[sharp-discuss] New SHARP/autoSHARP release (SHARP 2.2.0, Sushi/autoSHARP 3.4.0)

Clemens Vonrhein vonrhein at globalphasing.com
Wed Nov 9 17:28:06 GMT 2005


Dear SHARP/autoSHARP user,

We are pleased to announce the release of a new SHARP/autoSHARP
production version (SHARP 2.2.0 and Sushi/autoSHARP 3.4.0), which is
now available on our webserver at

       http://www.globalphasing.com/sharp/

Highlights include: heavy atom detection with SHELXC/SHELXD, parallel
version of SHARP, CCP4i interface to autoSHARP, Speed vs. Accuracy
'slider', Coot support, better analysis of residual maps, spherical HA
cluster repesentation, AMD64/Opteron support (the full list of new
features, improvement and fixes is available in the release notes from
the download page and in the attached file).

For installation instructions as well as update notes, please read the
release notes (available from the download page and attached) as well
as the various documentations on our WWW page.

-------------------------------------------------------------------

Any question or problem report should go to

        sharp-develop at globalphasing.com


Please use the tools available on the main SHARP/autoSHARP page for

   - download information (password)
   - licence keys
   - licence renewal

-------------------------------------------------------------------

Kind regards

The SHARP/autoSHARP developers

-- 

***************************************************************
* Clemens Vonrhein, Ph.D.     vonrhein AT GlobalPhasing DOT com
*
*  Global Phasing Ltd.
*  Sheraton House, Castle Park 
*  Cambridge CB3 0AX, UK
*--------------------------------------------------------------
* BUSTER Development Group      (http://www.globalphasing.com)
***************************************************************
-------------- next part --------------


SHARP 2.2.0 - release notes


  1. Introduction
  2. List of changes and notes
  3. Installation

-------------------------------------------------------------------------------


1. Introduction

These are the release notes for the new 2.2.0 production version of SHARP.
Between the previous versions 2.0.4 and the current 2.2.0 release, several
changes have occurred - mostly invisible to the user.

The current production version of SHARP (2.2.0) is intended as a drop-in
replacement of SHARP 2.0.4 (the previous production version). It can be run in
the same way as SHARP 2.0.4 using the updated interface (SUSHI 3.4.x).

This release has been tested on

  * Linux

    1. ia32: Pentium 4, Xeon, Athlon etc
    2. x86_64: AMD64, Opteron
    3. ia64: Itanium2

  * Mac OsX 10.4.X (aka Tiger)
  * SGI/Irix
  * HP Tru64 4.0F/5.X


  ##################################################################
  ##### IMPORTANT:
  ##### this release requires a new set of licence keys (so your
  ##### existing .licence file will not work): please request
  #####  - a licence reneal,
  #####  - additional licence keys or
  #####  - a complete new licence
  ##### (see http://www.globalphasing.com/sharp/)
  ##################################################################

-------------------------------------------------------------------------------


2. List of changes and notes


  1. Parallel excution using openMP

     A parallel version of SHARP using openMP is included in this release. This
     allows making use of several CPUs installed in a machine. It is available
     for linux (ia32/x86_64 and ia64/Itamium), SGI/Irix and Hp/Tru64. See the
     installation instructions on how to enable it.

  2. Spherically averaged clusters

     SHARP now has a model of the scattering from clusters using a spherically
     averaged description. More information can be found in the manual
     describing the Sharp INput file syntax (Appendix 3, keyword: SPHCLUSTER).

  3. MTZ files

     Since this current version has been linked against the CCP4 5.0.2 set of
     libraries (for handling MTZ files), the MTZ files produced will have this
     format. Therefore, the current release has been mainly tested (and is
     supported) under CCP4 5.0.2 (4.2.2 might still work - but you are
     encouraged to update to the latest 5.0.X release of CCP4). The upcoming
     CCP4 6.0 release should not pose any problem - since the underlying
     libraries for handling MTZ files are basically identically. If you
     encounter problems running this SHARP version in a CCP4 6.X environment,
     please let us know.

  4. This is a production release

     The code has been extensively tested on both simulated data and on all the
     real data sets at our disposal. It was in active beta testing for over 6
     months. We don't expect any significant difference in behaviour for this
     version (relative to the previous production version). However, would be
     grateful for any feedback from the users, especially those familiar with
     the previous versions of the program, about potential problems as well as
     overall code behaviour.

     Important : Please make sure to also read the release note for the latest
                 version of Sushi (which also contains the autoSHARP set of
                 programs and scripts).


-------------------------------------------------------------------------------


3. Installation

You will need to update your licence keys for this version; please go to the
main SHARP/autoSHARP page at

                 http://www.globalphasing.com/sharp/

and follow the instructions for licence renewal.

See also the main installation instructions as well as the upgrade notes at the
main SHARP/autoSHARP pages.

