CCP14 Homepage - Single Crystal and Powder Diffraction - Problems and Solutions - Some Starting links to Protein Crystallography Software/Macromolecular Crystallographic Software

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Collaborative Computational Project Number 14

for Single Crystal and Powder Diffraction

CCP14

Some Starting links to Protein Crystallography Software/Macromolecular Crystallographic Software

The CCP14 Homepage is at http://www.ccp14.ac.uk

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List of Software via UAB Center for Macromolecular Crystallography - http://www.cmc.uab.edu/
List of Software via UAB Center for Macromolecular Crystallography - http://ppcii.scripps.edu/links.html
List of Software via "Practical Protein Crystallography" homepage - http://imsb.au.dk/~mok/o/
MAIN (is an interactivelly driven computer program dealing with computational parts of macromolecular crystallography) : - http://www-bmb.ijs.si/doc/index.html. (Thanks to Lalji for this link)
Classification of Software for Macromolecular Crystallographers: - http://www-bmb.ijs.si/doc/other_index.html.
List of Software via PDB homepage - http://www.rcsb.org/pdb/software-list.html
Macromolecular Crystallography Program Documentation at CSB Yale University -
- Data Reduction and Analysis Applications - http://www.csb.yale.edu/userguides/datamanip/csb_hm_dm.html
- Table of Contents for Molecular Modeling and Simulation Applications - http://www.csb.yale.edu/model_toc.html
- Table of Contents for Model Analysis Applications - http://www.csb.yale.edu/model_anal.html
- Protein, DNA and Diffraction Databases - http://www.csb.yale.edu/userguides/databases/csb_hm_db.html
Macromolecular Crystallography Program Documentation at University of Massachusetts Medical School - http://bragg.ummed.edu/programs3a.html
DENZO Data Processing - http://www.hkl-xray.com
DPS/MacCHESS Data Processing - http://www.chess.cornell.edu/MacCHESS/processing_gui.html
PHASES Suite - http://www.imsb.au.dk/~mok/phases/phases.html
CCP4 Suite - http://www.dl.ac.uk/CCP/CCP4/main.html
- CCP14 FAQ's - http://www.dl.ac.uk/CCP/CCP4/FAQ/html/ccp4faq.html
- CCP14 Suite for LINUX in RPM format - http://imsb.au.dk/~mok/linux/dist/Scientific_Crystallography.html
- RPM Find - http://rufus.w3.org/linux/rpm2html/rpmfind.html
- PROLSQ Refinement (CCP4: Supported Program)
- REFMAC Refinement (CCP4: Supported Program)
SHELX refinement and structure solving program - http://shelx.uni-ac.gwdg.de/SHELX/index.html
TNT Macromolecular Refinement Package - http://www.uoxray.uoregon.edu/tnt/welcome.html
- TNT FAQ's - http://www.uoxray.uoregon.edu/tnt/faq.html
MAIN - interactivelly driven computer program dealing with computational parts of macromolecular crystallography - http://www-bmb.ijs.si/doc/
MICE - Molecular Sciences and Interaction Environments - http://mice.sdsc.edu/
CNS - Crystallography and NMR System - http://xplor.csb.yale.edu/cns_solve/
PROTEIN - A program system for the crystal structure analysis of macromolecules - http://www.biochem.mpg.de/PROTEIN/
SOLVE - Automated crystallographic structure solution for MIR and MAD - http://www.solve.lanl.gov/
- SOLVE Manual - http://www.solve.lanl.gov/manual/table-of-contents.html
Watncs - Pick water molecules which follow NCSs and sort out them to NCS asymmetric unit - http://gamma.mbb.ki.se/~guoguang/watncs.html
Conscript (A program for generating electron density isosurfaces for presentation in protein crystallography) - http://www.bioresi.com.au/conscript/
