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21 Open 29 Closed
21 Open 29 Closed
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Issues list

Total charge wrong in input file when seed atoms have charges in PDB
#57 opened Dec 19, 2024 by dwappett
Trimming procedure needs to recognise/appropriately deal with terminal residues
#56 opened Nov 20, 2024 by dwappett
MCs added to anchor CA or Ala SC in small models may disappear in bigger models
#55 opened Nov 15, 2024 by dwappett
Code needs to be added for driver "histidine" flag
#54 opened Nov 15, 2024 by dwappett
1
how do we safely convert "ligand" in probe/arpeggio output to "seed"?
#52 opened Aug 5, 2024 by natedey
Seed atoms being removed in distance-based trimming
#51 opened Jun 28, 2024 by dwappett
documentation of distance based approach needs to be clarified
#50 opened Jun 28, 2024 by natedey
Have RINRUS throw a warning if canonical amino acids have an atom type not shown in res_atoms.py
#42 opened Mar 15, 2024 by natedey
character justification of element names could be more flexible?
#41 opened Feb 27, 2024 by natedey
3
adding documentation that let the user know what indexes each component of the PDB files need to be. enhancement New feature or request
#36 opened Oct 11, 2023 by tsantaloci
5
Update pdb_dist_rank.py new distance method to not split water into SC or MC when the script includes hydrogens
#34 opened Mar 29, 2023 by tsantaloci
more flexible distance "center" enhancement New feature or request
#30 opened Jan 25, 2023 by natedey
@tsantaloci @tsuhagia
2
FSAPT GNMT example needs to be reworked
#29 opened Jan 24, 2023 by natedey
@natedey @tsantaloci
installation instructions need to be improved to eliminate path or pythonpath dependencies
#28 opened Jan 20, 2023 by natedey
2
Is instruction 6 for probe model creation correct?
#27 opened Jan 4, 2023 by natedey
@MiloCheng17 @tsuhagia
3
how to get probe/RINRUS to consider canonical amino acid as SIF "ligand" type
#24 opened Sep 28, 2022 by natedey
@MiloCheng17 @natedey
@tsantaloci @da02876 @tsuhagia
2
automating the treatment of seed canonical amino acids bug Something isn't working
#23 opened Sep 23, 2022 by natedey
@MiloCheng17 @tsuhagia
1
consistency needed in output file names
#20 opened Sep 20, 2022 by natedey
@tsantaloci
1
how to resolve ties from arpeggio (or probe)?
#17 opened Jun 15, 2022 by Jmller56
1
GenResAtoms.py should write a model_detail.dat file like v1 probe_freq_2pdb.py
#16 opened Jun 1, 2022 by Jmller56
3
need instructions on how to fake out GenResAtoms.py if we need to manually add a residue to seed
#15 opened Jun 1, 2022 by Jmller56
@MiloCheng17 @da02876
5
ProTip! no:milestone will show everything without a milestone.