Sushi 3.0.14 - release notes

Also note, that if you want to use the newly introduced viewers (like Moloc and/or XtalView) you need to

1. run the 'newmachine' command command for each machine:

         % cd $BDG_home
         % adm/bin/newmachine <machine name>
         

2. each user has to re-run the 'useSHARP' command, to add the capability to his/her ~/.mailcap file

3. edit the $BDG_home/bin/helpers.local file (have a look at the new $BDG_home/bin/helpers.local_template file for the new items that are required for these external viewers)

1. download all new packages

2. update your existing installation:

         % cd $BDG_home
         % adm/bin/kill_server
         % ./installSHARP -u
         

3. check all machines:

         % cd $BDG_home
         % foreach machine ( `ls machines/*/sharp.setup` )
           set machine=`dirname $machine`
           adm/bin/newmachine $machine
           end
         % adm/bin/restart_server
         

4. tell all users to rerun

         % $BDG_home/bin/useSHARP <user name>
         

Changes since version 3.0.13

• full support for SHARP 2.0.X version(s) in autoSHARP and Sushi - includes access to new features through the JavaScript SIN-file editor
• HA detection in autoSHARP:
  • automatic resolution cut-off for isomorphous/dispersive differences and anomalous differences in MAD
  • improvements in automatic deletion and addition of sides (during insection of residual maps)
  • several fixes/improvements to logic in detection via RANTAN
• important warnings are shown in main autoSHARP log file
• removed CCP4 < 4.X support in solvent flattening script
• some fixes in ARP/wARP script
• start to include proper NCS handling in autoSHARP
• added lot's of analysis about wavelength, f'/f" values in autoSHARP (and some more diagnostics that are MAD specific)
• update to documentation
• new example files for toxd and rnase (both CCP4 distributed datasets).
• this will be the last version to include SHARP 1.4.0 support!

Changes since version 3.0.12

• some minor (cosmetic) changes in the JavaScript SIN file editor.

Changes since version 3.0.11

• force POSIX compliant subshells under Tru64 - seems to be less buggy
• many fixes/changes to ARP/wARP interface: allows more control over convergence criteria, weights on phases and geometry (some only visible as EXPERT user). Also, added a few work-arounds for problems in programs from ARP/wARP 6.0.
• solvent flattening with a known model can now be done too by using just the mask based on this model. This could possible avoid bias towards the model.
• autoSHARP now supports PDB files as input for known sites (same naming convention as before). SO SHELXD sites can easily be included.
• Moloc viewer support

Changes since version 3.0.10

• support for CCP4 HA files as *.hatom files
• fix of small problem in optimizing of solvent content
• smallish clean-up in JavaScript code
• preparation for support of next major SHARP release
• fix when enantiomorph requires change of spacegroup (for screw axes)
• added some tools for running SHARP/autoSHARP effectively at synchrotron sites
• initial attempt to also support non-Netscape browsers (still flaky in JavaScript part)
• fix when no spacegroup symmetry explicitely given in autoSHARP input
• format of SIN file written by JavaScript SIN editor more in sync with the one written by SHARP
• added page with easy access/overview of all results (accessible from the main SHARP Control Panel)
• included better ARP/wARP 6.0 support: make use of improved main chain tracing algorithms

Changes since version 3.0.9

• Some cleanup in handling FFT/SFALL incompatibilities for axis ordering, map limits etc.
• compatible with CCP4 4.2.1 and ARP/wARP 6.0
• Interface to XtalView (Xfit)
• support for latest Apache httpd (1.3.26)