Release notes

SUSHI 3.0.15

• autoSHARP
  • added more checks throughout
  • can now be run independent of the httpd (i.e. with everything in single directory)
  • some changes/fixes to density modification (to speed things up) and ARP/wARP part (to build more) of autoSHARP
  • now does more than one pass through interpretation of residual maps: this way we can start from very few sites and add more during refinement/interpretation.
  • automatic building with ARP/wARP 6.0 now reports some basic stats
  • small changes so that handling of several molecules/asu becomes more automatic
  • more automation in defining starting heavy atom parameters (like temperature factors)
  • slightly changed defaults in HA detection
  • changes in automatic interpretation of residual maps - should be more robust now
• the problem with MTZ files seen but no column labels visible should be sorted
• tested with latest CCP4 release (4.2.2)
• tested with latest Perl release (5.8.0)

SUSHI 3.0.14

• some fixes in ARP/wARP script
• start to include proper NCS handling
• starting automatic resolution cut-offs for HA detection

SUSHI 3.0.13

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

SUSHI 3.0.12

• 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

SUSHI 3.0.11

• 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

SUSHI 3.0.10

• 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)

SUSHI 3.0.9

• several small bug fixes - mainly in installation.

SUSHI 3.0.8

• fixes in DM part of solvent flattening when dealing with really low resolution data (below 6A)
• fix in automatic interpretation of residual maps
• slightly altered ARP/wARP mode: now starts with density modified phases (apropriately dampened)
• fixes for spacegroup I422 in solvent flattening
• better handling when several SHARP/autoSHARP jobs of same id run at the same time (which the user should avoid anyway)
• fixes when the .hatom file for autoSHARP contains several atom types
• now the map after the last DM run in solvent flattening can be viewed
• support for CCP4 4.2 and Kevin Cowtans CCP4 for Linux distribution.

SUSHI 3.0.7

• small fixes in dealing with ARP/wARP 5.1 output
• fix in GETAX script (when allowing for monomer masks)

SUSHI 3.0.6

• improvements for viewing CCP4 o/p as HTML - not completely foolproof and tested though. Main problem is incomplete implemenations in various CCP4 programs!
• fix to version numbering in CCP4 when using Kevin Cowtan's CCP4 from http://www.ysbl.york.ac.uk/~cowtan/ccp4/ccp4.html
• small fix in automatic residual map interpretation
• maybe unnecessary fix in solvent flattening scripts when solvent content below 10% (which it probably shouldn't anyway)
• some fixes in job control (restart, continue etc)

SUSHI 3.0.5

• small bug fix in map viewing

SUSHI 3.0.4

• compatibility with Buffet 0.17.5 reached

SUSHI 3.0.3

• fixes minor typos in manual
• fixes bug when doing peak picking in pure SHARP electron density maps

SUSHI 3.0.2

• fixes bug in submission of jobs from the Phase Improvement and Interpretation Panel
• fixes possible problem in automatic interpretation of residual maps in autoSHARP
• fixes problems when user sets preferences to do HTMLized CCP4 log files (still not fully tested)

SUSHI 3.0.1

• minor bug fix release

SUSHI 3.0.0

• major new release: includes autoSHARP, additional density modification tools, interface to ARP/wARP.