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chothia numbering error of FR_L1

Submitted by Sbrendle on Mon, 2016-08-22 06:58
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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ROSIE - General

CDR are not being recognized

Submitted by wildchipiron on Mon, 2016-05-23 15:03
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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ROSIE - General

Can you change background color of pdb file pictures?

Submitted by AdoCbl on Sun, 2015-08-09 01:47
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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ROSIE - General

How to change your ROSIE username or password?

Submitted by AdoCbl on Sun, 2015-08-09 00:08
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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ROSIE - General

pKa job submitting problem

Submitted by syoifczeri on Tue, 2015-02-17 21:41
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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ROSIE - General

Problems with the RNA Denovo server

Submitted by mariaclausen on Tue, 2014-11-25 01:45
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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