You are here

Unsolved

The problem hasn't been solved

Academic e-mail adress verification

Category: 
ROSIE

Hi,

Could you please verify my academic email address so that I can access ROSIE via Github?

My institution name: National Center for Tumor Diseases Heidelberg, Germany - an institution of the German Cancer Research Center Heidelberg

Institution domain: @nct-heidelberg.de or @dkfz-heidelberg.de

Post Situation: 

ROSIE Queue not loading

Category: 
ROSIE

I've been trying to access my ROSIE queue, but it is stuck in the "loading queue data..." screen. I can access the "apps" and the "home" page just fine.

I used ROSIE a few months ago, and didn't had this problem. Now I'm trying to have access to a work I submitted to ROSIE but unfortunately this problem occurred.

Any help would be appreciated!

Post Situation: 

RECCESS-Rosetta Segmentation Fault with nonnatural residues

Category: 
Chemically Modified Residues

Hello,

 

I am trying to run the recess-turner function with the following command:

recces_turner.macosclangrelease -score:weights stepwise/rna/turner -seq1 gu  -seq2 [2MA]c -recces:n_cycle 9000000 -recces:temps 0.8 1 1.4 1.8 3 7 30 -st_weights 9.024828183205116 18.24157438187578 22.310063998885838 25.608533286161883 25.949659063278826 25.027484033009934 -recces:out_prefix ST -save_score_terms 

 

Post Situation: 

Antibody Structure Prediction - Error on antibody_H3 step: "Option matching -antibody:remodel not found in command line"

Category: 
Structure prediction

I'm trying to predict the structure of an antibody by following this Rosetta Antibody Modelling tutorial: https://meilerlab.org/wp-content/uploads/2022/02/RosettaAntibody_tutorial.pdf

At the 5th step, during the refinement of the model, I find the following error:

Post Situation: 

ERROR: ResidueType::add_ring: Requested atoms don't exist in this ResidueType!

Category: 
Compilation

Hi, all,

I am currently trying to run Rifdock, which I compiled according to the instructions in this repo (https://github.com/rifdock/rifdock). However, everytime I pass it a *.pdb input file, I get the following error:

=================================================== preparing target ===================================================

Post Situation: 

different relaxed energy scores for one same protein structure

Category: 
Scoring

Hello everyone,

 

By chance, I tried several times relax module for one same protein structure.

I got all different relaxed energy socres.

Which score is representive for this protein structure?

 

And of two similar structures mutated by 1 or 2 different positions, which structure can have the better structure?

By what criteria did you think that?

Post Situation: 

PyIgClassify cannot renumber and label CDRs my Nanobody-Antigen complex for RabD

Category: 
Design

Hi,

I've been trying to use the Anibody Designer but i was unable to use PyIgClassify webserver to renumber and label the CDRs in my PDB file. I am also unable to get it to find CDRs in any antibody pdb file even thoughs its within the database. I would also like to find the schema for how the CDRs are marked within the text of the renumbered PDB file. Any help would be appreciated.

 

Thanks,

Will

Post Situation: 

Pages

Subscribe to RSS - Unsolved