How has grade changed over time?
Improvement introduced in the July 2014 (1.2.9) grade release
Improvement introduced in the May 2014 (1.2.8) grade release
- Introduce check for the use of Mogul version 1.6 and if detected issue WARNING
that an update with speed improvement is now available.
Improvements introduced in 1.2.7 grade release (in snapshot release from February 2014)
- Include CONECT records in output PDB file to satisfy a user request
- Record total charge in comments to satisfy a user request
Improvements introduced in 1.2.6 grade release (in snapshot release from January 2014)
- Provide support for mogul from 2014 CSDS release, including
support for Mogul with in-house libraries
(only applicable for corporate customers with CCDC support).
- Protect against mogul infinite loop when presented with messed up mol2 file input.
- Improve description of method used included in output cif file (and consequently in BUSTER and buster-report output.
- Introduce optional output of restraints in SHELXL format with the ‑shelx, ‑shelxH
and ‑oshelx command line options.
Improvements introduced in 1.2.4 grade release (in snapshot release from June 2013)
- grade now allows use of environment variables to specify the location of
external helper tools as an alternative to finding from user's PATH.
- introduction of -checkdeps option for both grade and grade_PDB_ligand. This
includes test that problematic version of mogul is not being used.
- grade_PDB_ligand now provides a facility to set curl or wget options to
allow use in sites that use a proxy to limit external access.
- sort out grade bug failing to clean up temporary directory on exit.
Improvements introduced in 1.2.3 grade release (in snapshot release from November 2012)
- mol2 files containing positively charged phosphorous atoms will now work.
- mol2 files with titles with comments containing string "_ideal.pdb"
will now work.
- grade will now run without obabel being installed. Instead it tests
for obabel on path and gives a sensible warning and runs with
reduced functionality if it is not found.
- grade now runs recognise-compound utility as a matter of course. This
provides a warning that a user's new compound is already a known
PDB chemical component.
Improvements introduced in October 2012 (1.2.0) grade release
- Use override values for geometry around phosphates where mogul does
not have an opinion, since dynamo tends to get the angles much too
- "Planarity vetoes" from grade. grade information is now used to ensure
that like biphenyl rings are not wrongly set planar.
- set atomnames if supplied with mol2 with all atoms being named
after their element type ("C", "N" etc).
- mogul search performed by grade modified to allow small amount of
generalisation for bonds and angles but not torsion angles.
- fix issue with torsions not being enforced during QM step of grade
- introduce option -really_noH for ligands that do not have any hydrogen atoms
- grade_PDB_ligand option switch to v3 atomnames
- grade_PDB_ligand option -xdat to use experimental coordinates
from LigandExpo when no ideal coordinates are available.
- grade_PDB_ligand option -nonet to allow use from behind firewalls that
prevent the tool getting direct web access
- recognise-compound utility added to find whether ligand is already in
PDB chemical components definitions.
Improvements between the January 2011 (1.1.0) and November 2010 (1.0.1) releases of grade
- mol2 files are now converted to CIF using our own tool rather than
libcheck; we convert the SYBYL atom types to ccp4 atom types. This
allows improved atom typing, and removes a problem we saw
occasionally where libcheck added extra hydrogens to an input file
which already contained hydrogens.
- With the atom types in place, we can determine when a bond is
between sp3-hybridised atoms, and use this to analyse
mogul torsion output to determine when a bond should have a torsion
along it to ensure a staggered conformation.
- A customer requested an option for generating large planes rather
than our normal small planes; this has been added
- In response to a customer request, PDB files are now produced with
the atom occupancies set to 1 rather than 0.
Improvements between the October 2010 (1.0.0) and November 2010 (1.0.1) releases of grade
- The names of planes in the dictionaries are now no more than eight
characters long, which avoids a bug in refmac.
- Mogul is called with generalisation turned off, which avoids some
situations in which it produced wrong restraints.