[sharp-discuss] SHARP/autoSHARP release - October 2012
SHARP Developers
sharp-develop at globalphasing.com
Mon Oct 22 19:27:12 CEST 2012
Dear SHARP users,
We are pleased to announce the latest release of SHARP/autoSHARP, with
several important updates and fixes, including
* support for usage of spherical clusters in SUSHI.
* new automatic-building module (long_john_silver) using
BUCCANEER and PARROT by K. Cowtan.
* 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 litttle 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 and emX and pXpY network
interfaces.
Please see the release notes for more details.
--------------------------------------------------------------------
As usual, the software can be downloaded (and licences renewed) at
http://www.globalphasing.com/
If you have any questions, please refer to the SHARP/autoSHARP wiki at
http://www.globalphasing.com/sharp/wiki/ or contact us at
sharp-develop at globalphasing.com.
Kind regards
The SHARP developers
-------------- next part --------------
###################################################################
#
# This is the second SHARP/autoSHARP release in the 2.8.X/3.10.X
# series: SHARP 2.8.1 and autoSHARP 3.10.1 (October 22 2012). It is
# based on the previous 2.8.0/3.10.0 releases and available to
# academic and commercial users.
#
# These release notes cover SHARP, the autoSHARP pipeline and the
# Sushi graphical user interface.
#
###################################################################
#
# Copyright (C) 1995-2012 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 2.8.0/3.10.0 Oct 22 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:
* 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
===================================================================
Any feedback and remarks should be send to the SHARP developers:
sharp-develop at globalphasing.com
===================================================================
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