We've had reports that the plot generation at the end of a BUSTER run sometimes fail. This turns out to be due to a limitation in sftools where the length of filenames is restricted to be no longer than 192 characters. Normally this is not an issue, unless the autoBUSTER_scrdir parameter is manually set to something too long.
Note that this also impacts a BUSTER run from within a Pipedream job.
.../buster_maponly: line 338: .../bin/linux64_exe/cmdServer: No such file or directory
This can be worked around in two ways. Either by saying
buster_maponly \
BusterExe=$BDG_home/bin/darwin_exe/buster \
BusterCmdServer=$BDG_home/bin/darwin_exe/cmdServer \
...
or by making a symbolic link
cd $BDG_home/bin ln -s darwin_exe linux64_exe
The same issue relates to buster_rvalues.
There is a bug in fetch_PDB_gemmi when encountering reflection data in a given PDB entry containing only I+/I- (or F+/F-) data and not IMEAN (or F): the computation of IMEAN (or F) can miss incomplete acentric reflections, i.e. where e.g. only I+ or only I- is given.
This will be fixed in the next release.
There is a buglet in the core Perl interpreter distributed with many OS versions, that produces warning messages of the type
Use of uninitialized value in numeric eq (==) at /usr/lib/x86_64-linux-gnu/perl-base/IO/Select.pm line 68.
Although without effect on the functionality of a "pipedream", "buster-report", "rhofit" or "grade" job, they can still be disconcerting and plain ugly. The easiest solution is to surpress all warning messages from our perl scripts by adding "-X" to the perl invocation. This can be done e.g. by adding
export KeepFromEnv_BDG_perl="yes" export BDG_perl="/usr/bin/perl -X"
to $BDG_home/setup_local.sh and/or
setenv KeepFromEnv_BDG_perl "yes" setenv BDG_perl_arg "-X"
to $BDG_home/setup_local.csh. Alternatively, one could run the above commands also via e.g.
KeepFromEnv_BDG_perl="yes" BDG_perl_arg="-X" pipedream ... # bash/sh/zsh - or - env KeepFromEnv_BDG_perl="yes" BDG_perl_arg="-X" pipedream ... # tcsh/csh
To see if your particular perl version (as used by our programs) is affected by this issue, you can use the attached test_perl.sh script. Running
./test_perl.shcould return something like
##
## Testing perl environment/setup for BUSTER (Pipedream, buster-report etc)
## (for helpc contact us at buster-develop@GlobalPhasing.com)
##
BDG_home = /home/software/GPhL/BUSTER/20240123
BDG_perl = /usr/bin/perl (v5.34.0 - see "/usr/bin/perl -V" for more details)
### see: https://github.com/Perl/perl5/issues/18238
interaction with IPC::Cmd::run (GH 18238) = >>> WARNING <<<
$IO::Select::VERSION = 1.46
$IPC::Cmd::VERSION = 1.04
Perl version = 5.034000
= 5.34.0
(showing vulnerability of Ubuntu 22.04 LTS) or
##
## Testing perl environment/setup for BUSTER (Pipedream, buster-report etc)
## (for helpc contact us at buster-develop@GlobalPhasing.com)
##
BDG_home = /home/software/GPhL/BUSTER/20240123
BDG_perl = /bin/perl (v5.36.0 - see "/bin/perl -V" for more details)
### see: https://github.com/Perl/perl5/issues/18238
interaction with IPC::Cmd::run (GH 18238) = OK
$IO::Select::VERSION = 1.49
$IPC::Cmd::VERSION = 1.04
Perl version = 5.036000
= 5.36.0
(showing Debian 12 bookworm being fixed).
The bug was introduced (it seems) at v1.42 of Perl's IO::Select and fixed at v1.48 with this bug report.
Some URLs for compound files have changed at the EBI - which requires applying a patch to $BDG_home/scripts/grade_PDB_ligand:
98c98
< my ($version,$vdate) = ("1.2.20","Dec 01 2020");
---
> my ($version,$vdate) = ("1.2.21","Feb 14 2024");
360c360
< my $msdpfx = "ftp://ftp.ebi.ac.uk/pub/databases/msd/pdbechem_v2/".substr($ligid,0,1)."/$ligid";
---
> my $msdpfx = "https://www.ebi.ac.uk/pdbe/static/files/pdbechem_v2/$ligid";
596c598
< my $py="ftp://ftp.ebi.ac.uk/pub/databases/msd/pdbechem_v2/".substr($ligid,0,1)."/$ligid";
---
> my $py="https://www.ebi.ac.uk/pdbe/static/files/pdbechem_v2/$ligid";