You are here

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

Post Situation: 

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

Post Situation: 

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]" ?

Post Situation: 

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.

Post Situation: 

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

Post Situation: 

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!)

Post Situation: 

Pages

Subscribe to RSS - ROSIE