IssuesPage201603

Known Issues in 20160324 (stable) BUSTER release or subsequent (snapshot) releases:

• Introduction
• Name clash with ATSAS package (resulting in grade failures) - fixed in (snapshot) release 20160923
• Pipedream regression in snapshot 20160706 release - fixed in (snapshot) release 20160708
• buster-report failure when generating PDF output - fixed in (snapshot) release 20160923

Introduction

Please also check the BUSTER home page and the news page for updates and snapshot releases.

Name clash with ATSAS package (resulting in grade failures) - fixed in (snapshot) release 20160923

If you see an error when running 'grade'

getopt error: unknown option: --silent

the most likely reason is a nameclash (for 'pdb2seq' command) between our command and a identically named program from the ATSAS (EMBL-Hamburg, bioSAXS) that is often installed directly into the system directories /usr/bin and therefore causes this problem.

A solution is to set environment variable BDG_UseOldPathAtStart to yes before running grade - using one of the following mechanisms:

• for bash/ksh/sh/zsh:

       export BDG_UseOldPathAtStart="yes"
       grade ...

       BDG_UseOldPathAtStart="yes" grade ...

• for tcsh/csh

       setenv BDG_UseOldPathAtStart "yes"
       grade ...

       env BDG_UseOldPathAtStart="yes" grade ...
 

Pipedream regression in snapshot 20160706 release - fixed in (snapshot) release 20160708

When running Pipedream from images and having high enough multiplicity to create the F(early)/F(late) datasets intended to analyse for radiation damage:

• Pipedream will stop with an error about column names
• This has been fixed in the (snapshot) release 20160708 - please ensure to update!
• A workaround is to run Pipedream with

            % pipedream -apcommands "autoPROC_ScaleEarlyLateCreate=no" ...
 

buster-report failure when generating PDF output - fixed in (snapshot) release 20160923

When generating the PDF version of buster-report and BCORR (B-factor correlation restraints) outliers are to be reported: this leads to a pdflatex failure with a message like

ERROR>     ! Missing $ inserted.
ERROR>     <inserted text>
ERROR>                     $
ERROR>     l.36 ...Worst is     6.2 \(\sigma\)   -44.66 Angs^
ERROR>                                                       2 A|202:C(TRP)=A|203:N(ALA)\\
ERROR>     
ERROR>     ?
ERROR>     ! Emergency stop.
ERROR>     <inserted text>
ERROR>                     $
ERROR>     l.36 ...Worst is     6.2 \(\sigma\)   -44.66 Angs^
ERROR>                                                       2 A|202:C(TRP)=A|203:N(ALA)\\
ERROR>     
ERROR>     !  ==> Fatal error occurred, no output PDF file produced!
ERROR>     Transcript written on report.log.

One possible workaround at the moment is to run

% find YourBusterOutputDir -name "screen_[a-z]*" \
    -exec grep -l "Angs^2" {} ";" | xargs sed -i "s/Angs^2/Angs**2/g"

and then

% buster-report	-d YourBusterOutputDir -dreport	YourBusterOutputDir.report

This should work when using buster-report standalone, but not when using "refine -report ...".

This will be corrected in the next (snapshot) release.