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Rosetta Server

getting right protonation state from PKa of Rosie

Category: 
ROSIE

Hello,

Does the pdb file in the output folder of pKa give us the right protonation state of pdb file?

Also, there are two options in pKa program in ROSEI:

1.Pack side chains and protonation states of the residues neighboring the target residue during pKa calculations

2.Pre-pack the side chains and protonation states of all the residues in the input PDB before pKa calculations

 

which one should  we use to get the right protonation state?

 

Post Situation: 

FARFAR2 error

Category: 
Structure prediction
Nucleic Acids
ROSIE

Hi ROSIE and FARFAR2 team,

       I used FARFAR2 to test the 3D structure prediction of several RNAs two weeks ago with native PDB uploaded. But all the jobs were finally dead with the error message "2-rescore_to_native_or_lowest". Could you tell me why this happened? You can find the sequence, 2D structure, and native PDB in the attachment.

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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  

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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.

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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: 

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