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backrub application, resfile, and pivot_residues

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backrub application, resfile, and pivot_residues
#1

Hi,

I've been attempting to use the "backrub" app to model mutations while allowing flexibility of the backbone in specific protein stretches.

It appears adding the resfile (with or without mutations specified) causes backbone flexibility across the entire output structure and not restricted to the protein stretches specified by -pivot_residues.

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Example:

The following command outputs structures with backbones changes in regions specified by -pivot residues:

backrub.linuxgccrelease -database /rosetta-3.5/rosetta_database/ -s 1MI5.pdb -ignore_unrecognized_res -backrub:ntrials 10000 -pivot_residues 209 210 211 212 213 214 215 216 217 218 219 220 235 236 237 238 239 240 241 275 276 277 278 279 280 281 282 283 284 285 286 287 288 321 322 323 324 325 326 327 328 329 330 345 346 347 348 349 350 351 352 353 390 391 392 393 394 395 396 397 398 399 400

The following command outputs structures with backbone changes nearly everywhere in the protein complex:

backrub.linuxgccrelease -database /rosetta-3.5/rosetta_database/ -s 1MI5.pdb -ignore_unrecognized_res -backrub:ntrials 10000 -pivot_residues 209 210 211 212 213 214 215 216 217 218 219 220 235 236 237 238 239 240 241 275 276 277 278 279 280 281 282 283 284 285 286 287 288 321 322 323 324 325 326 327 328 329 330 345 346 347 348 349 350 351 352 353 390 391 392 393 394 395 396 397 398 399 400 -resfile resfile

where resfile:

NATRO

start

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Is something off here? I'd like to just implement backbone flexibility in specific regions upon making mutations specified by resfile. 

The same scenario occurs when the resfile has mutations listed.

 

Thanks,
Tyler

 

Category: 
Post Situation: 
Tue, 2016-12-06 14:46
tylerborrman