# ROSIE

Rosetta Server

## chothia numbering error of FR_L1

Category:
ROSIE

I submitted a Heavy and lIght chain sequence with and without the 'multiple template grafting' and H3 loop modeling and recived the same errors each time- "Chothia numbering of FR_L1".

Does anyone know how to get around this error so that the antibody will be modeled? job #'s 24670, 24671

thank you

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## supercharge problems

Category:
ROSIE

Dear Professor Bryan Der,

Thank you very much for your great server. I've come across two essential questions using your techniques and I really need your help so I can continue working on my PhD thesis.

I've used both supercharge methods:

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## CDR are not being recognized

Category:
ROSIE

Hi!!

I had been suscesfully using ROSIE to generate Fab models for a while and lately the server has not able to recognize the CDRL3 and CDRH3 in my antibody sequences. I also tried a sequence that was previously used and modeled but now the server gave an error

ERROR: CDR L3 cannot be recognized !!!  L3 pattern: C[A-Z]{1,15}(L|F|V|S)G[A-Z](G|Y)

and I dont undestand why  the CDR cant not be recognized now. The pattern of the input seqeunces looks correct.

I would really aprreacite some help in this matter

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## industrial example of ROSETTA modeled protein

Category:
ROSIE

This is a general question,

Is there any example of proteins modeled by ROSETTA  which is currently being used in industry, whether it is enzymes or therapeutics or any other biomolecules?

Thanks.

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## 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

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Category:
ROSIE

http://rosie.rosettacommons.org/signup lets you set up a new account, and
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?

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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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