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IDProjectCategoryView StatusDate SubmittedLast Update
0000199Rosetta[All Projects] Crashpublic2013-03-06 18:592013-03-15 10:59
Assigned Todelucasl 
PlatformAll platformsOSAnyOS VersionAny
Product VersionAll 
Fixed in Version 
Summary0000199: 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:

for the tetramer
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. "
TagsNo tags attached.
Application(s) Affectedall
Command Line Usedanything that scores a protein
Developer OptionsConfirmed As Bug
Fixed in SVN Version54296
Attached Files

- Relationships

-  Notes
delucasl (Administrator)
2013-03-07 20:47

OK well it's definitely not a problem with membrane scoring thats for sure
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

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