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: <sharp-develop@GlobalPhasing.com>
###################################################################
#
# 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 2.8.2/3.10.2 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/run_autoSHARP.sh -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
protocols.
* 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
filenames)
- version 7.4 (changes due to changed format of refinement
statistics)
* 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.
Fixes:
* 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 aStar.sh (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
===================================================================
Fixes:
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
tool.
* support for latest SHELXC/D versions.
For information regarding the latest SHELXC/D version please refer
to the official documentation at
http://shelx.uni-ac.gwdg.de/SHELX/
and especially
http://shelx.uni-ac.gwdg.de/SHELX/changes.php
* 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
Fixes:
* 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
model.
* 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:
http://www.globalphasing.com/sharp/wiki/
* 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
Fixes:
* modified Perl code to work with latest Perl version 5.12
* fixed I41 hand inversion
* made I4122 hand inversion consistent with documentation in CCP4
(reindexing.doc)
* 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
2.6.x
To check the version of the kernel on a particular system, run the
following command:
uname -r