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?
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?
> 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.
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).