whatif - "WHAT IF is a versatile protein structure analysis program that can be used for mutant prediction, structure verification, molecular graphics" - http://www.sander.embl-heidelberg.de/whatif/
SnB - Shake-and-Bake - Structure Solution - http://www.hwi.buffalo.edu/SnB/
LIGPLOT - Program for automatically plotting protein-ligand interactions - http://www.biochem.ucl.ac.uk/bsm/ligplot/ligplot.html
HBPLUS - program for calculating hydrogen bonds and hydrophobic contacts for plotting by LIGPLOT - http://www.biochem.ucl.ac.uk/~mcdonald/hbplus/home.html
Procheck - A program that checks the stereochemical quality of a protein structure - http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html
Profit - A program for fitting protein structures on to each other - http://www.biochem.ucl.ac.uk/~martin/programs/index.html#profit
PROCOMP - Compares residue-by-residue geometry of a set of closely-related protein structures. - http://www.biochem.ucl.ac.uk/~roman/procheck_comp/procheck_comp.html
- NT Version - ftp://www-structure.llnl.gov/Procheck_NT/
NACCESS - program for computing solvent accessible areas - http://sjh.bi.umist.ac.uk/naccess.html
AMBER - Assisted Model Building with Energy Refinement - http://www.amber.ucsf.edu/amber/amber.html
ARP and WARP Phasing Software - http://www.embl-hamburg.de/ARP
Cai X.-J. Zhang's Molecular Replacement Package - http://omrf.uokhsc.edu/~zhangc/mrx/mrx.html
Michael S. Chapman's Real Space Refinement Package - http://www.sb.fsu.edu/~rsref/
Buster - (A program for recovering missing phase information by Bayesian inference) - http://lagrange.mrc-lmb.cam.ac.uk/
SHARP (A Statistical Heavy Atom Refinement and Phasing program) - http://lagrange.mrc-lmb.cam.ac.uk/sharp/SharpHome.phtml
The Biochemist's ToolBox (links to databases, etc) - http://www.biochem.ualberta.ca/Biochem/BioLinks.html
3D Reconstruction (Cryo-electron microscopy (Virus reconstruction), etc)- http://biocomp.stanford.edu/3dreconstruction/index.html
EMBL Virus Structures Image Database - http://www.embl-heidelberg.de/ExternalInfo/fuller/icos0.html
EMBL Virus Structures Image Database - http://www.bocklabs.wisc.edu/virusviztop.html
Image Library of Biologial Macromolecules Image Database - http://www.imb-jena.de/IMAGE.html
Molecules-R-Us (NIH) Image Database - http://molbio.info.nih.gov/doc/mrus/mol_r_us.html
SWISS-3DIMAGE Annotated 3-D Image Database - http://www.expasy.ch/sw3d/sw3d-top.html
An Internet course on The Principles of Protein Structure - http://www.cryst.bbk.ac.uk/PPS/index.html
SWISS-MODEL - An Automated Comparative Protein Modelling Server - http://www.expasy.ch/swissmod/SWISS-MODEL.html
Glaxo Wellcome Experimental Research presents the Swiss-PdbViewer Software for Mac PC SGI and Linux - http://www.expasy.ch/spdbv/mainpage.htm
- Includes tutorials explaining "how to compute molecular surfaces, electrostatic potentials and how to perform energy minimization directly from the program".
- Australian Mirror - http://expasy.proteome.org.au/spdbv/
- Taiwan Mirror - http://expasy.nhri.org.tw/spdbv/
- Israel Mirror - http://inn-prot.weizmann.ac.il/spdbv/mainpage.htm
- Examples Page - http://chemb16.leidenuniv.nl/~armand/ including pictures page http://chemb16.leidenuniv.nl/~armand/pict.html (Very withit site - also appeciates importance of quake and has relevant quake link - http://www.planetquake.com)
PovRay (Persistance of Vision Raytracing software) - http://www.povray.org
X-plor (Yale) - http://xplor.csb.yale.edu/xplor-info/
- XPLOR Manual - http://xplor.csb.yale.edu/xplor-info/xploronline.html
