UPDATE: the issues described here have been resolved in newer versions of our software. Please do not run old and unsupported software, but ensure to update to the latest version.

Content:

Combined patch: sushi_20130614.diff.

ARP/wARP 7.3 bug

ARP/wARP 7.3 has a problem when used from SHARP/autoSHARP (where we do want to use phased refinement during model building using Hendrickson-Lattman coefficients). The file arp_warp_7.3/share/auto_tracing.sh needs to be modified from 

if ( "$arguments[$index_phaselabin]" && $arguments[$index_twin] ) then

to 

if ( "$arguments[$index_phaselabin]" != '' && $arguments[$index_twin] ) then

See also the discussion on sharp-discuss and the ARP/wARP FAQ for 7.3.

Bug affecting decision-making about model-building module to use

You might see messages like 

/sharp-2.8.1/bin/sharp/detect.sh: line 545: [: 2.00: binary operator expected

or 

/sharp-2.8.1/bin/sharp/detect.sh: 545: [: Float_GT: unexpected operator

caused by a typo in bin/sharp/detect.sh. Line 545 should be changed from 

[ Float_GT $resh $autoSHARP_DETECT_ModelBuildingResLim ] ); then

to 

( Float_GT $resh $autoSHARP_DETECT_ModelBuildingResLim ) ); then

Without this change the new building module long_john_silver (using PIRATE and BUCCANEER from K. Cowtan) will not be used as intended when

With the above patch applied, normal operation is reinstated.

Support for SHELX version 2013

To support the latest SHELX version (with changes to various output formats), two patches need to be applied:

Map-plotting for LJS results

There is a buglet in the map-plotting routine preventing maps from the parrot/buccaneer (LJS) module to be calculated correctly. Please apply the following patch