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The EMBL-HH Automated Crystal Structure Determination Platform

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Version 1.08 includes
  • Addition of Radiation Induced Phasing (RIP) phasing
  • Addition of MRRIP phasing
  • Addition of S-SAD phasing
  • ARP/wARP 7.0.1 updated to 7.1
  • CCP4 ccp4-6.0.2 updated to ccp4-6.1.1
  • Addition of Beta version of SHELXE for model building
  • Addition of RESOLVE for sequence docking to SHLEXE polyala model in MRSAD/MRRIP protocol
  • Addition of SAD function for ARP/wARP model building in MRSAD/MRRIP protocol
  • Refinement for model generated from modelbuilding program in in MRSAD/MRRIP protocol
  • Iterative model building using BUCCANER for low resolution data in MRSAD/MRRIP
  • Cluster analysis of SHELXD trails in weak cases
  • Addition of SITCOM for comparison of heavy atom sites from SHELXD
  • Version 1.07 includes
  • ARP/wARP 6.1 updated to 7.0.1
  • Addition of PHASER for SAD phasing in MRSAD protocol
  • A direct link to MRSAD from experimental phasing. The MRSAD protocol has the ability to complete the model (as much as is possible) from poor or partial models resulting from experimental phasing. MRSAD protocol can be also accessed separately at Auto-Rickshaw server.
  • Addition of PIRATE for density modification for the molecular replacement case
  • Improved heavy atom detection protocol.
  • Improvement in heavy atom hand determination.
  • Automatic correction of number of molecules in the asymmetric unit when number of molecules in asymmetric unit is underestimated.
  • Improvement in NCS-operator detection based on heavy atom sites or for MRSAD determined from PDB.
  • Additional option for d*trek data input (prefix must be .ref ) AR can accept, XDS, SCALEPACK and MTZ format of intensity data
  • Automatic refinement of a model using CNS and REFMAC5.
  • Bug fixed in the parallel space group execution for experimental phasing, MR and MRSAD phasing (this should be used when there is ambiguity in space group determination)
  • DPS2AR module for offline job submission to AR (for an example see XDSwiki page).

  • Version 1.06 includes
  • Option for MRSAD phasing and model completion
  • Model preparation using MrBUMP for phased molecular replacement
  • Dual fragment phasing using OASIS-2006
  • Link to output log file

  • Version 1.05 includes
  • Upgrade of CCP4 and SHARP programs
  • HELICAP is replaced by ALBE ( An ARP/wARP module for tracing helices and strands)

  • Version 1.04 includes
  • Now XDS processed data (XDS_ASCII.HKL) as input
  • Users have choice to upload MTZ, SCA or XDS file or combination of these.
  • Make sure that scaled data contains anomalous information.
  • space group parallelization Select "Automatic" from space group menu.
  • Version 1.03 includes
  • Option for Phased molecular replacement
  • Preliminary molecular replacement (user provides search model)
  • Dual fragement phasing for SAD and SIRAS
  • Automated material and method output with references upon successful
  • structure determination.
  • Improved model building protocol
  • Improved decision making at heavy atom refinement and phasing step
  • Improved Graphical User Interface
  • Version 1.02 includes
  • MTZ or SCA files or combination of both as input. Make sure that SCA files contain "H K L I+ SIGI+ I- SIGI-" format, and MTZ files contain "H K L I+ SIGI+ I- SIGI-" labels.
  • 4W-MAD phasing protocol
  • Improved protocol for automatic determination of enantiomeric space group and correct hand of the heavy atom sites.
  • Further improvement in the decision parameters at the density modification
  • step
  • Interface of the result page with JMOL (java based molecular visualization
  • program, for detail see www.jmol.org) to view your partial/complete structure.
  • A link to heavy atom co-ordinates and NCS-operators if found
  • Pull down menu for the node (no need to give computer's name but choose your respective institute),
  • Pull down menu for "Number of expected heavy atoms per monomer" and "Number of monomers in asymmetric unit".
  • No need to give password, PX project number and project name
  • For help, click on the relevent text.

  • Version 1.01 includes
  • All crystallographic programs as in the previous version but now including HELICAP (Thanks to Victor) for helix building
  • SIRAS phasing protocol
  • Automatic determination of enantiomeric space group
  • Improved protocol for substructure solution for weak cases
  • 20% faster Beamline Version
  • Pull down menu for the beamline node, no need to give IP code.
  • Protein sequence input in free format
  • Improved help menu for "Beamline" and "Advanced" version
  • Further improvement in the Decision parameters
  • Three different user-definable dissemination levels for X-ray data
  • >li>Password access for the User (password is same as for Beamline database access).
    Version 1.00 includes
  • SAD, 2W-MAD and 3W-MAD phasing protocol
  • Automatic determination of resolution cut-off
  • Decision-makers (Panjikar et al 2005,Acta Cryst. D61, 449-457. )
  • NCS-averaging whenever necessary
  • Four levels of hand determination
  • Help page for input parameters


  • Last Edited: 08.09.2009 by Santosh Panjikar