Loop extensions at the end of chains

[Anonymous]

I am trying to model the ends of a protein structure that extend beyond what I have in the PDB file. I tried using the FloppyTails protocol but that seemed to only work for really long tails (> 30aa) and gave me a segmentation fault when I tried to make them shorter (3-10 aa). Does anyone know of a way to use the loop prediction or modify the floopy tails protocol to get this to work?

thanks
James

[Anonymous]

I never tried FloppyTail with a short tail, but I’m surprised that it failed. Can you describe the segfault further?

What have you tried in the traditional loop modeling protocol? I think it will work as-is if you tell it CCD-style loop closure (it will actually just skip the closure step).

[Anonymous]

After some digging into the code I realized there was a function being called that was specific to the authors original project. It was looking for specific residues in the example pdb file. When these were removed it failed. When that function was commented out and recompiled the rest of the program ran fine and produces floopy tails of any lengtth.

thanks
James

> I am trying to model the ends of a protein structure that extend beyond what I have in the PDB file. I tried using the FloppyTails protocol but that seemed to only work for really long tails (> 30aa) and gave me a segmentation fault when I tried to make them shorter (3-10 aa). Does anyone know of a way to use the loop prediction or modify the floopy tails protocol to get this to work?
>
> thanks
> James

[Anonymous]

I left it that way so it would work out-of-the-box for the experiments described in the paper it accompanies – did I not make it clear enough in the documentation? Let me know if you think I can improve the documentation….

[Anonymous]

Sorry to bother you with this, I should have figured it out before posting to the forum. After knowing what the problem is the manual make sense, but at first I figured that it would just print out things specific to that system and didn’t know that it would fail completely. I would suggest just putting stronger language such as saying that this must be removed or it won’t work for any system but the example.

thanks for the help

James

> I am trying to model the ends of a protein structure that extend beyond what I have in the PDB file. I tried using the FloppyTails protocol but that seemed to only work for really long tails (> 30aa) and gave me a segmentation fault when I tried to make them shorter (3-10 aa). Does anyone know of a way to use the loop prediction or modify the floopy tails protocol to get this to work?
>
> thanks
> James

[Author]

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