Only 430 models are generated for membrane prediction

[Anonymous]

Dear all,

I try to predict the structure of a membrane protein with 4 transmembrane helices and 290 amino acids. I set the output by flag: out:nstruct 9999.
But the membrane_abinitio mode can only generate 430 models. I have tried 3 times. Each run gives 430 models.

Could anyone help me?

[Anonymous]

What is the exit status? Does it exit normally, or is it giving an error message?

What changes if you try nstruct 429, 430, 431?

[Anonymous]

> What is the exit status? Does it exit normally, or is it giving an error message?
>
> What changes if you try nstruct 429, 430, 431?

It exit normally. No error message is reported.
I tried nstruct 1 and it worked.

In addition, I find some confusing flags.

nstruct | 1 | I| Number of times to process each input PDB
shuffle_nstruct | 1 | I| total number of decoys to produce

These are in the help message.

[Anonymous]

shuffle_nstruct should only take effect if you also pass the shuffle flag – this is used for certain modes to randomize the order that jobs are processed (specifically, it’s used on BOINC in the Rosetta@home project).

You’re welcome to try shuffle_nstruct but I don’t think it will help.

There are two option system commands that may help track this error down. First, -options::user will repeat the loaded options at the beginning of the run. This is useful for making sure Rosetta read your options file properly. Second, -show_accessed_options will print at the end of the run all the options whose value was checked – this will tell you if you’ve specified options that didn’t do anything. (You can’t use both these options in the same run – checking which ones are specified on command line for options::user will screw up the latter flag by marking all of the as used).

[Author]

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