Known Issues in 20210716 BUSTER release:

Failure during installation on case-insenstive filesystems (like APFS on MacOS) (fixed)


UPDATE ("Fri, Jul 23 2021, 10:30 UTC"): The download packages (GPhL_BUSTER_snapshot_20210716.darwin.tar and have been replaced with the fixed versions. The fixes shown below (for this particular issue) should no longer be necessary for downloads after that time.


During installation on a case-insensitive filesystem (ie a filesystem where there is no difference between a file called "File.txt" and one called "file.txt"), you will probably see an error like

NOTE : Installation of BUSTER completed

NOTE: Installing Grade2 version:1.0.0, build:1.0.0-rc1

ERROR: file "Grade2.darwin.tar.gz" not found

ERROR: during "./" - see above

Since a change to a case-sensitive format would require a complete reformatting of the disk (including loss of all data and use of backups), this is not really an option here. In order to fix our installation files the following procedure can be used:

  • We assume that you have downloaded the two files GPhL_BUSTER_snapshot_20210716.darwin.tar and into ~/Downloads (please adapt the following commands accordingly)
  • Open a terminal and go to the directory with the downloaded files, e.g.
        cd ~/Downloads
  • Create a temporary directory and go there via
        mkdir tmpfix
        cd tmpfix
  • Move the relevant files there
        mv ../GPhL_BUSTER_snapshot_20210716* .
        mv ../ .
  • Run the script via
        chmod +x

This should result in a new set of files


that could be used for installation of our software on those case-insensitive filesystems. Thanks to Kevin Battaile for reporting this issue.

MacOS 11

Please be aware that CSD 2021 is currently unsupported on MacOS 11 (Big Sur) and therefore Grade (grade and grade_PDB_Ligand) as well as buster-report are not supported on that platform. Support for MacOS 11 is expected in a forthcoming update to CSD.

Potentially slow Gnuplot on CentOS8

We've had reports of long execution times for previous releases of BUSTER (or Pipedream) on CentOS8 due to our distributed Gnuplot binary taking a very long time. We can partly reproduce this (although not quite to the same extent), but hope that the binary distributed with this release will on CentOS8 behave similar to other Linux distributions.

If you still experience problems, we would recommend the installation of an OS-specific version of Gnuplot on those systems.

As root, run

    yum install gnuplot

and as software installer run

    echo "setenv BDG_TOOL_GNUPLOT \"/usr/bin/gnuplot\"" >> $BDG_home/setup_local.csh
    echo "export BDG_TOOL_GNUPLOT=\"/usr/bin/gnuplot\"" >> $BDG_home/

The setting of the environment variable BDG_TOOL_GNUPLOT will ensure the use of the newly installed OS-version of "gnuplot".

Remember that CentOS8 will reach end-of-life on December 31, 2021, while CentOS7 is still supported til June 30th, 2024!

Coot 0.9.6 regression in conjunction with visualise-geometry-coot

The latest Coot version 0.9.6 (e.g. distributed as part of the 7.1.016 update of CCP4) stops with an error when running visualise-geometry-coot: this is due to changes in Coot that removed the no-coot-tips function.

You can fix that by removing the corresponding line 11 in $BDG_home/scripts/problem-gui.scheme, e.g. using

  sed -i "s/^(no-coot-tips)//g" $BDG_home/scripts/problem-gui.scheme

(or any editor of your choice).

buster-report failure after MapOnly run (fixed in 20211020 release)

Because a run with

  refine -M MapOnly ...

will not create deposition-ready BUSTER_model.cif and BUSTER_refln.cif files at the moment, buster-report will complain about missing files and fail to produce a full report. To fix this (for the moment), please run with

  refine nsmall=1 nbig=2 ...

instead if the creation of a full report even after (basically) no refinement step is important to you. We will fix this for the next release.

aB_deposition_combine on MacOS (fixed in 20211020 release)

Running something like

    aB_deposition_combine -aP /where/ever/autoPROC/dir BUSTER_model.cif BUSTER_refln.cif

will most probably fail on MacOS systems with an error message like

awk: illegal statement
 input record number 2, file 
 source line number 7
awk: illegal statement
 input record number 3, file 
 source line number 7

(the same command run on Linux systems will work as expected). This will be fixed in the next release.

Thanks to Mike Norris for reporting.