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!
In case you want to switch back to using the compound PDB file directly within the Mogul analysis stage (by setting the environment variable BDG_MOGUL_USE_PDB to a non-empty value), you also need to modify line 208 of $BDG_home/scripts/buster-report-lib/Abt_ligands.pm from
MOGUL MOLECULE FILE $aus.mol2
to
MOGUL MOLECULE FILE $mogul_molin
When depositing a BUSTER-refined model using the BUSTER_model.cif file that contains one or several compound restraint dictionaries, the PDB OneDep deposition system might give an error message
Coordinate format check returned an error ...
This could be caused by a typo in the chiral restraint sections upon deposition preparation. Please change the sections
_chem_comp_chir.gphl_atom_id_1 _chem_comp_chir.gphl_atom_id_1 _chem_comp_chir.gphl_atom_id_1
to
_chem_comp_chir.gphl_atom_id_1 _chem_comp_chir.gphl_atom_id_2 _chem_comp_chir.gphl_atom_id_3
to avoid this duplication.
Please note that this is unrelated to the actual restraint dictionaries used during refinement: it only happens during the generation of the BUSTER_model.cif file in order to mark non-standard PDBx/mmCIF items with an adequate prefix. This will be fixed in the next release.