Release Notes - SHARP 2.8.5 and autoSHARP 3.10.5 (16 June 2015)

This is the fifth SHARP/autoSHARP release in the 2.8.X/3.10.X series: SHARP 2.8.5 and autoSHARP 3.10.5 (16 June 2015). It is based on the previous 2.8.4/3.10.4 releases and available to academic and commercial users.

These release notes cover SHARP, the autoSHARP pipeline and the Sushi graphical user interface.

Any feedback and remarks should be send to the SHARP developers: <>

# Copyright   (C) 1995-2015 by Global Phasing Limited
#             All rights reserved.
#             This software is proprietary to and embodies the
#             confidential technology of Global Phasing Limited
#             (GPhL). Possession, use, duplication or dissemination of
#             the software is authorised only pursuant to a valid
#             written licence from GPhL.
# Authors:    G. Bricogne, E. Blanc, E. de la Fortelle, C. Flensburg,
#             J. Irwin, P. Keller, W. Paciorek, P. Roversi, A. Sharff,
#             O. Smart, C. Vonrhein, T. Womack
# References: G. Bricogne, C. Vonrhein, C. Flensburg, M. Schiltz &
#             W. Paciorek. (2003). Generation, representation and flow
#             of phase information in structure determination: recent
#             developments in and around SHARP 2.0. Acta Cryst. D59,
#             2023-2030.
#             C. Vonrhein, E. Blanc, P. Roversi & G. Bricogne
#             (2007). Automated structure solution with
#             autoSHARP. Methods Mol Biol 364, 215-30.

 Changes relative to 2.8.4/3.10.4                      Jun 16 2015

Improvements and changes:


   * create scripts for Coot to be run directly: separate scripts for
     the different stages of HA-detection, phasing,
     density-modification and model-building are available. This
     simplifies the viewing of results for users.

   * report date, directory, user name in top of the .autoSHARP file

   * added safety-check for unset/missing "wvlid" (wavelength
     identifier) and "fmid"/"smid" (amplitude/sigma)

   * the help message ( -h) now also includes an
     example for a Ta6Br12 cluster as heavy-atom compound.

 * when presenting MTZ files as part of the autoSHARP results: also
   report which columns should be used for various map
   computations. This simplifies the viewing of results in Coot based
   on those MTZ files.

 * the command-line for running "Long John Silver" (K. Cowtan's PARROT
   and BUCCANEER) as part of autoSHARP is better reported in a way
   that would allow a user to run this tool stand-alone.

 * the skeleton representation in the Coot scripts (for visualising
   electron density maps) have been improved with the help of
   P. Emsley.



   * safeguard against MTZ column names with ":" characters

   * fix bug in awk construct (triggered by non-GNU awk binary on OsX)

   * when starting from known positions of sites: ensure the
     symbolic links in the Results directory aren't confused by this.

 * autoSHARP:

   * fixed buglet that resulted in badly formatted solvent content
     presented in map tools for LJS results (when run through httpd

   * depending on the ARP/wARP version used, the final PDB file was
     not presented in the output HTML page.

   * automatic interpretation of LLG residual maps was confused when
     multiple iterations of parameter refinement (in SHARP) and this
     analysis were combined with the need of f'/f" parameter

   * if no ARP/wARP installation is available (or not configured),
     keep running "Long John Silver" building tool instead of
     producing an error.

 Changes relative to 2.8.3/3.10.3                      Mar 16 2015

Improvements and changes:

 * The setup scripts have been consolidate. The installation will
   create two different files setup.{csh,sh} and setup-admin.{csh,sh}
   for two different tasks:

     setup.{csh,sh} : for users of the software (sets SHARP_home
                      environment variable and puts
                      into the users PATH)

     setup-admin.{csh,sh} : for administrators of the software (puts
                      commands for adding users, configuring the
                      software and machines into the PATH)

   Only the setup.{csh,sh} files need to be put into a users setup
   e.g. via

     if [ -r /where/ever/sharp/ ]; then
       . /where/ever/sharp/

   (for bash/sh-users) or

     if ( -r /where/ever/sharp/setup.csh ) then
       source /where/ever/sharp/setup.csh

   (for csh/tcsh users).

 * Changed writing of LLG residual maps from SHARP: instead of writing
   real and imaginary part of the structure factor it now writes
   amplitude and phase. This should make it much easier to load the
   resid.mtz file into a Coot session and show residual maps.

