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Running CstFileToTheozyme for Mono-Atomic Metal

Submitted by Jhreed on Fri, 2016-07-08 13:43
Category: 
Design

Hi everyone,

I'm running into issues making a proper .cst file for a mono-atomic metal ion. I've tried to follow Wang, et. al. 2010 Protein Science paper, but am cannot get it right. I've attached my cst and flags files.

I've also attached the error file that comes up when I attempt to run CstFileToTheozyme.

The ZN.params file has been very slightly modified to have NAME ZN2 and IO_STRING ZN2 Z.

Thanks!

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Rosetta 3 - General

error--rosetta fragment‐based refinement protocol for refinement against EM density

Submitted by gsuchunli on Wed, 2016-07-06 10:35
Category: 
Fragment Generation

I am trying to use rosetta fragment‐based refinement protocol for refinement against EM density. My script is attached.

It always complaints:

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Rosetta 3 - Applications

calculate RMSD (RNA modelling)

Submitted by obdulia on Tue, 2016-07-05 01:58
Category: 
Nucleic Acids

Dears

With RNA modelling in Rosetta, how may i get the RMSD to a native structure for the whole set of generated models? I forgot to run the rna_denovo.linuxgccrelease with the -native flag and now, i would like to measure the RMSD for the obtained models (.out file) agaisnt the crystallographic structure.

Thanks a lot in advance

Best Regards

Obdulia

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Rosetta 3 - General

scoring input pdbs as the same as docking score

Submitted by hamedkhakzad on Fri, 2016-07-01 07:15
Category: 
Scoring

Hi everyone,

I'm writing a pilot app in Rosetta and I want to cluster results (all pdbs) of global dock. After calculating the scores, they are completly different with the original scores I got from docking_protocol. I'm using following codes:

        core::scoring::ScoreFunctionOP scorefxn( core::scoring::get_score_function() );
        ( *scorefxn )( init_pose );

I found that the input pdbs do not have sidechains, however using following command just made the scores better but the difference is still remained:

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Rosetta 3 - Applications

How to restart RASREC run

Submitted by aep on Fri, 2016-07-01 04:39
Category: 
Structure prediction

Greetings.

I had a long RASREC run (with distance restraints) crash due to a stack overflow error. I'm reading that it is possible to restart the run and have it pick up where it left off with respect to decoys but do not know how exactly to do that without overwriting the existing batch files. What would be the command line for a proper restart in MPI mode (I'm working with a moab scheduler script)? Thank you!

 

 

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Rosetta 3 - Applications

revert_design_to_native app comparison to FavorNativeResidue mover

Submitted by nwhoppe on Wed, 2016-06-29 14:35
Category: 
Design

Hello,

I am currently designing ligand-binding protiens, but designs are returned with more mutations than I would like. In order to reduce this number, I currently use the revert_design_to_native app, but I recently read about about the FavorNativeResidue mover. However, I am unsure of the differences in function between the two. I made two small sets of designs with the FavorNativeResidue bonus set to 0.5 and 1.5, and I ran revert_design_to_native on those designs with the same thresholds, respectivley. 

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Rosetta 3 - Applications

Rebuilding the structure from unknown residues

Submitted by sushreet on Mon, 2016-06-27 09:32
Category: 
Structure prediction

Hi,

I am trying to rebuild the structure from unknown residues (UNK). I have the corresponding EM map and sequence but the PDB file is missing some residues and rest is given as "UNK". I am trying to build an all-atom model using Rosetta. Please suggest as Rosetta does not accept any undefined residues. Any input is welcome.

 

Thanks

Sushree

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Rosetta 3 - Applications

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