Known Issues¶
Please check the online version of this issues page: https://gphl.gitlab.io/grade2_docs/issues.html as this is updated frequently as new issues arise.
Issues found with Grade2 version 1.3.2
¶
Getting Grade2 to work with CSD release 2023.1 released April 2023¶
This problem affects all versions of Grade2 and will be fixed in the next Grade2 release
Grade2 terminates with a "CSDNotFoundException"¶
Grade2 -P, --PDB_ligand failed for some PDB components (now fixed)¶
The problem affected all versions of Grade2 but has been fixed by PDBe. Big thanks to the PDBe team, particularly Ibrahim Roshan for the fix.
Issues found with Grade2 version 1.3.1
(Distributed with BUSTER 20230217)¶
Issues found with Grade2 version 1.3.0
(Distributed with BUSTER 20221121)¶
Grade2 does not properly handle SMILES with some ambiguous chirals¶
Bug fixed #559 in Grade2 release
1.3.1
.
Issues for Grade2 version 1.2.0
(Grade2 Update Release 31 March 2022)¶
Issues for Grade2 version 1.1.0
(Distributed with BUSTER 20220203)¶
Grade2 cannot read a MOL2 file of a charged molecule when it has atomic partial charges¶
Bug fixed #444 in Grade2 release
1.2.0
.
Grade2 restraint dictionaries cannot be read by Coot because of long InChI records¶
Bug fixed #438 in Grade2 release
1.2.0
.
On MacOS 10.15 using NFS - there may be problems running Grade2¶
Issues for Grade2 version 1.0.0
(Distributed with BUSTER 20210716 and 20211020)¶
Grade2 cannot read a MOL2 file of a charged molecule when it has atomic partial charges¶
Please see section above - Bug fixed #444 in Grade2 release
1.2.0
.
Grade2 restraint dictionaries cannot be read by Coot because of long InChI records¶
Please see section above - Bug fixed #438 in Grade2 release
1.2.0
.
On MacOS, Grade2 does not work with latest CSD Release 2021.2 (September 2021)¶
Bug fixed #390 in Grade2 release
1.1.0
.
On MacOS installation of (or update to) 2021.1 CSD Release (July 2021) causes Grade2 to crash¶
Bug fixed #390 in Grade2 release
1.1.0
.
Bug: input from MOL2 file that has atom names containing lower case letters¶
Bug fixed #324 in Grade2 release
1.1.0
.
Bug: grade2 will fail if the environment variable PYTHONPATH
is set¶
Bug fixed #349 in Grade2 release
1.1.0
.
Bug: "Suggestion: to view/edit the restraints, use one of the commands" gives wrong filenames when --out is used¶
Bug fixed #333 in Grade2 release
1.1.0
.
.
(the blank lines above are included so that hyperlinks to issues above work better).
Please check the online version of this issues page: https://gphl.gitlab.io/grade2_docs/issues.html as this is updated frequently as new issues arise.