 * The need to obtain a separate licence key for each machine on which
   the software is to be run has been removed for academic users: a
   single valid licence key will now work on any number of machines.


 * Fixed hanging of interactive script when no
   model-building was requested.

 * Fix in presenting results when running interactive
   script with an initial set of sites (instead letting it do the
   heavy atom detection itself).

 * Try to recreate during installation the way CCP4 sets the
   environment variable CCP4_SCR including a dynamic part (user name):
   the resulting $SHARP_home/machines/*/ccp4.setup file(s) should now
   also contain this and not have the user id of the installer account

   This can be switched off (to have previous default behaviour) by
   setting the environment variable AdjustCcp4ScrForUser to "no"
   before running the installation.

 * Fixed a bug when running autoSHARP through the CCP4i interface and
   declaring neither sequence nor molecular weight or number of

 * Handle cases in autoSHARP where a site that has been refined to
   nearly zero occupancy by SHARP is actually on a special position
   and therefore didn't get recognized as a removable site during LLG
   residual map analysis. This resulted in running the same
   SHARP/LLG-analysis loop multiple times.

Please also check the next block of release notes for recent changes.

 Changes relative to 2.8.2/3.10.2                      Mar 04 2015

Improvements and changes:

 * A command-line tool for running autoSHARP that can easily be
   incorporated into the workflow. See

     $SHARP_home/bin/sharp/ -h

   for detailed usage help.

 * SHARP and SCALA2SHARP: increase maximum number of batches from 10k
   to 100k. This makes it possible to handle advanced data collection

 * Support for CCP4 6.5 (and removed support for CCP4 versions prior
   to 6.3.0).

 * Support for SHELXC version 2014/2 and SHELXD version 2013/2

 * Support for ARP/wARP:
   - version 7.5 (changes due to changed default prefix of output
   - version 7.4 (changes due to changed format of refinement

 * new arguments to 'Long John Silver' script:

   -ncsrad (to set ncs-mask-filter-radius in PARROT)

   -free (MTZ column label for test-set flag (default = FreeR_flag)

 * autoSHARP will now use the same test for the 'Long John Silver'
   (PARROT/BUCCANEER) auto-building at lower resolution, that it
   already uses for the ARP/wARP path at higher resolution. If a large
   enough number of residues are built/docked the loop over density
   modification and auto-building will be stopped.

 * When running the non-default fast option in autoSHARP: change to
   use smaller steps during optimisation of solvent content since
   otherwise it can easily go into silly solvent content ranges for
   structures with exceptionally large/low solvent content.

 * Improved checking of SHELXC/SHELXD version to give more meaningful
   messages to user.

 * autoSHARP will now not use FHSCAL for MIR/SIR scaling: if the
   derivatives are higher resolution than the native it will not
   output those higher reflection data. It now uses SCALEIT instead
   for all cases.


 * Fixed issue where jobs gave an erroneous warning (about solution
   not being good enough while it clearly was).

 * fixed problem with input SCA-files for structures with cell
   dimensions above 999.999 A

 * when only running model building using PARROT/BUCCANEER ("Long John
   Silver"), fix problem if subsequent density modification jobs came
   up with identical solvent content (by chance): this used to trigger
   an error.

 * added test to (jiffy for visualising maps/models directly
   from HTML file produced via CCP4i autoSHARP task) to handle
   SHARP_home environmental variable correctly.

 * fixes in 'Long John Silver' script when getting NCS operators from
   PARROT (however: NCS operators written by PARROT up to at least
   version 1.0.2 are buggy)

<-- Below are the Release Notes for the previous stable release -->

 Changes relative to 2.8.1/3.10.1                      19 Jun 2013


 autoSHARP improvements:

 * stop complaining about spacegroup differences for cases like P1211
   versus P21, ie. simply a difference in notation.

 * fix handling of f'/f" values when using an initial/partial model
   for heavy-atom substructure solution via SHARP: when used in
   multi-wavelength MAD the values for the second (and following)
   wavelengths were wrongly assigned.

 * give a bit more information why we would prefer the peak, infl,
   hrem etc nomenclature for SHELXC/D.

 * fixed menu for plotting maps after automatic-building with LJS

 * support for latest SHELXC/D versions.

   For information regarding the latest SHELXC/D version please refer
   to the official documentation at

   and especially

 * automatically translate all spaces to underscore in project name.

