Unsolved

I tried to do some loop modeling and now I have this strange problem. Loop modeling no longer works even though I've used it in the past.
Rosetta seems to think that there are no residues in the pose although relax works fine on the same pdb. I tried a very simple test (see below) to try to get it to work but the result is the same. The same problem occurs in both OSX and LInux. What could be the source of this problem?

With the release version I get this message:
ERROR: Start pose and native pose don't match in length

With the debug version I get this message:

Hi,

I want to know two things about a design experiment involving loop modeling:-
1. I have a database of loop conformations, that I have extracted from PDB. I want to model those conformations onto a beta-hairpin structure. How can I do that ??
2. Is it possible to apply de-novo folding protocol only for the loop-sequence, keeping the hairpin sequence unaltered.

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Bharat

Hey everyone, I'm trying to compile in mpi mode on a cluster. I used:
./scons.py bin mode=release cxx=icc extras=mpi

First, everything looked good but almost after 3 hours latter i had an error;


src/protocols/features/ReportToDB.cc(107): warning #780: using-declaration ignored -- it refers to the current namespace
using protocols::features::ProteinRMSDFeatures;
^
src/protocols/features/ReportToDB.cc(108): warning #780: using-declaration ignored -- it refers to the current namespace
using protocols::features::ProtocolFeatures;
^

I'm using an ab initio script to preform a structure calculation with NOE restraints (i,i+3 or longer). The _fa NOE file, as I understand it, only activates at one stage. Is it better to create a centroid file for earlier stages of the calculation? Is it necessary ?

As well, would someone be willing to share a structure generation script with me ? I'm sure I could be doing it better. As things go, I have method to generate a little protein structure from NOEs and coordinate a Zn ion with 3xCys/1xHis, below. I would appreciate the help to make it better and more efficient.