what is “-relax:sequence” ?

[Anonymous]

in the user guide for “how to prepare structures for use in Rosetta”, Steven C. recommended to use -relax:sequence. What is this parameter? It seems relax manual only mentions -relax:fast -relax:thorough, and the deprecated -relax:classic.

[Anonymous]

Steven Combs passes this along:

“The problem with this question is that myke [Mike Tyka] changed relax to default to fast relax. Before, in 3.2, which the tutorial was written for, sequence relax was fast relax. If they are using 3.4, sequence relax stands for a set of paramaters for relax that changes the behaviour of relax at certain points. We never use sequence relax. We only run fast relax, which is the default beahviour in the relax application in 3.4.”

[attesor]

Thanks for your reply, smlewis!
I guess the reply from Steven may be interpreted as: “-relax:sequence is not recommended in v3.4 (because it changes the behaviour of relax, somehow)”, right? One should try to use -relax:fast.

Also, I checked the help page of relax in v3.4 (relax.linuxgccrelease –help), it seems -relax:fast is default to false:
” relax: | | |
fast | false | B| Do a preset, small cycle number FastRelax
“

[Anonymous]

Hi attesor,

That is incorrect. Relax defaults to fast relax. If you want any different type of relax, you must specify it with the flag -relax:classic or something different.

The flag -relax:sequence is fast relax, but a much shorter version of it. I personally only use the default relax (fast) when I run relax on my proteins.

Steven C.

[attesor]

and I saw “-relax:quick” in the manual.

“For virtually all situations it should be sufficient to use either -relax:quick or -relax:thorough and not worry about all the options.”

Does it have any difference from “-relax:fast” ? Or they are just synonyms?

[Anonymous]

As far as defaults: If you look at src/protocols/relax/util.cc:generate_relax_from_cmd, you’ll see that it’s a long if-elseif-elseif tree, with fast as the default choice. You are correct that the boolean command line argument (probably incorrectly) defaults false…

[attesor]

I see. Maybe just the help doc is not updated. Thanks!

[attesor]

Thanks, Steven C. I tested both -relax:sequence and -relax:fast on my protein (~60 aa). Both runtime and RE score are very similar. But I guess I will stick to -relax:fast as there is few documentation about -relax:sequence. And I suggest to update the corresponding user guide page when you got time. Thanks again!

[Anonymous]

I’ve never heard of it. It’s more likely a misprint than a synonym. Where did you see it…?

[attesor]

it appears twice in v3.3 manual:
http://www.rosettacommons.org/manuals/rosetta3.3_user_guide/d6/d41/relax_commands.html
twice in v3.4 manual:
http://www.rosettacommons.org/manuals/archive/rosetta3.4_user_guide/d6/d41/relax_commands.html

and v3.4 actually did not complain about the parameter and swallowed it.

[Anonymous]

OK, I opened the code up:

} else if ( option[ OptionKeys::relax::quick ]() ){
protocol = new FastRelax( scorefxn, option[ OptionKeys::relax::default_repeats ]() );
} else if ( option[ OptionKeys::relax::fast ]() ) {
protocol = new FastRelax( scorefxn, option[ OptionKeys::relax::default_repeats ]() );

Assuming the flags aren’t accessed somewhere else, they’re synonyms.

[Author]

Posts