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IDProjectCategoryView StatusDate SubmittedLast Update
0000186Rosetta[All Projects] Input Handlingpublic2013-03-01 10:222013-03-01 10:53
Assigned Tosmlewis 
PlatformAll platformsOSAnyOS VersionAny
Product Version 
Fixed in Version 
Summary0000186: Should ignore_zero_occupancy default true or false?
DescriptionMinicon 2013 defaults discussion #1:

Currently, Rosetta ignores all atoms with zero occupancy (the penultimate PDB column). If it's a sidechain, Rosetta will auto-rebuild the sidechain. If it's a backbone, Rosetta deletes the whole residue (standard behavior if any of {N, CA, C, O} are missing). This is controlled by -ignore_zero_occupancy, which defaults true, but could be false.
Additional InformationArguments in favor of changing the default from true to false (start reading zero occupancy atoms):

-This is a major class of user error on the message boards
-On the "principle of least surprise", we should match what molecular viewers (pymol) do - read in all the atoms.

Arguments against:
-These are often garbage coordinates, especially sidechains, we should not treat them as accurate. (This may be ameliorated by repacking zero-occupancy residues through the existing repack_missing_sidechains system).

This bug will stay open for "a while", and then the default will change from true->false (with the fix above) unless objections are noted.
Tagsforums, Minicon_2013_defaults, user_support
Application(s) Affectedignore_zero_occupancy
Command Line Usedpdb reader, ignore_zero_occupancy
Developer Options
Fixed in SVN Version
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- Issue History
Date Modified Username Field Change
2013-03-01 10:22 smlewis New Issue
2013-03-01 10:23 smlewis Assigned To => smlewis
2013-03-01 10:23 smlewis Status new => assigned
2013-03-01 10:23 smlewis Category Incorrect Results => Input Handling
2013-03-01 10:53 smlewis Tag Attached: Minicon_2013_defaults
2013-03-01 10:53 smlewis Tag Attached: forums
2013-03-01 10:53 smlewis Tag Attached: user_support

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