Member Site › Forums › Rosetta 3 › Rosetta 3 – Applications › variable length fragments for Ab initio
- This topic has 7 replies, 2 voices, and was last updated 9 years, 8 months ago by
Anonymous.
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July 1, 2015 at 1:13 pm #2219
Anonymous
Is it possible to ask Rosetta Ab initio application to read in a fragment file containing fragments of variable length generated by myself? If so, would it also have any impact to later stage analysis?
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July 3, 2015 at 9:20 pm #11087
Anonymous
While there has been some work on using different length fragments in abinito, I’m unaware of anything concrete that has been released using that.
For the most part, abinitio is set up to use fixed length fragments, and normally would expect two sets of fragments, one short (typically 3 aa) and one long (typically 9 aa).
There should be some flexibility in how long the fragments are. (e.g. you could try 5-mers and 13-mers … stick to odd lengths, though.), and depending on the exact protocol you might be able to do more than two (e.g. 3-mers, 9-mers and 15-mers), but I don’t believe there’s any facility to read mixed-length fragments from a single file.
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July 6, 2015 at 1:35 pm #11093
Anonymous
this sounds like I can hack it by grouping fragments according to their lengths (odd length) and saving them into different frag files. Does this sound reasonable?
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July 7, 2015 at 11:33 pm #11095
Anonymous
It does sound like a reasonable first step to try.
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July 28, 2015 at 4:18 pm #11105
Anonymous
I built my own 3-residue / 5-residue / 9-residue fragment libraries. 3mer and 9mer libraries work very well with Rosetta. I then tried adding 5-residue fragments using argument -frag5, Rosetta simply ignored that.
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August 6, 2015 at 3:42 pm #11111
Anonymous
The frag5 option is only used by FlexPepDock.
For abinito, it looks like you can use the -fragA and -fragB options instead of -frag9 and -frag3 (respectively) for non-standard size fragments … I haven’t tested this yet, though.
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August 10, 2015 at 3:45 pm #11133
Anonymous
Could you provide with more details, rmoretti? I only found:
std::string frag_large_file, frag_small_file;
if (option[ in::file::fragA ].user()) {
frag_large_file = option[ in::file::fragA ]();
} else {
frag_large_file = option[ in::file::frag9 ]();
}if (option[ in::file::fragB ].user()) {
frag_small_file = option[ in::file::fragB ]();
} else {
frag_small_file = option[ in::file::frag3 ]();
} -
August 18, 2015 at 11:47 pm #11150
Anonymous
That’s the relevant section of the code, yes.
My understanding is that the fragment file reader is intelligent to know what size fragments are being loaded from the file, so it will load fragments as the appropriate size. (So technically you could load your 5-mers and 13-mers with -in:file:frag3 and -in:file:frag9, but I wouldn’t recommend it, for your own sanity.)
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