Molecular Structure Determination Packages Supported at Pittsburgh Supercomputing Center (PSC), Carnegie Mellon University - http://www.psc.edu/general/software/categories/molecular_structure_determination.html
X-plor (MSI) - http://www.msi.com/about/offers/xplor/index.html
Xsight (MSI) suite - http://www.msi.com/solutions/products/insight/modules/xsight.html
XtalView Refinement, fitting and graphics (Structure and Contour Map) - http://www.sdsc.edu/CCMS/Packages/XTALVIEW/xtalview.html and http://www.scripps.edu/pub/dem-web/
TURBO_FRODO Web site - http://afmb.cnrs-mrs.fr/TURBO_FRODO/turbo.html
- "Turbo-Frodo reads and displays X-ray density maps. Electron density maps are calculated by the program Mappage, available in most crystallographic packages"
- TURBO_FRODO Image Gallery - http://afmb.cnrs-mrs.fr/TURBO_FRODO/gallery.html
- TURBO_FRODO FAQs - http://afmb.cnrs-mrs.fr/TURBO_FRODO/faq.html
TURBO_FRODO Description with on-line manual - http://www.med.yale.edu/computing/acadcomp/research/turbo/turbo_descrip.html
MAPS (an automated program for Multiple Alignment of Protein Structures) - http://gamma.mbb.ki.se/~guoguang/maps.html | http://bioinfo1.mbfys.lu.se/TOP/maps.html
List of available programs from Guoguang Lu - http://bioinfo1.mbfys.lu.se/~guoguang/prog.html
- DIFLIST Checking the atoms with negative value in Fo-Fc map
- DOMID Identify protein domains from 3d structures
- FINDNCS find out NCS operations from heavy atom sites
- FIT A structure comparison utility program
- FOCUS A program which draw the atoms, bonds and their density maps
- MAPS An automated program for Multiple Alignment of Protein Structures
- MATROT An utility program for rotation functions
- PATTERN A precession simulation program (figure)
- PSHIF Detect domain movement
- PERCENT calculate percentage of completness
- PDBSYMOP give symmetric operations to PDB
- REINDEX reindex the ascii hkl reflxn file by a transform matrix
- ROTCENTR rotate and translate molecule
- TOP An automatic structure comparison program (Web server)
- WATNCS Pick waters which follow NCSs and sort out to NCS assymetric unit
FRODO/TOM Molecular Modelling Program - http://www.iucr.org/sincris-top/logiciel/prg-frodo.html
Online Documentation for Macromolecular software (Frodo, etc, etc, etc) - http://www.imb-jena.de/www_sbx/sbx_dhp_od.html
"O" (includes links to other software) Graphics - http://imsb.au.dk/~mok/o/
- O FAQ's - http://imsb.au.dk/~mok/o/ofaq/ofaq.html
- MolScript documentation in SGML format - http://imsb.au.dk/~mok/o/molscript/molscript.html
MolScript v. 2.0 Graphics (MolScript: The Official Web Site) - http://www.avatar.se/molscript/
- Links to:
- The OpenGL Organization web site - http://www.opengl.org
- The OpenGL WWW Center at SGI. - http://www.sgi.com/Technology/openGL/
- The OpenGL Web Site at SGI. - http://reality.sgi.com/opengl/
- Mesa, by Brian Paul: the OpenGL look-alike 3D-rendering software library - http://www.ssec.wisc.edu/~brianp/Mesa.html
- The VRML Consortium. - http://www.vrml.org/
Spock is a full-featured molecular graphics program, knows about crystallographic symmetry (and also allows shared screens/conferencing over the internet): http://quorum.tamu.edu/spock/
- Image Gallery (looks very nifty) - http://quorum.tamu.edu/spock/images.html
RasMol and Chime Graphics - http://www.umass.edu/microbio/rasmol/
Herbert Bernsteins version of RasMol Graphics - http://www.bernstein-plus-sons.com/software/rasmol/doc/rasmol.html
Raster3D Graphics - http://www.bmsc.washington.edu/raster3d/