-------------------------------------------------------------------------------
http://www.globalphasing.com, <sharp-develop at GlobalPhasing.com>
Last modification: 26.10.05
-------------- next part --------------
###################################################################
#                 Sushi 3.4.0 - release notes                     #
###################################################################


 1. Introduction
 2. List of changes (new features, improvements, fixes)
 3. Installation
 4. Upgrade
 5. Installing the autoSHARP CCP4i GUI

===================================================================

1. Introduction

This is the new production release of the SHARP/autoSHARP interface
package (Sushi). It includes the graphical user interface as well as
autoSHARP. Apart from the documentation you are currently reading,
there is extensive information available on our WWW page (especially
the Sushi 3.4.X and general upgrade notes).

This release has been tested on

  * Linux

    1. ia32: Pentium 4, Xeon, Athlon etc
    2. x86_64: AMD64, Opteron
    3. ia64: Itanium2

  * Mac OsX 10.4.X (aka Tiger)
  * SGI/Irix
  * HP Tru64 4.0F/5.X (note: SHELXC/SHELXD will not work on 4.0X systems)

  ##################################################################
  ##### IMPORTANT:
  ##### this release requires a new set of licence keys (so your
  ##### existing .licence file will not work): please request
  #####  - a licence reneal,
  #####  - additional licence keys or
  #####  - a complete new licence
  ##### (see http://www.globalphasing.com/sharp/)
  ##################################################################

-------------------------------------------------------------------

2. Changes since version 3.2.3


  1. autoSHARP - new features:

     o The detection of the heavy atom substructure can now also be
       done with the SHELXC/SHELXD programs by G. Sheldrick. This is
       now the recommended way, although some internal parameters
       might still benefit from fine- tuning. As an alternative, the
       RANTAN procedure is also still available.

     o The user can now decide, if autoSHARP should use some
       short-cuts (hopefully speeding up the calculation but at the
       cost of less accuracy) or use the full set of features (being
       as accurate as possible, but maybe a little bit slower). This
       is done as a Speed/ Accuracy setting in the interface. The main
       shortcuts that will speed up a calculation are done at the
       following steps:

       # data analysis and scaling (fewer outlier checks, so some
         problems with the given data might be missed);

       # heavy atom detection with SHELXD (fewer trials, which might
         miss the correct solution if the data or substructure signal
         isn't of high quality);

       # density modification (larger steps and fewer cycles during
         optimisation of solvent content, so that the correct number
         of molecules might be missed when a large number of
         NCS-related molecules is present);

       # automatic building using ARP/wARP (more frequent building
         steps and fewer cycles, possibly resulting in fewer residues
         being built or not all chains docked into sequence);

     o A new CCP4i interface for running autoSHARP is available: this
       has been tested with CCP4 5.0.2. The program output still uses
       HTML, so it is advisable to view these with a browser (Mozilla,
       Firefox, Internet Explorer ...). Please note: this mode of
       operation does not require a running httpd.

     o Support for viewing results (maps and models) with Coot by
       P. Emsley.

     o When estimating the most likely number of molecules per in the
       asymmetric unit (before any heavy atoms have been found and
       before an optimised solvent content is available), the Matthews
       coefficient probabilities by Kantardjieff & Rupp (Protein
       Science 12, 1865) are implemented.

     o During the analysis of residual maps (to update and check the
       current heavy atom model), an automatic decision based on SHARP
       residual maps (LLG maps) is done for the refinement of
       anomalous scattering factors f'/f''.

     o When deciding which is the correct hand (and also when the
       solvent content is optimised), a new score is used for density
       modification: CC/ Contrast (CC is the correlation between E2 of
       density-modified map and observed data and show how well the
       density modification fits with the observed data; Contrast is
       the ratio between the standard deviation of density in the
       solvent region and the standard deviation of density in the
       'protein' region - this is a measure how macromolecule-like the
       modified density appears).

     o When several datasets are given (e.g. for a MAD experiment) and
       the space group allows it, all datasets are checked for
       alternate indexing to give the best agreement to the first
       dataset. These happens for space groups: P4 (75), P41 (76), P42
       (77), P43 (78), I4 (79), I41 (80), P3 (143), P31 (144), P32
       (145), H3 (146), P312 (149), P3112 (151), P3212 (153), P321
       (150), P3121 (152), P3221 (154), H32 (155), P6 (168), P61
       (169), P65 (170), P62 (171), P64 (172), P63 (173), P23 (195),
       F23 (196), I23 (197), P213 (198) and I213 (199). Also, the
       consistency of screw- axis components in all datasets is
       checked.

     o New reflection file formats are supported: unmerged SCALEPACK
       and SHELX HKLF 4 format files.

     o During the analysis of log-likelihood gradient (LLG) maps from
       SHARP (residual maps): already refined heavy atoms sites might
       be deleted if the standard uncertainty of their heavy atom
       occupancy parameter is too large.

     o To facilitate the connection of external helpers (to view
       results using Mozilla/Firefox directly from the HTML log files
       with e.g. O, Coot, Xfit etc), a new script is provided
       (add2rdf.sh) that will modify each users browser configuration
       (as long as it is found in ~/.firefox or
       ~/.mozilla/firefox/). A similar script for Konqueror
       (add2konq.sh) is available too - although not as well tested.

     o An autoSHARP paper should be out quite soon:

       Vonrhein, C, Blanc, E., Roversi, P and Bricogne,
       G. (2005). Automated structure solution with autoSHARP. In
       "Crystallographic Methods", S Doublie, Ed., Humana Press,
       Totowa, NJ, submitted.

