Dear all,
Run ab_initio folding , the first step I have to get the fragmet picker first. Can I use the Null_fragment protocol to get fragment. Because I have only the fasta sequence.
Thank you so much and best regards,
Tuong Vy
Category:
Post Situation:
Unless you have special requirements (and assuming you're an academic user), it's highly recommended to just use the fragment server at http://www.robetta.org/ - it works with just the sequence, and saves a bunch of headaches in getting things set up.
If that's not going to work for you, you may want to clarify what you're trying to accomplish - what special restrictions, limitations, or requirements feed into your decision to make fragments locally. How are you intending to set up the Null_fragment protocol?
Note that it's probably not productive to do fragment picking with "just" a sequence - you'll want to bring in secondary structure prediction at least. Although that can be done by running external programs on your fasta sequence. (Getting those external files set up is most of the headaches of running the fragment picker locally.)
Thank you so much rmoretti,
I am not an academic user for this. It is working now.
Many Thanks