0000149: Feature Request: loop RMSD mode - MantisBT

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ID

Project

Category

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Date Submitted

Last Update

0000149

Rosetta

[All Projects] Incorrect Results

public

2012-10-29 11:34

2013-02-21 09:10

Reporter

smlewis

Assigned To

Priority

low

Severity

minor

Reproducibility

always

Status

new

Resolution

open

Platform

OS

OS Version

Product Version

Fixed in Version

Summary

0000149: Feature Request: loop RMSD mode

Description

Is there a command-line only method (I guess RosettaScripts counts) to calculate loop RMSDs? All of the methods with which I am familiar (um, -native on score_jd2) produce whole-structure RMSD, which is not correct when doing loop modeling with only localized variation.

LoopAnalyzer (pilot/smlewis) would be a good place for me to add this (promoting it along the way) if it doesn't exist already.

Tags

No tags attached.

Application(s) Affected

score_jd2, LoopAnalyzer, loopmodel

Command Line Used

feature request

Developer Options

Feature Request

Fixed in SVN Version

Relationships

Notes
(0000125) weitzner (Developer) 2012-10-31 11:41	Part of the difficulty in providing this sort of functionality is the way that alignments are done for the purpose of calculating loop rmsd. I can point you to a function in protocols::loops that calculates what you want, but, afaik, there is not an application to simply calculate this. It would be simple-ish to write one. I'd be happy to talk with you about it offline.

(0000140) smlewis (Administrator) 2013-02-21 09:10	https://www.rosettacommons.org/content/how-make-benchmark#comment-5856 [^]

Issue History
Date Modified	Username	Field	Change
2012-10-29 11:34	smlewis	New Issue
2012-10-31 11:41	weitzner	Note Added: 0000125
2013-02-21 09:10	smlewis	Note Added: 0000140

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