0000202: in fa_standard_05.2009_icoor, many atoms have X instead of VIRT for mm atom type

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0000202

Rosetta

[All Projects] Bad Coding

public

2013-03-12 16:56

2013-03-13 11:07

Reporter

smlewis

Assigned To

Priority

low

Severity

minor

Reproducibility

always

Status

new

Resolution

open

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OS Version

Product Version

Trunk

Fixed in Version

Summary

0000202: in fa_standard_05.2009_icoor, many atoms have X instead of VIRT for mm atom type

Description

14:53:46 ~/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
7,9c7,9
< ATOM MG Mg2p VIRT 2.00
< ATOM V1 VIRT VIRT 0.00
< ATOM V2 VIRT VIRT 0.00
---
> 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

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No tags attached.

Application(s) Affected

mm scoring, fa_standard_icoor

Command Line Used

N/A

Developer Options

Fixed in SVN Version

Attached Files

Relationships

related to

0000004

resolved

delucasl

molfile_to_params misassigns mm atom types

Notes
(0000163) 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?

(0000164) 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