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ID | Project | Category | View Status | Date Submitted | Last Update | ||||||||
0000186 | Rosetta | [All Projects] Input Handling | public | 2013-03-01 10:22 | 2013-03-01 10:53 | ||||||||
Reporter | smlewis | ||||||||||||
Assigned To | smlewis | ||||||||||||
Priority | low | Severity | minor | Reproducibility | always | ||||||||
Status | assigned | Resolution | open | ||||||||||
Platform | All platforms | OS | Any | OS Version | Any | ||||||||
Product Version | |||||||||||||
Fixed in Version | |||||||||||||
Summary | 0000186: Should ignore_zero_occupancy default true or false? | ||||||||||||
Description | Minicon 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 Information | Arguments 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. | ||||||||||||
Tags | forums, Minicon_2013_defaults, user_support | ||||||||||||
Application(s) Affected | ignore_zero_occupancy | ||||||||||||
Command Line Used | pdb reader, ignore_zero_occupancy | ||||||||||||
Developer Options | |||||||||||||
Fixed in SVN Version | |||||||||||||
Attached Files | |||||||||||||
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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