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I've got two doubts

Submitted by jrcf on Sun, 2016-01-10 07:45
Category: 
Structure prediction

Hello guys.

I've got two doubts.


First: someone tell me of an article that explains why for example be between 100,000 and 200,000 decoy to abinitio or 15000 decoy for comparative modeling?


Second: to see the articles in the case of e.g. abinitio is informed that were N decoy, if 100,000, my doubt; was produced a total of 100,000 or 100,000 was requested in the script?

Thank you all for the help

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Rosetta 3 - General

LIGAND APPEARS TO BE DOCKED INTO EMPTY SPACE

Submitted by gabeliluo1 on Wed, 2016-01-06 16:23
Category: 
Docking

Hello All,

My docking results, when viewed together with the input protein structure, appear to be docked into open space.

I have confirmed that the hint coordinates I supplied are correct.

Any ideas why this is happening?

Thanks!

Gabe

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ROSIE - General

Fusing C-terminal or N-terminal segments onto proteins using Remodel

Submitted by achambe on Tue, 2016-01-05 09:39
Category: 
Structure prediction
Design
Loop Modeling

Hi I am trying to fuse a structure onto a designed protein structure at the C-terminus using the following command:

remodel.linuxgccrelease -s model3.pdb -remodel:RemodelLoopMover:bypass_closure -remodel:domainFusion:insert_segment_from_pdb model4.pdb -remodel:blueprint model3.blueprint -use_input_sc -num_trajectory 3 -save_top 1 -database <PATH> -overwrite -out:file:scorefile model3.sc

model3.pdb covers the range: 1-393

model4 covers the range: 290 - 393

Where the blueprint has the following general format:

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Rosetta 3 - General

Symmetry definition for apolar helix

Submitted by vanrooyenjason on Tue, 2016-01-05 05:20
Category: 
Symmetry

Hi,

I am struggling to generate a symmdef file for a helical model and I am hoping someone can help.

The helical parameters are as follows: rise = 17 Angstrom with 4.674 subunits per turn. The helix is apolar i.e. the ends of the helix are the same as related by 180 degree rotation. The repeating unit is a dimer with C2 symmetry. In the attached pdb (ca only to avoid upload limit) the A and B chains form the dimer which is related to the next C/D pair by the helical symmetry I mentioned.

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Rosetta 3 - Applications

Fusing C-terminal or N-terminal segments onto proteins using Remodel

Submitted by achambe on Mon, 2016-01-04 11:26
Category: 
Design
Loop Modeling

Hi, I am trying to replace the C-terminal segment of a designed protein with that taken from a crystral structure using the Remodel module with the DomainFusion flag turned on. I have tried several different tweaks to the arrangment however the gist of it is that I use the following command. 

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Rosetta 3 - Applications

Error score_scatter_plot.py

Submitted by jrcf on Wed, 2015-12-30 05:46
Category: 
Structure prediction

Hi guys,

I'm using a tutorial for analysis my results of abinitio, in the step for "identify the best socring models" using this script  "~/rosetta_workshop/Rosetta/main/source/bin/combine_silent.default.linuxgccrelease -database ~/rosetta_workshop/Rosetta/main/database/ -in:file:silent 2LZM_0*.out -in:file:silent_struct_type binary -in:file:fullatom -out:output -out:file:silent 2LZM_all_models_silent.out -out:file:silent_struct_type binary -out:file:fullatom"

I has this error

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Rosetta 3 - General

Unit tests on a non-Intel CPU

Submitted by yuvals on Sun, 2015-12-27 07:03
Category: 
Compilation

Hello Rosetta forum!

I've been trying to run Rosetta (2015wk39) on an IBM Power8 machine. It has 64-bit PowerPC processors, which, according to our CS department, have been set up to work with little-endian byte ordering. Rosetta compiles fine* but I've been getting failures when running unit-tests.

I've attached the full log, and the epilogue is attached inline at the end of this message. Of all failed tests, I can only find details to the test_rotamer_trials test, which have the following error:

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Rosetta 3 - Build/Install

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