       Steps that involve use of external programs will give clear
       reference to publications: make sure to cite all programs used.

  2. autoSHARP - improvements:

     o The handling of off-origin peaks in native Patterson has been
       improved.

     o Some unnecessary warnings in initial checks are now avoided -
       to prevent some confusion.

     o A better automatic analysis of MAD wavelengths is done. Since
       the heavy atom detection with SHELXC/SHELXD require a correct
       identification of each wavelength by name, it is recommended to
       use some 'standard' convention as identifiers of the different
       wavelengths (as a fall-back plan for autoSHARP): peak, infl,
       hrem, lrem.

     o Better residual map analysis: avoid adding C-Sites with same
       G-Site and keep track of already removed sites. This should cut
       down on the number of (sometimes unnecessary) cycles between
       refinement of heavy atom model (SHARP) and the analysis/update.

     o During density modification, extreme values of solvent content
       are now avoided: this should stabilise this step in cases of
       very low (around 20%) or very high (above 70%) solvent content.

     o The interface to ARP/wARP for the automatic building of models
       into density modified maps has been updated to 6.1.1
       logic. This should now be very similar to the currently
       distributed ARP/wARP 'warpNtrace' mode.  Therefore, it might be
       beneficial to use the distributed ARP/wARP interface with data
       out of SHARP/autoSHARP. However, some settings in the ARP/wARP
       interface within autoSHARP have been optimised to work best
       with data coming out of SHARP/autoSHARP - so it is worth trying
       both!

     o If the resolution is not high enough for doing complete
       auto-building with ARP/wARP, the helix-building module of
       ARP/wARP will be used for getting at least part of an initial
       model (if there are helices).

     o The description of spherical cluster refinement (SPHCLUSTER
       keyword) has been improved in the distributed documentation. An
       example Sharp INput (SIN) file is available in
       $BDG_home/docs/sharp/doc.

     o Reflection files don't need to have an extension of *.data.mtz
       (or *.data.sca, *.data.hkl) anymore: a plain *.mtz file is
       sufficient.

     o During scaling of different datasets relative to each other:
       the low resolution analysis and adjustment of a low resolution
       cut-off have been stabilised.

     o Some more checks regarding the sequence file have been added.

     o If the data was processed with some resolutions shells excluded
       due to ice-rings on the images, potential problems during
       scaling/analysis are caught.

     o Job submission:

       # problems should be analysed better

       # support for PBS/OpenPBS

       # more meaningful job names for queueing systems


  3. autoSHARP - fixed bugs:

     o switching hand for P3121/P3221

     o interface to ARP/wARP: inclusion of heavy atoms

     o adjustment of no. of molecules and no. of heavy atoms based on
       Matthews coefficient now takes user-given information better
       into account

     o better handling of CCP4 4.2.2/5.0.2 differences in MTZ file
       header (regarding space group and Project/Crystal/Wavelength
       (Dataset ID) information)


-------------------------------------------------------------------

3. Installation

The easiest way to install everything from scratch:

  1. Download all necessary packages. This requires a password - which
     should have been sent to you at the time of licence acceptance
     (but it is changed regularly, so see also the password reminder
     page).

  2. follow the installation instructions, especially the typical
     installation scenarios. E.g.:

       % cd /where/ever/sharp
       % ./installSHARP -F


-------------------------------------------------------------------

4. Upgrade

Alternatively, if you want to upgrade your existing SHARP/autoSHARP
installation:

  1. Download all new packages. This requires a password - which
     should have been sent to you at the time of licence acceptance
     (but it is changed regularly, so see also the password reminder
     page).

  2. unpack files and update your configuration (in the so-called
     $BDG_home directory):

       % cd /where/ever/sharp

       % source ./setup.csh              # for csh/tcsh
         - or -
       % . ./setup.sh                    # for sh/bash/ksh

       % adm/bin/kill_server
       % ./installSHARP -U

  3. see also the Sushi 3.4.X and general upgrade notes.

-------------------------------------------------------------------

5. To install the autoSHARP CCP4i GUI:

  * start CCP4i

  * open "System Administration" (at the right side)

  * select "Install Tasks"

  * for the "Task archive", browse to the installation directory of
    SHARP/autoSHARP and select the file autoSHARP_CCP4i.tar.gz

  * click "Apply" and then quit/restart ccp4i

  * there should now be a task autoSHARP in the "Experimental Phasing"
    module and also in the "Program list" (by default new tasks are
    installed at the end of the list).

-------------------------------------------------------------------------------
Clemens Vonrhein, sharp-develop at GlobalPhasing.com
Last modification: 09.11.05


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