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ROSIE

Rosetta Server

Can you change background color of pdb file pictures?

Category: 
ROSIE

In the output of ROSIE docking2 and symmetric_docking jobs,
many pdb files are shown as cartoons with rainbow coloring
and black backgrounds. Is it possible to have an option that
would change the background color of these images to white
and perhaps render these images with a thin black outline
around the cartoon shape? I think this would use less toner
when printing and yield clearer printouts. Also, could you
include these images in the tar archive one gets via the link
"[Download all job files as tar archive]" ?

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How to change your ROSIE username or password?

Category: 
ROSIE

Is there a way to change your ROSIE username or password?
http://rosie.rosettacommons.org/signup lets you set up a new account, and
http://rosie.rosettacommons.org/password_reset lets you change your password,
but the new password is chosen for you and sent to you in an e-mail,
which isn't the most private way to do things.

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pKa job submitting problem

Category: 
ROSIE

Hello

I tried to submit a job to calculate residue pKa in the protein (http://rosie.graylab.jhu.edu/pka/submit)
But...

after input PDB file I clicked "Submit" and stopped at "Submitting pKa job...".

Is that caused by my data error ?

or, Is there a pKa application in the Rosseta 3.5 for standalone calculation?

Thanks for your help

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Problems with the RNA Denovo server

Category: 
ROSIE

Hello,
I have problems using the RNA Denovo protocol on the web server. I try to get a structure for a duplex RNA, with a bulge, and the calculations fail, giving the error message: Protocol failed to produce any results! (File output/protein-0.out not found!)

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download decoy structures as .tar file?

Category: 
ROSIE

I am new to ROSIE (in fact new to Rosetta). I was able to submit some dockin runs and get the results. I want to download the 1000 decoy structures for doing my own post-docking analysis but I cant figure out how to download them as .tar / .zip file.

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Antibody protocol: unusual antibodies, and chainbreaks

Category: 
Structure prediction
Loop Modeling
ROSIE

Hello,
I am doing a research internship, on modelling some antibodies recognizing a short peptide from a conserved part of the gp41 protein of the HIV1 virus and simulating their docking.

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Supercharge server

Category: 
ROSIE

When I looked up the supercharge queue, I found many jobs have been holding since June.
Most of them are not even started yet. I know rosie is getting busier, and I am wondering how long it will take to run one project these days.
Is there a technical problem with the supercharge program (the server is down for some reason..?)?

Thank you for your attention,
YC

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Ligand Docking Protocol now available for academic users

Category: 
ROSIE

Hi Everyone,

Our ROSIE Server now have Ligand Docking Protocol (developed in Meiler Lab at http://www.meilerlab.org ) open for academic users. Please visit http://rosie.graylab.jhu.edu/ligand_docking for documentation and job submission.

Best,

Sergey.

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