- This topic has 9 replies, 3 voices, and was last updated 11 years, 1 month ago by Anonymous.
November 7, 2012 at 8:02 am #1454Anonymous
I am using the following protocol which someone used in the forum to build loop based on crystal structure. I am going to fix the left part of the region since they are from crystal structure and I find that all the regions are rebuild by Rosetta. I am just wondering, where is the problem?
thank you very much
November 7, 2012 at 3:43 pm #8040Anonymous
Double check your loop file….
November 7, 2012 at 3:51 pm #8041Anonymous
What does “left part” mean…?
November 7, 2012 at 5:27 pm #8045Anonymous
I checked many times, and I don’t know where the problem it is…..
November 7, 2012 at 5:32 pm #8046Anonymous
Is the backbone moving or just the sidechains? What do the occupancies of the moving region look like in the PDB (are they nonzero)? Post the loop file (just paste it into the text box).
November 7, 2012 at 6:28 pm #8047Anonymous
both backbone and side chain moves. I trying to include the hydrogen as the input file, but it always claim loop definition out of range. So, I removed all hydrogen as initial structure. Here is the loop file:
LOOP 193 208 200 0 1
November 7, 2012 at 6:57 pm #8049Anonymous
thanks for kind comments. In fact, I remubered the residues from 1…..
November 7, 2012 at 7:20 pm #8050Anonymous
You have fastrelax turned on – try turning that off. I don’t know if fastrelax limits itself to just the defined loop.
November 7, 2012 at 7:56 pm #8051Anonymous
IC, it works now. However, I find my disfulde bridge was borken…..
November 7, 2012 at 6:45 pm #8048Anonymous
If those values are meant to be PDB numberings, you need to include the PDB chain; for example
LOOP 193A 208A 200A 0 1
Rosetta interprets wthem as 1-indexed residue IDs (whole pose numbered starting from 1) normally.
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