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How to score the crystal structure?

Hi All,

I have a control system in which the co-crystal structure is determined. I would like to have rosetta only score the input pdb without docking, so that I can compare the crystal coordinates with the results. I would also like to be able to score the prepacked structure used for the actual studies.

I used the flag -run:score_only and this worked, but there was a file and a pdb file. Also, the rms was 30 in the score file. I re-ran and sure enough, the score was different, indicating that it is actually docking not merely scoring.

The flags I used were:

Post Situation: 

loop modeling during enzyme design?

Dear developers:

I noticed that some loop modeling options (e.g. kic_looop_sampling) are now included for the enzyme_design.linuxgccrelease protocol in Rosetta3.3.

It seems that the capacity to remodel loops in the substrate-binding pocket will significantly improve the enzyme_design protocol. But since this has not been mentioned in any papers or tutorials, are the loop modeling options fully working now, or are they still under development?

Thanks for reading...

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fragment_picker with fasta only

I would like to generate a fragment library based on a sequence. I tried running the fragment_picker demos in rosetta3.3/rosetta_demos/fragment_picker and it seems I need to include a pdb and also psipred (.ss2) file. The documentation seems to say that only vall .fasta .wghts are mandatory. I only have sequence -- can I still run this protocol?

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ERROR: unrecognized atomtype property VIRTUAL

I have built Rosetta3.3 using gcc-4.3 which went smoothly without errors. While running any rosetta script(xml file) using rosetta_scripts.linuxgccrelease, i am getting the error 'unrecognized atomtype property VIRTUAL'. When the same script is run using rosetta_scripts.linuxgccdebug, the error doesn't occur. Please suggest me the solution for this error. Following is the error i am getting.

protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job

ERROR: unrecognized atomtype property VIRTUAL
ERROR:: Exit from: src/core/chemical/ line: 108

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Can not build the parallel version of rosetta-2.3.1 (the SnugDock). Help!!

Hi all,

I was trying to build a parallel version of Rosetta-2.3.1(SnugDock) on my workstation. My OS is RHEL 5.4(32-bit), and I use Openmpi-1.4.3.

I tried to compile it as I did to Rosetta2.3.0 on the same computer and the very same OS and MPI compilier, but it didn't work.

I got the following errors:

###################### undefined reference to `pathways::pathways_generator_main(bool&)'
collect2: ld return 1
make: *** [rosetta.mpilam] error 1


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Calling A Protocol From Another Protocol


I am having trouble calling other movers from the protocol I created and cannot find a solution. Maybe it is obvious again, but I cannot see it.

I modified the minirosetta routine to call my protocol (SymEns), which looks like the following code. This works fine and indeed generates useful output.

SymEnsProtocolOP assembly_mover = new SymEnsProtocol;
protocols::moves::symmetry::SetupForSymmetryMoverOP setup_mover = new protocols::moves::symmetry::SetupForSymmetryMover;

Post Situation: 


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