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farfar2 not submitting jobs

Category: 
ROSIE

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.

Post Situation: 

how to control alignment for energy_based_clustering

Category: 
Docking

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?

Post Situation: 

Error when trying to use xml script to design PDB

Category: 
Design

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"/>

Post Situation: 

Which application/mover should I use to evaluate the ddg between apo enzyme and enzyme binding with transition state?

Category: 
Enzyme Design

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.

Post Situation: 

Rosie login email verification

Category: 
ROSIE

Hi there,

I would also like to ask for an email address confirmation to access ROSIE via Github. Could you please help me with the verification?

My institution is the Fraunhofer Institute for Cell Therapy and Immunology (IZI)

Domain: @izi.fraunhofer.de

Thank you very much!

Dominik

Post Situation: 

Challenge with applying AntibodyCDRGrafter method and MinMover method

Category: 
PyRosetta

I've been trying to trial designing antibody CDRs. Thus far I haven't had much luck applying standard methods. I've converted my antibody to AHO scheme with PyIgClassify and applied the cleanATOM method, however, I am still running into the following error prompt. Any recommendations on how to resolve this, would be great.

I've applied the AntibodyInfo method and am able to print the antibody with the sequences of each CDR, so I don't think the first portion about start and end not being contained is correct.

Post Situation: 

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