Unsolved

Hello ROSIE and FARFAR2 team,

I've been trying to submit a RNA structure prediction using FARFAR2 and it is not working. Namely, when I press to submit the job, the submitting window pops up and it never submits the job. I tried changing the computer and browser, but unfortunatelly the "error" still remains.

Thank you very much for your attention.

Hi,

I am using the energy_based_clustering application to cluster results from a protein-protein global docking job. One of the partners is kept fixed, so I would like to cluster based on the RMSD of the moving partner alone, without any alignment. I assume that the clustering algorithm is aligning the whole structure to minimize RMSD. Is this correct? If it is, is there a way to skip the alignment and calculate the RMSD directly from the input structures?

I am trying to mutate and relax the 7ah0 pdb using the following xml script:

<ROSETTASCRIPTS>

<SCOREFXNS>

<ScoreFunction name="sfxn" weights="ref2015"/>

</SCOREFXNS>

<RESIDUE_SELECTORS>

<Index name="res1" resnums="388A"/>

<Index name="res2" resnums="389A"/>

<Index name="res3" resnums="390A"/>

<Index name="res4" resnums="391A"/>

<Index name="res5" resnums="392A"/>

Hi everyone:

        I used Enzyme Design application to get a series of enzymes with ligand(transition state of my target reaction). Now I want to inspect the free energetic change upon the protein transition state binding. 

        So I first look into the ddg_monomer application, and I find this application is suitable for comparing ddg energy between wild-type protein and its mutant structures. This can't meet my needs.