UPDATE ("Fri, Jul 23 2021, 10:30 UTC"): The download packages (GPhL_BUSTER_snapshot_20210716.darwin.tar and GPhL_BUSTER_snapshot_20210716_install.sh) 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 "./install_Grade2.sh" - 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:
cd ~/Downloadsmkdir tmpfix cd tmpfix
mv ../GPhL_BUSTER_snapshot_20210716* . mv ../fix_20210716_macOS.sh .
chmod +x fix_20210716_macOS.sh ./fix_20210716_macOS.sh
This should result in a new set of files
GPhL_BUSTER_snapshot_20210716.darwin.tar GPhL_BUSTER_snapshot_20210716_install.sh
that could be used for installation of our software on those case-insensitive filesystems. Thanks to Kevin Battaile for reporting this issue.
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.
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/setup_local.sh
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!
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).
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.
Running something like
aB_deposition_combine -aP /where/ever/autoPROC/dir BUSTER_model.cif BUSTER_refln.cifwill 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.