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Need help figuring out the meaning and cause of an error

Submitted by AleksanderK on Fri, 2019-05-03 11:02
Category: 
PyRosetta

I run into this problem when trying to use prepend_polymer_residue_before_seqpos and I can't understand what it really means and, most importantly, what its cause is and how to prevent it from happening. There's a screenshot of the error in the attached pic. 

Assertion `moving_connection.icoor().is_internal() && fixed_connection.icoor().is_internal()` failed
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PyRosetta - General

script recommendations? for high res docking from low res

Submitted by Amy F on Wed, 2019-05-01 07:59
Category: 
Docking

Hi:

Is there a rosetta or pyrosetta script  (or general protocol) you would recommend for a pdb that already has a small molecule ligand docked in a low resolution docking model?

I used Zhang lab's BP Slim server to get this lo res docking, and now what I need to do is refine that model to high res, atomic scale.

 

thank you all so much, I am learning rapidly from this most generous and helpful community.  - Amy

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PyRosetta - Scripts

missing atom number 5 atom name CB

Submitted by ajaniharesh on Fri, 2019-04-26 12:08
Category: 
Docking

I am contacting you because I am getting an error in results with Rosetta. Successfully finished protein-protein docking. I can see in the output that following lines complaining about missing atoms. I have prepared protein in ICM, Molsoft. I checked the input file those I have given as input.pdb, there were no missing any CB atoms in all amino acid. Docking finished successfully and generated score value. Do you think this missing atom will make any impact in score value? Let me know how can solve this problem. 

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Rosetta 3 - Applications

D100 Docking script error test.output

Submitted by Amy F on Fri, 2019-04-26 08:29
Category: 
Docking

Hi:  I have researched this error I am getting, but don't see any reference to it.   Thanks in advance for any help.

When I run

 

python D100_Docking.py --pdb_filename /81q1D100_Dock/ferudock81q1cds.clean.pdb --jobs 400 --job_output 81q1_docking_output --translation 3 --rotation 8 --PyMOLMover_ip off
 

I can't get past this error with the constant seed:

In [1]: import optparse

In [2]: from pyrosetta import *

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PyRosetta - Scripts

Installing rna_denovo

Submitted by Tanusree Chaudhuri on Thu, 2019-04-25 23:59
Category: 
Nucleic Acids

Hi,

I tried using the Rosetta RNA tertiary structure modeling pipeline as described in your article "Modeling complex RNA tertiary folds with Rosetta."

My build is correct.

But every time I try to run

helix_preassemble_setup.py -secstruct sec.txt -fasta fasta.fasta

I am getting error as

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Rosetta++ - Build/Install

LHOC script problem in Rosetta Antibody

Submitted by ziheng@mit.edu on Thu, 2019-04-25 14:19
Category: 
Structure prediction

Hi all,

I'm getting a problem running the LHOC angle script in the antibody modeling protocol. To reproduce:

python -m pdb ../rosetta/main/source/scripts/python/public/plot_VL_VH_orientational_coordinates/plot_LHOC.py -h3_fasc H3_modeling_scores.fasc -graft_dir grafting -output_dir vhvl

I have uploaded the H3_modeling_scores.fasc file and the contents of the grafting directory. Here is the error message:

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Rosetta 3 - General

Highly negative total score

Submitted by Ruchi_P_Jain on Wed, 2019-04-24 19:55
Category: 
Docking

I have performed a docking between a protein and a 15 residue peptide using flex pep dock. I have got a total score of around -1347, is this considered as good docking ? I am unable to predict whether the docking can be considered or not. Please help me. Thanks in advance:

The total score and other factors are as follows:

total_score

I_sc

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Rosetta 3 - Applications

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