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The problem hasn't been solved

ERROR: filtered_alignments.size() > 0

I've been successfully running comparative modeling jobs, but when I tried a new template pdb, I got the following error:

ERROR: filtered_alignments.size() > 0
ERROR:: Exit from: src/protocols/comparative_modeling/ line: 167

and the program stops.

I am having the darndest time trying to debug this. Has anyone run across this error before?


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Relax protocol details for Rosetta 3.1


I've searched for details of what exactly the relax protocol does. I know that it does "agressive sampling" and basically just minimises the Rosetta energy. Is there anywhere I can get more detail than that? I've looked through the Rosetta publications and many describe different aspects of Rosetta but I haven't found any that describe specific protocols or applications. I understand that these protocols keep evolving and therefore cannot be described "for once and for all" so, is my search in vain?

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membrane protein packing prediction

Hi, fellows:
We have two transmembrane peptide from two separate membrane proteins and we would like to see how they pack. The conformation of helix 1, i.e., tilt angle w.r.t the membrane etc, is determined by NMR. For the second helix, we currently take it as an ideal helix. The tilt angle for helix 2 is also known. This problem is similar to the glycophorin A packing problem addressed in "Toward high-resolution prediction and design of transmembrane helical protein structures".

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using defined WATERS in PACKING


does anybody have experience or ideas on how to involve waters in a packing/design process?
I want to repack a protein but want to make sure to include some water filled cavities. Is there a way to define waters or a sort of placeholder, though explicite waters would be better, so that the design-packer can generate a suitable surrounding.

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Reading and writing structures using streams

Is there any way to read (write) structures (pdbs) using a python stream?
Couldn't find any clue in PyRosetta's documentation, so I guess its not a standard feature.. but I'm wondering whether there's a hack people use to in order to enable it..


Lior Z.

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Good Afternoon,

We were wondering if Rosetta3.3 had the ability to use scoring as described in

RosettaHoles: Rapid assessment of protein core packing for structure prediction, refinement, design, and validation by Will Sheffler and David Baker

We have searched the forum for how to utilize it but were not able to find a solution.

Any help would be greatly appreciated.


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