- This topic has 3 replies, 2 voices, and was last updated 11 years, 9 months ago by Anonymous.
February 22, 2012 at 7:04 pm #1170Anonymous
I have a protein with a loop and I want to made a single mutation or small insertion in the loop.
Do I need to prepare a new fragment file for protein which has a single mutation in the loop, or can I use the fragment file from parent protein?
Is it possible to avoid regeneration of the fragment file, as it takes a lot of time?
Thank you for you help.
February 22, 2012 at 7:56 pm #6676Anonymous
Fragment generation is two steps. The hard-for-users step is secondary structure prediction generation, mostly because it relies on half a dozen bits of scattered software. The actual fragment generation is not that hard – if you already have SS predictions in hand, it’s pretty fast with the demo included in 3.3.
Errors in the input sequence (point mutations) are only relevant insofar as they affect the secondary structure prediction. If your mutation is going to turn a loop into a loop, it won’t matter. If your mutation is going to turn a helix-preferring region into a loop-preferring region, it can matter.
Errors in the _length_ of the sequence are hugely important. That will produce the equivalent of a frameshift mutation in the fragment file – all the fragments will apply to the wrong frames. You should regenerate fragments for indels. Rosetta will probably refuse to accept a fragment file with a different length from the protein.
If you have the SS predictions for the old sequence, you can manually edit those to include your indel (if it’s in a loop, just assign it the SS preference of its neighbors), then rerun only the second step of fragment picking. Or just let Robetta do it.
February 23, 2012 at 3:22 pm #6680Anonymous
So I understand that I can rerun only the second step of fragment picking using a flag file,
but this file call *.checkpoint file which has data for parent protein sequence.
Is it OK? Or I need to modify it some how?
Thank you again for your help.
February 23, 2012 at 4:16 pm #6681Anonymous
You will want to alter all of the inputs to fragment picking to match your new sequence. I haven’t used the checkpoint file; when I’ve done it with only a psipred_ss2 file. I don’t know how to alter the file for your purposes.
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