| Program name | Description | Website or manual | To use it |
|---|---|---|---|
| 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 may be saved as either tiff or postscript files. Adxv will display data from most current detectors. | manual | |
|
adxv -usage (for getting started)
| |||
| align | A program for quick alignment of structures. | ||
|
/progs/align.exe
| |||
| APBS | A software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. | manual | |
|
apbs your-input-file
(or from the pymol menu: Plugins > APBS electrostatics) | |||
| ARP/WARP | A package for automated protein model building and structure refinement. It is based on a unified approach to the structure solution process by combining electron density interpretation using the concept of the hybrid model, pattern recognition in an electron density map and maximum likelihood model parameter refinement. | web | |
|
source /progs/ccp4-7.1/bin/ccp4.setup-sh
Start ccp4i by typing: ccp4i In the ccp4i menu: Model building > ARP/wARP | |||
| Autodock | A suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. AutoGrid pre-calculates these grids. | web | |
|
autodock4
or for autogrid: autogrid4 | |||
| BUSTER | A software system for crystallographic structure refinement by Bayesian statistical methods, from the creators of SHARP. | web | |
|
ask your system administrator for a BUSTER account on neo
| |||
| Canal | A program for analyzing the output from Curves+ applied to a single structure or to MD trajectory files. It makes a statistical analysis including parameter correlations and prepares files for graphical output concerning spatial or time series and histograms. Canal can also analyse data libraries from multiple structures or trajectories. | manual | |
|
[see manual for input file]
/progs/curves/canal | |||
| CCP4 | Collection of crystallography programs. Collaborative Computational Project, Number 4. 1994. | web | |
|
source /progs/ccp4-7.1/bin/ccp4.setup-sh
to start the graphical user interface, type: ccp4i | |||
| Chimera | Molecular graphics program | web | |
|
In a terminal window type: chimera
|
|||
| CNS | Crystallography & NMR System (CNS) is the result of an international collaborative effort among several research groups. The program has been designed to provide a flexible multi-level hierachical approach for the most commonly used algorithms in macromolecular structure determination. Highlights include heavy atom searching, experimental phasing (including MAD and MIR), density modification, crystallographic refinement with maximum likelihood targets, and NMR structure calculation using NOEs, J-coupling, chemical shift, and dipolar coupling data. | web | |
|
Parallel version, use max. 8 threads for jobs with FFT routines, single thread for all other jobs. Run in bash.
source /progs/cns_solve_1.3b/cns_solve_env_sh export OMP_NUM_THREADS=8 run program by: cns_par < input.file > output.file | |||
| Coot | A program for model building, completion and validation. Coot displays maps and models and allows model manipulations such as idealization, real space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers, Ramachandran plots... | web | |
|
Coot is part of the CCP4 distribution, if you have the ccp4 environment set-up, then type:
coot Coot lecture/workshop video with Dr. Paul Emsley at NIH (May 2009) Streaming for Windows: http://www-mslmb.niddk.nih.gov/local-mslmb/Video_512K.wmv Streaming for Mac: http://www-mslmb.niddk.nih.gov/local-mslmb/Video_512K_Stream.rm ) | |||
| CryoSPARC | A state of the art scientific software platform for cryo-electron microscopy (cryo-EM) used in research and drug discovery pipelines. | web | |
|
[once you have an account set up, it runs inside firefox]
localhost:39000 | |||
| Curves+ | A complete rewrite of the Curves approach for analysing the structure of nucleic acids. It respects the international conventions for nucleic acid analysis, runs much faster and provides new data, notably on groove geometries. | web | |
|
[see the manual for input file]
/progs/curves/Cur+ | |||
| EPMR | A program that finds crystallographic molecular replacement solutions using an evolutionary search algorithm. The program directly optimizes the three rotational and three positional parameters for the search model with respect to the correlation coefficient between Fo and Fc. | web | |
|
export OMP_NUM_THREADS=12 (or similar, otherwise it will use all processors)
/progs/epmr-lin64 | |||
| HBPLUS | HBPLUS inputs a Brookhaven Protein Database format file, and outputs a list of potential hydrogen bonds. Prerequisite for Ligplot. | web | |
|
export nucdir=/progs/nucplot
alias nucplot='/progs/nucplot/nucplot.scr' export hbdir=/progs/hbplus alias hbplus='/progs/hbplus/hbplus' | |||
| HKL 2000 | A program package based on the extended versions of Denzo, Xdisplayf and Scalepack. It consists of several subprograms coordinated by the graphical command center. The most important new elements are: strategy and simulation, 3-D processing, mosaicity refinement during processing, variable spot size, easy change of the space group, report generation, etc. | web | |
