0000199: SymE is broken (or probably never worked to begin with )

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Date Submitted

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0000199

Rosetta

[All Projects] Crash

public

2013-03-06 18:59

2013-03-15 10:59

Reporter

delucasl

Assigned To

delucasl

Priority

high

Severity

minor

Reproducibility

always

Status

resolved

Resolution

fixed

Platform

All platforms

Any

OS Version

Any

Product Version

All

Fixed in Version

Summary

0000199: SymE is broken (or probably never worked to begin with )

Description

"Hi Sam,

I for the life of me could not get a BugTracker account (the image to join isn't there, so I can't sign up!), so I decided to email you.

I did a couple of things after we talked this morning. I ran both the monomer and assembled tetramer (in membrane mode, fixbb) with the symE flags (-score:symE_units 4; -score:symE_bonus 100). The tetramer didn't work (rosetta_scripts.default.linuxgccdebug: src/core/scoring/MembraneTopology.hh:133: bool core::scoring::MembraneTopology::allow_scoring(utility::pointer::ReferenceCount::Size) const: Assertion `seqpos <= allow_scoring_.size()' failed.
Got some signal... It is:6) , but the monomer did run, it just did fixbb normally. The tetramer error appears to be a membrane issue...?

I have all of this sorted in my directory:

~duranam/learning/SymE_bonus/tet
for the tetramer
~duranam/learning/SymE_bonus/
for the monomer trial

97_aligned.pdb is my sequence and structurally symmetric (2-fold inverted) protein. I know I can run fixbb on the tetramer and get the same mutations for each chain, but I am looking for a way to maintain the symmetry within the protomer/monomer. "

Tags

No tags attached.

Application(s) Affected

all

Command Line Used

anything that scores a protein

Developer Options

Confirmed As Bug

Fixed in SVN Version

54296

Attached Files

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Notes
(0000162) delucasl (Administrator) 2013-03-07 20:47	OK well it's definitely not a problem with membrane scoring thats for sure

(0000174) delucasl (Administrator) 2013-03-15 10:59	The symE_bonus scoring term was a terrible idea. it has been replaced with a mover called FavorSymmetricSequence. The old score term code will be removed soon.

Issue History
Date Modified	Username	Field	Change
2013-03-06 18:59	delucasl	New Issue
2013-03-06 18:59	delucasl	Status	new => assigned
2013-03-06 18:59	delucasl	Assigned To	=> delucasl
2013-03-07 20:47	delucasl	Note Added: 0000162
2013-03-15 10:59	delucasl	Fixed in SVN Version	=> 54296
2013-03-15 10:59	delucasl	Note Added: 0000174
2013-03-15 10:59	delucasl	Status	assigned => resolved
2013-03-15 10:59	delucasl	Resolution	open => fixed