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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 |
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| 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 | | |
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| 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.
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| 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 |
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| Application(s) Affected | ignore_zero_occupancy |
| Command Line Used | pdb reader, ignore_zero_occupancy |
| Developer Options | |
| Fixed in SVN Version | |
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| Attached Files | |
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