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comparative modelling and broker

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comparative modelling and broker


I am trying to perform an abinitio modelling of the full-length structure of a two domains protein, having the crystal structure of the Nterminal one. If I try to use a similar protocol as the demo of comparative modelling with end extension the program stops with the following error:

ERROR: moving_connection.icoor().is_internal() && fixed_connection.icoor().is_internal()
ERROR:: Exit from: src/core/conformation/ line: 100

sometimes the first pdb that comes out is ok, but when it crashes, the position of both domains is strangely far away.

Thanks in advance!


Post Situation: 
Tue, 2013-02-05 08:33

This isn't really enough evidence to help us debug the problem. I can tell you that in general, this is an error that occurs when adding residues to a pose; probably it is occurring when Rosetta is tacking the unknown-portion residues onto the known-portion residues.

My best guess is a misalignment or misnumbering in the input files; for example your alignment inputs tell Rosetta that there are 100 residues in the N-terminal domain, but it only contains 96 readable residues (perhaps because of nonzero occupancies, or undetected funny numbering). This guess is a little inconsistent with the "sometimes it crashes, sometimes it works but wrong" aspect, but very consistent with what historically causes problems for this sort of modeling.

Tue, 2013-02-05 12:46


thanks for the response

I checked the pdb and I didn't find anything unusual

the broker.arg is identical as the demo and the files I am using are almost the same:


CLAIMER RigidChunkClaimer
REGION_FILE S_0029.pdb_1_126.region
PDB_FILE S_0029.pdb


RIGID 1 126 0 0 0

the only different thing is that I am trying to model the C-terminal domain. I also saw the following in the output:

protocols.general_abinitio: (0) AbrelaxMover: S_0001
loops: (0) Extended: (-3,+0) LOOP 124 326 0 0 0
protocols.topo_broker: (0) Enlarged loops:
protocols.topo_broker: (0) LOOP begin end cut skip_rate extended
protocols.topo_broker: (0) LOOP 124 326 0 0 0

this is not right because the modelling part is between the residue 127 and the end (position 199). What I found completely weird is that the first cycle worked fine, with a pdb at the end with 199 residues all connected. But in the second cycle the error appears and both domains are too far away from each other.



Wed, 2013-02-06 06:36

sorry...I solved the problem. I didn't realize that I have to start with the full-length protein as a model


Wed, 2013-02-06 08:11

Glad to hear it!

Wed, 2013-02-06 08:19