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


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>     ! 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>     !  ==> 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

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

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