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How to run PLOT LHOC on Results from Rosie Server

Category: 
ROSIE

Hi,

 I am using Rosie antibody server for modeling antibody. In order to validate the model i need to run the PLOT LHOC script on the output results from Rosie server. However while running the script i am only getting the graph for the final model and not the template. kindly can anybody share the comand for running the PLOT LHOC script. Also whether the template used for the calculation by PLOT LHOC is grafted model or the original template PDB.

Thanking you

Dr. Suji george  

Post Situation: 

Incorporating Rosetta Binary and Database to a Web Server Pipeline

Category: 
Design
Scoring
Enzyme Design
Constraints
Small Molecules
ROSIE

Our lab is planning to design a web server, and we would like to incorporate one of the binaries and the corresponding Rosetta database in our pipeline. 

We would like to incorporate Rosetta's supercharge binary (https://www.rosettacommons.org/docs/latest/application_documentation/design/supercharge) along with the corresponding common database in our web server as a component of our web server pipeline.

Post Situation: 

Fv modelling Job Mab_Top 「№33253」

Category: 
ROSIE

Hi all,

I am having problems using the ROSIE antibody section for comparative modelling of a Fv fragments, job number 33253 (Mab_Top).
Previous attempents have failed, and now I made a modification on the N-terminus (because this is was not fully sequenced) and the job is flaged as finished altough without any structure, as well as without reports of potencial errors.

I guess that there was any problem with the modelling since the CPU time used was so small 0.0147222222222.

Post Situation: 

weights for pH_protocol

Category: 
ROSIE

Dear all,

I have been recently testing pH_protocol to calculate the pKa of one of my proteins. In the original paper, the authors include the weights function to be used with the protocol:

fa_atr 0.8

fa_rep 0.44

fa_sol 0.65

fa_intra_rep 0.004

fa_dun 0.56

hbond_lr_bb 1.17

hbond_sr_bb 1.17

hbond_bb_sc 1.17

hbond_sc 1.1

hack_elec 1.0

e_pH 1.0

ref 1.0 

 

Post Situation: 

Sequence Tolerance Failed

Category: 
ROSIE

Dear all,

 

I submitted six jobs to Rosie (28069 through 28074) under the username dstork. They failed quickly with no error messages beyond "Failed * Tech support has been notified of this error" anywhere that I can see. After waiting a few weeks the issue hasn't been resolved. What can I do to get this job to work?

Thanks,

-Devon

Post Situation: 

Ligand docking error Could not find essential file trigger-00001.ligand_docking_protocol

Category: 
ROSIE

Hello,

My attempts at ligand docking on Rosie (e.g. job 26146)  keep failing after less than 15min. I am getting no input error. The json logs return the error:

  "log": "\nCould not find essential file trigger-00001.ligand_docking_protocol/score.sf in DB!\n", 


I used Frog2 to generate my ligand sdf file and Chimera to estimate the starting x,y,z coordinates.

Any hints at what I might be doing wrong?

 

thanks,

Isabelle

Post Situation: 

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