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IDProjectCategoryView StatusDate SubmittedLast Update
0000202Rosetta[All Projects] Bad Codingpublic2013-03-12 16:562013-03-13 11:07
Assigned To 
PlatformOSOS Version
Product VersionTrunk 
Fixed in Version 
Summary0000202: in fa_standard_05.2009_icoor, many atoms have X instead of VIRT for mm atom type
Description14:53:46 ~/rosetta/rosetta_database/chemical/residue_type_sets> diff fa_standard/residue_types/metal_ions/MG.params fa_standard_05.2009_icoor/residue_types/metal_ions/MG.params
< ATOM MG Mg2p VIRT 2.00
> ATOM MG Mg2p X 2.00
> ATOM V1 VIRT X 0.00
> ATOM V2 VIRT X 0.00

VIRT is the appropriate mm atom type for virtual atoms (and Mg, unless we get magnesium parameters) - X triggers crashes, but VIRT triggers "do not score this atom for mm purposes"

This is likely true in many places but I only checked MG.params
TagsNo tags attached.
Application(s) Affectedmm scoring, fa_standard_icoor
Command Line UsedN/A
Developer Options
Fixed in SVN Version
Attached Files

- Relationships
related to 0000004resolveddelucasl molfile_to_params misassigns mm atom types 

-  Notes
delucasl (Administrator)
2013-03-12 17:00
edited on: 2013-03-13 11:07

When I resolved bug 0000004 I kept the default behavior (assign mm type as X). See the close note on that report. Should we flip this switch?

smlewis (Administrator)
2013-03-13 11:05

These icoor files long predate bug 0000004 anyway. I say flip the switch, the MM torsion parameters treat X as bad and VIRT as nonexistent...probably nonexistence is better than badness. Generally the user is responsible for checking the atom typing anyway.

As an aside - there's no need to paste URLs - just do a # sign and then digits, and it will automagically make a link to the bug, even with strikethrough for solved bugs!

- Issue History
Date Modified Username Field Change
2013-03-12 16:56 smlewis New Issue
2013-03-12 17:00 delucasl Note Added: 0000163
2013-03-12 17:01 delucasl Relationship added related to 0000004
2013-03-13 11:05 smlewis Note Added: 0000164
2013-03-13 11:07 delucasl Note Edited: 0000163 View Revisions

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