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How to determine the value size in block of *.cst files?

Category: 
Design

HELLO, everyone,

I am a begineer of Rosetta de nevo peotein design and want to design an enzyme using rosettamatch, however it is complicated even i have read its method carefully. Recently, I am trying to use demos, and i found that are really helpful and important. But some used files need to be made by hand, such as the *.cst file. The question is how to determine the value size in block of *.cst files to constrain a ligand and residue interaction, including :

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Need help figuring out the meaning and cause of an error

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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script recommendations? for high res docking from low res

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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missing atom number 5 atom name CB

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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D100 Docking script error test.output

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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Installing rna_denovo

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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LHOC script problem in Rosetta Antibody

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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