loop modeling

[Anonymous]

Hi
I am trying to do some loop modeling calculations. I found that after creating the template pdb from the parent pdb and the zones file, there were no HB atoms corresponding to any residue. Is that normal?
When I model the loop I find that the output pdb has these HB atoms at weird positions. I have just outputted one structure for testing. Is this just a consequence of not outputting numerous structures ( will these HB atoms find their correct position on calculating several structures? Also, if a loop is one residue long, how do I define it in the loops file…for example if the parent and query proteins have the same sequence between residues 45-50 and 52-57, how should I incorporate the 51st residue as a loop (is writing LOOP 50 52 0.0 0.0 good enough?)

I am attaching my template pdb and outputted structure (as png and text files) for your convenience.

Thanks
Ishita Sengupta.

[Anonymous]

By “zones file” do you mean the file with “LOOP start stop cut”? Which executeable are you using? (I’m not used to the terminology for normal loop modeling, maybe it’s used in the enzyme code? Abinitio code?)

[Anonymous]

By zones file, I mean the file that is used to specify which portions to copy from the parent to the template pdb. here is the link:
http://www.rosettacommons.org/guide/Comparative+Modeling+with+Rosetta

I am running the calculations on rosettav 3.1. The loops while is to specify which parts of the template need to be rebuilt.

[Anonymous]

James Thompson tells me that that documentation is ancient, and you should try this instead:

http://www.rosettacommons.org/manuals/archive/rosetta3.2.1_user_guide/app_comparative_modeling.html

[Author]

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