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How to use rewrite_rosetta_script.py to update XML script file?

Category: 
Design

Hello!

I am trying to run the default XML script to change the specificity of a protein so that it binds to a DNA sequence of interest. For this I am referring to the book Redesigning the specificity of protein-DNA interactions with Rosetta

Thyme S, Baker D. Redesigning the specificity of protein-DNA interactions with Rosetta. Methods Mol Biol. 2014;1123:265-82. doi: 10.1007/978-1-62703-968-0_17. PMID: 24510272.

However I am getting the following error message.

Post Situation: 

Cartesian_ddG mutfile error

Category: 
Design
Constraints

hello gus,

When i use catesian-ddg for protein stability, i want saturation site by all amino acied. but I Set  "1 A ALLAA" OR "C 1 ALLAA"(first site is  cys), all error.

and i type "total 9 

1

C 1 A 

C 1  W 

C 1  F 

C 1  I
.....  " Enumerative method is OK. So, how I set mutfile more easy and clearly ? help!

Post Situation: 

Error about rifdocking step 12

Category: 
Design

Hello, everyone I prepared paper_interface_design_pilot_commands. List when I did RIFdocking step 12 Running a pilot job. When I ran the commands, the error occurred: 

basic.io.database: Database file opened: scoring/score_functions/sap_sasa_calib.dat
WARNING!! DALPHABALL output nan at index 140724834832176
DALPHABALL output indicies not matching! 1!=140724834832176

Post Situation: 

Error about rifdocking

Category: 
Design

Hello, everyone I prepared paper_interface_design_pilot_commands. List when I did RIFdocking step 12 Running a pilot job. When I ran the commands, the error occurred: 

basic.io.database: Database file opened: scoring/score_functions/sap_sasa_calib.dat
WARNING!! DALPHABALL output nan at index 140724834832176
DALPHABALL output indicies not matching! 1!=140724834832176

Post Situation: 

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