plots of the most informative statistics of INTEGRATE.LP, CORRECT.LP and XDSSTAT.LP are generated for each dataset. A plot comparing Rmeas, I/sig and Completeness of all the processed datasets is generated. You can also generate plots for datasets that have been processed using XDS without XDSi. Note that this software requires 'kpdf' to display its output.

yes yes yes

XDSSTAT

- a home-brewn program that prints various statistics (that are not available from XDS itself) in the form of tables and images.

yes yes yes

XDS-Viewer

- an X-ray diffraction and control image viewing utility for data processed using the XDS program package.

yes yes yes

XIA2

- an automated data reduction system designed to work from raw diffraction data and a little metadata, and produce usefully reduced data in a form suitable to immediately start phasing and structure solution, e.g. through Mr BUMP or your favorite experimental phasing suite.

yes yes yes