Abinitio Relax Error from -kill_hairpins

[Anonymous]

I am using Rosetta 3.5 to predict protein structures using AbinitioRelax protocol.
When I specify -kill_hairpins I always got the following errors:

ERROR: [ERROR] invalid header input for kill_hairpins file.
ERROR:: Exit from: src/core/scoring/SS_Killhairpins_Info.cc line: 375
Exception :

[ERROR] EXCN_utility_exit has been thrown from: src/core/scoring/SS_Killhairpins_Info.cc line: 375
ERROR: [ERROR] invalid header input for kill_hairpins file.

The file specified by -kill_hairpins was generated by Robetta server and has a suffix .psipred_ss2. I compared the content to the example file 1elwA.psipred_ss2. Only the first line of comment was missing:

# PSIPRED HFORMAT (PSIPRED V2.6 by David Jones)

I add it back and still no luck.

I would like to try this parameter because “-kill_hairpins ./input_files/1elwA.psipred_ss2 Setup hairpin killing in score (kill hairpin file or psipred file). This option is useful for all-beta or alpha-beta proteins ……”

[Anonymous]

See the following thread for details: https://www.rosettacommons.org/content/killhairpin-error

Basically, the format of the file changed between Rosetta 3.3 and Rosetta 3.4

[Anonymous]

OK, I will manually add a header line. Which should I use? “ANTI” or “PARA”?

[Anonymous]

Rocco, what would be the best approach to fix this here? Change the format back/find out why it was changed in the first place, or have the code spit out the error explicitly stating that the format changed? Or have Robetta spit out the correct format? I updated the ab-initio docs mentioning that the format changed and pointed to that post. We should update the demo as well.

[Anonymous]

They stand for “paralell” and “antiparallel” – use whichever corresponds to the hairpins you wish to kill. – You’re probably looking at antiparallel hairpins, unless you have something special going on.

[Anonymous]

At this point the ideal way to handle it would likely be to make it such that the file reader automatically chooses which format to use based on the input format. A second-best solution would be printing an error which makes it clear the input format has changed.

[Anonymous]

I do want to kill anti-parallel hairpins. It seems I need to specify two key words in the header. So I am going to use:

# PSIPRED ANTI ANTI

would that make sense?

[Anonymous]

Yes, that would be the appropriate header line, then.

[Author]

Posts