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The problem hasn't been solved

Fold and Dock - chains not in contact


I wonder if anyone can suggest a solution, I am attempting to perform a fold and dock calculation. however, in about 80% of the structures generated by Fold and Dock the chains are not in contact with one another. On top of this, in about 5% of the cases I have actual overlapping of the structures (eg a helix (Ca not just side chains) will exist in the same position for each monomer)).

The command I am using can be found here

Thanks for your help

Post Situation: 

Biopython error in mac os x


I am new with mac osx and rosetta. I have rosetta 3.3 installed and have trouble with installation of biopython 1.59. on my mac os 10.7, have already installed Xcode 4.3.2. I have pasted the error message. Any help would be highly appreciated.

$cd biopython-1.59
$sudo python install
running install
running build
running build_py
creating build
creating build/lib.macosx-10.7-intel-2.7
creating build/lib.macosx-10.7-intel-2.7/Bio
copying Bio/ -> build/lib.macosx-10.7-intel-2.7/Bio
copying Bio/ -> build/lib.macosx-10.7-intel-2.7/Bio

Post Situation: 

input_score_filter not taken by program cluster ?

Hi, I have Rosetta 3.4 here.
When I run cluster using parameter -cluster:input_score_filter , it seems to me the parameter is just ignored and all decoys (no matter its score is higher or lower than the limit) are considered. I got the same results no matter I set the parameter or not. I read the source file at rosetta_source/src/apps/public/ and it seems variable input_score_filter is not used (together with some other parameters). Function GatherPosesMover::set_filter in rosetta_source/src/protocols/cluster/ seems never invoked anywhere.

Post Situation: 

Trouble building rosetta3.4 on Mac OsX 10.5.8

I have unpacked all of the files but each time that I enter scons bin mode=release I keep getting this read out:

josh-spegmans-macbook-pro:rosetta_source joshspegman$ scons bin mode=release
scons: Reading SConscript files ...
Running versioning script ... sh: git: command not found
Done. (0.1 seconds)
scons: done reading SConscript files.
scons: Building targets ...

Post Situation: - protocols.docking.DockingInitialPerturbation: moving together failed. Aborting DockingSlideIntoContact.

When I run the docking script, it starts out ok, but, as the run progresses, the ligands are being placed further and further from the target substrate. Also, I get the message "protocols.docking.DockingInitialPerturbation: moving together failed. Aborting DockingSlideIntoContact."

Is there any way to constrain where the movers will place the ligands? I'm using the following command line options: --pdb_filename hard_to_dock.pdb --partners AB_C --jobs 1000 --job_output docked --translation 3 --rotation 8 --PyMOL_Mover_ip off

Post Situation: 

Incorrect Jump being set in RosettaScripts docking mover

I'm trying to dock three chains with RosettaScripts with Rosetta 3.3. Docking chain C to chains AB. I.E. the partner string would be AB_C. It appears that no matter what jump number I use in the docking tag in RosettaScripts, it always tries to dock the second and third chains to the first chain of the structure (always 1_23) corresponding to a jump number of 1. Is this a known issue with the docking mover in Rosetta Scripts?

Post Situation: 


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