 * decision making about low-resolution model building was broken: the
   new long_john_silver tool was not used for data below 2.5A if the
   'fast' autoSHARP option was set.

 Changes relative to 2.8.0/3.10.0                      22 Oct 2012

Improvements and changes:

 * support for usage of spherical clusters in SUSHI.

 * new automatic-building module (long_john_silver) using BUCCANEER
   and PARROT by K. Cowtan.

 * support for SHELXD (beta) version 2011/5 in autoSHARP, including
   the parallelized binaries shelxd_mp and shelxd_mp64.

 * support for ARP/wARP 7.2 and 7.3 as well as CCP4 6.3.0

 * removed support for Xfit/XtalView, Moloc and Quanta viewers

 * improved output and checks for the part in autoSHARP dealing with
   an initial/partial input model

 * new renaming feature within the file-upload facilty


 * automatically translate all spaces to underscore in project name.

 * correctly fetch MTZ files (for map plotting) from GETAX
   (NCS-detection) runs in case of negative self-rotation angles.

 * deal better with low-resolution (<= 6A) data in the NCS-detection
   (GETAX) part: DM can't determine an appropriate scale and we need
   to set this by hand (as well as switching off histogram matching
   because of that).

 * avoid printing link to wrong cross-table listing in SHELXD HA
   detection step (when running several trials).

 * in SHARP, allow underscore (_) as part of project name and also a
   longer title (180 characters)

 Changes relative to 2.6.0/3.8.0                       20 Jul 2011

New features:

 * given an initial PDB model, autoSHARP can use phases calculated
   from this file to detect heavy atom sites through SHARP's
   residual/LLG maps.

   This feature was present in SHARP since its beginning, but required
   a little bit more user intervention. Putting it into autoSHARP
   should make it easier to find heavy atom sites from a poor initial

 * Support for 64-bit binaries on linux.

 * Support for emX and pXpY network interfaces.

Improvements and changes:

 * updated to handle also ARP/wARP 7.1 and most likely the upcoming 7.2

 * clarified autoSHARP interface regarding sequence file, number of
   sites, wavelength and f'/f" values.

 * added new helper (pir2pir) for automatic detection and correction
   of common issues with sequence files - in particular converts a
   FASTA sequence into internal format

 * consolidate usage of PRIOR cards in the SHARP Input Editor

 * added spacegroups 2018 and 3018

 * cleanup of different documentation links, mainly to point to
   official SHARP Wiki at:

 * use fixed ordinate range of relative-occupancy plots of shelxd 
   solutions for quick quality assessment

 * support for up to 9999 number of batches in MRF-mode

 * automatically set environment variables: ATOMSF, SYMINFO, SPHCLUSTER


 * modified Perl code to work with latest Perl version 5.12

 * fixed I41 hand inversion

 * made I4122 hand inversion consistent with documentation in CCP4

 * fixed map-plotting issue for ARP/wARP maps

 * several fixes to make PKMAPS program more robust (eq. when analysing
   LLG maps for additional sites)

 * fixed typo that prevented usage of resolution-dependent initial
   HAT_B value (in case no Wilson plot could be calculated for very
   low-resolution data)

 * fixup some (non-standard) space group numbers and add I2

 * fixed problems in parameter refinement (SHARP hanging) due to
   problems in anisotropic tensor construction

 * fix spurious crashes when calling LRINFO(CCP4)

 * fix handling of multi-batch MRF cases

 * fix a memory leak in file_open

 * correct error handling when unable to write '.status' file

#### NOTES

  The 32-bit Linux distributions of Global Phasing's software will
  work on systems running relatively old kernels (versions
  2.4.x). Most mainstream server and desktop Linux distributions that
  are currently under active maintenance are based on the newer 2.6.x
  kernel series.

  The current 32-bit release will be the last to support Linux systems
  based on the 2.4.x kernel. Future distributions (including patches
  and minor updates) of our software for all Linux systems released
  after this one can only be relied on to work on systems running
  kernels from the 2.6.x series.

  This is only a significant change for our 32-bit distribution: our
  64-bit distributions for Linux have always required kernel version

  To check the version of the kernel on a particular system, run the
  following command:

      uname -r        

Any feedback and remarks should be send to the SHARP developers: <>, <>
Last modified: 19.06.2013