|
HKL2000
| |||
| Mosflm | A program for integrating single crystal diffraction data from a wide variety of modern area detectors, e.g. from Mar Research, Rigaku/MSC, ADSC, DIP etc. | web | |
|
[also works from the ccp4i GUI or]
imosflm | |||
| Naccess | Naccess calculates the atomic accessible surface defined by rolling a probe of given size around a van der Waals surface. This program is an implimentation of the method of Lee and Richards (1971) J.Mol.Biol.55, 379-400. which does just that. The program is dimensioned for up to 20000 atoms, and allows the variation of the probe size and atomic radii by the user. | web | |
|
/progs/naccess2.1.1/naccess your_pdbfile.pdb
| |||
| NAMD | A parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR. | web | |
|
[example for 8 processor run, where your configuration file is input.conf:]
charmrun ++local +p8 namd2 input.conf > logfile & | |||
| NUCPLOT | Can generate schematic diagrams automatically - directly from the 3D coordinates of the complex as found in a given PDB file. The program works for any single- or double-stranded protein-DNA, DNA-ligand and protein-RNA complexes. | web | |
|
export nucdir=/progs/nucplot
alias nucplot='/progs/nucplot/nucplot.scr' export hbdir=/progs/hbplus alias hbplus='/progs/hbplus/hbplus' | |||
| O | Molecular graphics software with powerful interface. | manual | |
|
setenv ODAT /progs/o13/data
[if you have hardware stereo: setenv DIALS SG , setenv STEREO on] /progs/o13/lin_ono | |||
| PDB2PQR | A package that automates many of the common tasks of preparing structures for continuum electrostatics calculations (APBS), providing a platform-independent utility for converting protein files in PDB format to PQR format. | web | |
|
it can be run from pymol or chimera as part of APBS
| |||
| Phaser | A crystallographic software for phasing macromolecular crystal structures with maximum likelihood techniques. | web | |
|
source /progs/ccp4-7.1/bin/ccp4.setup-sh
start the ccp4 GUI by typing: ccp4i ccp4i menu > molecular replacement > phaser [can be also run from inside Phenix] | |||
| Phenix | PHENIX is a new software suite for the automated determination of macromolecular structures using X-ray crystallography and CryoEM. | web | |
|
. /usr/local/phenix-1.19.2-4158/phenix_env.sh
then type phenix in your work directory | |||
| Pymol | A molecular graphics system with an embedded Python interpreter designed for real-time visualization and rapid generation of high-quality molecular graphics images and animations. | web | |
|
In a terminal window type: pymol
Licensed version documentation, please do not redistribute: http://www-mslmb.niddk.nih.gov/local-mslmb/Quick_Reference.pdf (4 pages) http://www-mslmb.niddk.nih.gov/local-mslmb/Getting_Started_1.pdf (33 pages) http://www-mslmb.niddk.nih.gov/local-mslmb/Getting_Started_2.pdf (26 pages) http://www-mslmb.niddk.nih.gov/local-mslmb/Typed_Commands.pdf (23 pages) http://www-mslmb.niddk.nih.gov/local-mslmb/Expressing_Selections.pdf (24 pages) | |||
| Resolve | A program that improves electron density maps by using a statistical approach to combine experimental X-ray diffraction information with knowledge about the expected characteristics of an electron density map of a macromolecule. Fully integrated into Phenix. | web | |
|
From the Phenix interface: Resolve density modification
| |||
| SHARP | A powerful phasing program based on maximum likelihood methods. | web | |
|
[ask your system administrator for a new sharp account]
logged into neo (ssh -X yourusername@neo) type: firefox -no-remote neo:8080 | |||
| SHELX | A set of programs for crystal structure determination from single-crystal diffraction data. | web | |
|
[Incorporated into the ccp4 program suite]
from ccp4i menu > Experimental phasing > Shelx) | |||
| VMD | A molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. | web | |
|
vmd
| |||
| WHAT IF | Many options are available to visualize proteins (see the menus GRAFIC for normal molecular display, GRATWO for two dimensional graphics, GRAEXT for special effects, COLOUR to colour atoms, residues, molecules, PSTPLT for postscript plots, etc). | web | |
|
/home/vriend/whatif/DO_WHATIF.COM
| |||
| X-util | Collection of crystallographic utility programs from the Uppsala Software Factory. Programs included are: moleman, hetze, xplo2d, pacman, oops, ave, crave, mapman, mappage, mama, mave, etc. | manuals | |
|
The programs are located at:
/progs/xutil_linux/ /progs/rave_linux/ /progs/dejavu_linux/ | |||
| X3DNA | Package for analyzing and rebuilding 3-dimensional nucleic acid structures. | web | |
|
export X3DNA=/progs/X3DNA
export PATH=/progs/X3DNA/bin:$PATH [command line help: ] find_pair -h | |||
| XDS | For processing single-crystal monochromatic diffraction data recorded by the rotation method. XDS can process data images from CCD-, imaging-plate, and multiwire-detectors in a variety of formats. | web | |
|
export PATH=/progs/XDS-INTEL64_Linux_x86_64:$PATH
input files located under: /progs/XDS-INTEL64_Linux_x86_64/XDS_html_doc/html_doc/INPUT_templates/ to run the XDS GUI type: xdsgui | |||
