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Molprobity2
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Write up improvements made to SuiteName along the way and send to Jane and Dave for progress report
#77
russell-taylor
closed
3 years ago
0
Deploy cctbx including new MolProbity on AWS Graviton2 processors
#76
russell-taylor
closed
2 years ago
7
Find an example CCTBX program to base the SuiteName integration on
#75
russell-taylor
closed
3 years ago
1
Add a comment that the default doesn't use the satellite widths and tell how to turn it on with the new flag
#74
russell-taylor
closed
3 years ago
1
Remove the dominant bin column in the SatelliteData table
#73
russell-taylor
closed
3 years ago
1
Fill the README.md with information about running SuiteName and its inputs
#72
russell-taylor
closed
3 years ago
0
Kinemage files: ignore headers and append all lists into one and handle 7-parameter files
#71
russell-taylor
closed
3 years ago
0
CCTBX SuiteName Integration
#70
russell-taylor
opened
3 years ago
0
Ask Christopher to get a script that will report both alternates when there are two
#69
russell-taylor
closed
3 years ago
0
Send 4z4d output to Dave and Jane for them to inspect what is happening on lines 18-20
#68
russell-taylor
closed
3 years ago
0
Upgrade SuiteName
#67
russell-taylor
opened
3 years ago
0
Consider adding orientationPenalty for other Movers besides flips
#66
russell-taylor
closed
1 year ago
1
Determine what is happening with RotMethyls
#65
russell-taylor
closed
3 years ago
1
Consider how to output the annotated XYZ structure along with what optimizations should be done
#64
russell-taylor
closed
3 years ago
0
Consider doing internal sums for bumpSubScore and hubScore in atomScore() as doubles
#63
russell-taylor
closed
2 years ago
1
Probe should do optimal Hydrogen placement on nearby waters during scoring
#62
russell-taylor
closed
2 years ago
0
Upgrade Probe
#61
russell-taylor
opened
3 years ago
0
Consider changing Reduce's behavior based on the resolution of the input structure
#60
russell-taylor
opened
3 years ago
0
Consider a remediator for reading old-format PDB files into Reduce and Probe
#59
russell-taylor
opened
3 years ago
0
Hydrogenate vs. reduce tests are not working for me on some input files
#58
russell-taylor
closed
1 year ago
8
Different outcomes when running Reduce in two phases vs. one phase
#57
russell-taylor
closed
3 years ago
33
Check speed of reduce with -FLIP option in the new develop branch compared to the original
#56
russell-taylor
closed
3 years ago
3
Support running probe from within cctbx to get the scores
#55
russell-taylor
closed
2 years ago
2
Reduce should never make covalent bonds to waters
#54
russell-taylor
closed
3 years ago
3
Get Mage compiling again
#53
russell-taylor
closed
3 years ago
1
Phenix.reduce Adding spurious hydrogens
#52
russell-taylor
opened
3 years ago
2
His are incorrect in 103M.pdb
#51
russell-taylor
closed
1 year ago
1
Determine modes of operation for cctbx/Reduce
#50
russell-taylor
closed
2 years ago
4
Get CCTBX compiling on my laptop using SCons/Visual Studio
#49
russell-taylor
closed
3 years ago
6
[Duplicate issue]
#48
russell-taylor
closed
3 years ago
1
Determine license for new software going forward
#47
russell-taylor
closed
3 years ago
3
Consider replacing all new/delete with smart pointers
#46
russell-taylor
closed
2 years ago
1
Consider replacing the pointer in the middle of _bnded in RotDonor.h
#45
russell-taylor
closed
3 years ago
1
Update Reduce README's and add LICENSE files
#44
russell-taylor
closed
2 years ago
2
Remove unused source files from Reduce
#43
russell-taylor
closed
3 years ago
0
Consider adding knowledge of charge for better placement in Reduce in the future
#42
russell-taylor
opened
3 years ago
0
Reduce seems to claim an abandoned clique search when all default orientations are selected
#41
russell-taylor
closed
3 years ago
2
Flipkin script should handle 2-character chainIDs
#40
russell-taylor
closed
1 year ago
1
Why is the CMake-built new version of Reduce so much slower than the Makefile-built old version?
#39
russell-taylor
closed
3 years ago
3
Add structures to Reduce regression tests
#38
russell-taylor
closed
3 years ago
1
Add regression test of Methyl rotations in Reduce
#37
russell-taylor
closed
3 years ago
1
Speed up neighbor calculation
#36
russell-taylor
closed
2 years ago
2
Early return from genHydrogens()
#35
russell-taylor
closed
3 years ago
3
Run 5a1a for Reduce and Hydrogenate conditions and send result to Jane
#34
russell-taylor
closed
3 years ago
1
Consider changing invalidation approach in analyzeRes when "N" on non amino acids
#33
russell-taylor
closed
2 years ago
1
RotAromMethyl::finalize() should also check for valid() atoms
#32
russell-taylor
closed
3 years ago
1
Are multiple placements for an AtomPlacementPlan valid?
#31
russell-taylor
closed
3 years ago
3
Run static code analysis on Reduce and fix resulting issues
#30
russell-taylor
closed
2 years ago
1
One of the hydrogens on a HEM methyl group should be perpendicular to the ring
#29
russell-taylor
closed
3 years ago
2
Reduce should print a warning when it finds a ligand that it does not recognize
#28
russell-taylor
closed
3 years ago
1
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