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Segmentation fault on antibody structure prediction

Submitted by dkesar on Fri, 2021-06-04 19:09
Category: 
Structure prediction

On running antibody.macosclangrelease I was getting a segmentation fault. Now on switching to antibody.static.macosclangrelease I got the following error: SCS_BlastFilter_nonmatching_prolines::apply: Error! Could not cast SCS_Results to SCS_BlastResult

I was able to predict the structures for rest of my antibody models, I don't understand why this particular sequence is giving me a hard time.

 

 

 

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Rosetta 3 - General

FastRelax Refinement severe clashes

Submitted by Victor Tobiasson on Thu, 2021-05-20 06:55
Category: 
Structure prediction

Dear Rosetta community,

I am working with Rosetta version 2020.08.61146. have run into an issue of massive clashes when refining a part of a ribosome structure using FastRelax. I have previously used Fast Relax extensivly as a preliminary refinement step and its usually works wonders. This has been on individual chains and now I want to try to relax an entire subunit however Fast Relax seems to tear a few nucleotides apart. I attached images pre and post FastRelax as well as my RosettaScripts XML and shell output. 

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Rosetta 3 - Applications

Using NCAA

Submitted by ate on Sat, 2021-05-01 02:52
Category: 
Structure prediction

Hello,

I am trying to build peptide sequences containing NCAA to use for FlexPepDocking. After getting params file and rotlib file, when I am using fixbb to do mutation, I encounter with this error “COULD NOT FIND TORSION PARAMS FOR 30 30 6 31” it shows there is no parameters for C-N-C-CA

I would really appreciate it if someone could let me know how I can build my peptide sequence containing NCAA without ignoring this torsion (i.e., importing 0 1 180.00 for related parameter in mm_torsion_params.txt)

 

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Rosetta 3 - General

trRosetta protocol Segmentation Fault

Submitted by nc-ring on Wed, 2021-04-28 11:57
Category: 
Structure prediction

Hello,

So I've been trying to implement the new trRosetta protocol and I keep getting a segmentation fault error. Is there any idea what I might be doing incorrectly? The Rosetta Crash Log is below and is followed by the output logs (both raw text files are also included as attachments).

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Rosetta 3 - Applications

RosettaCM/hybridize

Submitted by kywei on Wed, 2021-04-28 09:56
Category: 
Structure prediction

Has anyone had trouble with the Hybridize mover in RosettaScripts in the lastest weekly release Rosetta 2021.16 (Release date: Friday, April 23, 2021)? My script that works with older releases has stopped working and seg faults in Stage 4. Other movers, for example FastRelax, work.

Any help is much appreciated! Thanks.

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Rosetta 3 - Applications

How to use base_pair_constraint for RNA as a constraint term？

Submitted by yels on Sat, 2021-04-03 01:19
Category: 
Structure prediction

https://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/14.00-RNA-Basics.ipynb

The above tells me that an RNA low-resolution potential

(rna_lowres_sf = core.scoring.ScoreFunctionFactory.create_score_function("rna/denovo/rna_lores_with_rnp_aug.wts"))

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