The DNA modelling course HomePage
- http://lcvmwww.epfl.ch/~lcvm/dna_teaching/index.html
Web cutter.
- "Webcutter is an on-line tool for restriction mapping nucleotide sequences. It features: Customizable enzyme database Monthly enzyme updates Automatic sequence search-and-input Quick links to gene searches Worldwide accessibility via internet "
- http://firstmarket.com/firstmarket/cutter/
- http://www.medkem.gu.se/cutter/
PovChem
- "PovChem takes molecules in the PDB format, lets you to set up a picture with fine control over details of the illustration - colors, atom and bond radii, view orientation, etc. It will even calculate and display hydrogen bonds."
- http://www.ChemicalGraphics.com/PovChem/
DNA (organics and proteins) Graphics Created with PovChem for Windows, Mac and UNIX
- http://www.chemicalgraphics.com/paul/DNA.html
Ribbons Software Home Page (Molecular Graphics)
- http://sgce.cbse.uab.edu/ribbons/
Other molecular graphics sites
- http://www.avatar.se/molscript/other_molgraph.html
MOLMOL - MOLecule analysis and MOLecule display
- http://www.mol.biol.ethz.ch/wuthrich/software/molmol/
PREPI
- "PREPI is a molecular graphics program which can be used to EASILY produce and interactively manipulate many different types of molecular representations (cartoons) as well as providing quantative information on secondary structural topology. The program is not just limited to proteins, but can also show cartoon representations of NUCLEIC ACIDS."
- http://www.bmm.icnet.uk/people/suhail/prepi.html
WHAT IF
- "WHAT IF is a versatile protein structure analysis program that can be used for mutant prediction, structure verification, molecular graphics, etc."
- http://www.cmbi.kun.nl/whatif/
3D modeling homepage
- http://swift.embl-heidelberg.de/
3D modeling services
- http://swift.embl-heidelberg.de/future/other.html
BIOcomputing 3D modelling unit servers
- "PredictProtein. Multiple alignments; predictions of secondary structure, accessibility, and helical transmembrane regions; (threading); evaluation of prediction accuracy. K2D Protein secondary structure prediction from CD spectra. PROPSEARCH Compositional search of sequence databases using a sequence or experimental amino acid analysis data. MAXSPROUT (Re)constructing full coordinates from C-alpha atoms. DALI. Comparison of protein structures in 3D Protein Structure Verification 'BIOTECH' Protein Structure Verification server. Small molecule topology maker The PRODRG server takes a small molecule and produces WHATIF and GROMOS topology files."
- http://swift.embl-heidelberg.de/servers/
The EMBL-Heidelberg Amino Acid Analysis Server
- http://www.embl-heidelberg.de/aaa.html
3D modelling services
- "DSSP: Definition of Secondary Structure of Proteins FSSP: Families of Structurally Similar Proteins HSSP: Homology-derived Secondary Structure of Proteins PDBSELECT: Unique subset of 3-D protein structures PDBFINDER: Your entry into the PDB database PDBREPORT: Structure verification reports for PDB structures GPCRDB: G protein-coupled receptor (GPCR) data Modules in extracellular proteins"
- http://swift.embl-heidelberg.de/future/databases.html
DNA Sequence & Structural Analyses
- (almost every link imaginable relating to DNA sequence analysis plus DNA to protein sequencing)
- "DNA Sequence Homology Analysis and Searching DNA/RNA Structure & Function Analyses Multifunction Search & Data Retrieval Searchers Nucleotide Sequence Alignment Servers Sequence Manipulation Tools Miscellaneous Analyses "
- http://www.unl.edu/stc-95/ResTools/biotools/biotools16.html

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