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The vall.jul19.2011.gz Database

Submitted by ac.research on Fri, 2017-09-01 02:29
Category: 
Fragment Generation

Dear All,

 

Is there a URL or FTP to download the vall.jul19.2011.gz database?

I know the database resides in {ROSETTA}//tools/fragment_tools/

But if I want to direct someone to just download the database without downloading Rosetta and uncompressing it (for example to use PyRosetta independently than Rosetta). Does a URL or FTP to download the database exists?

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Rosetta 3 - General

Fragment Picking in PyRosetta

Submitted by ac.research on Thu, 2017-08-31 04:48
Category: 
Fragment Generation

Dear All,

 

Is there a tutorial that can show how to preform fragment picking in PyRosetta? I want to generate fragments for many structures and I do not want to overwhelm the Robetta server, thus I want to preform it in-house.

 

Any help on how or where to start to generate fragments using PyRosetta? I found that there is a mover FragmentPicker() in  pyrosetta.rosetta.protocols.frag_picker but I do not know how to use it.

 

This is my code so far:

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PyRosetta - General

-loops:fa_input not found in command line top-level context

Submitted by swarekwood on Thu, 2017-08-24 03:15
Category: 
Loop Modeling

Hi everybody!

I'm trying to learn how to use Rosetta in de novo protein design. I use this article as a manual: https://www.ncbi.nlm.nih.gov/pubmed/23744289

It doesn't work for me at some point. Namely, when I go to step 13 (Running the comparative modeling job), I try to execute the following command in the terminal:

./loopmodel.default.linuxgccrelease @modeling.options -database rosetta_database -nstruct 100

But the response is:

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Rosetta 3 - Applications

Ligand Docking with Rosetta Scripts memory problem

Submitted by Swillard on Thu, 2017-08-17 14:59
Category: 
Docking

Hi,

I am trying to dock a small molecule with holo dimer protein (153 aa, 1 Cu and 1 Zn per chain). I followed the Ligand Docking Tutorial and it all works fine until I try to generate more than ~50 output structures. Using both MPI and default builds, all 8 GB of RAM and 5 GB of Swap are slowly filled up until my linux system kills the program. Below I have listed different commands and how many strucures it generated before swamping memory. The basic options file and xml file is attached is attached.

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Rosetta 3 - Applications

Protein Docking Error

Submitted by ac.research on Thu, 2017-08-17 02:57
Category: 
Docking

Dear All,

 

I am learning how to do protein-ligand docking and I am following the Rosetta built-in tutorial: https://www.rosettacommons.org/demos/latest/tutorials/ligand_docking/ligand_docking_tutorial

 

I did not change anything whatsoever. I used the same tutorial files (as is) and attempted to run the calculation as such:

{PATH_TO_ROSETTA}/main/source/bin/rosetta_scripts.linuxgccrelease @options

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Rosetta 3 - General

Muting output in pyrosetta

Submitted by SenyorDrew on Mon, 2017-08-14 08:13
Category: 
Design

Hi,

I have a function in pyrosetta that performs repack, and I call this function many times.   Right now I get tracer output from core.pack.task:

e.g.

core.pack.task: Packer task: initialize from command line() 
core.pack.pack_rotamers: built 143 rotamers at 8 positions.

Is there a way to mute this output ONLY while in my function? i.e. I'd like to mute this output and then turn it back on later in my script?  

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PyRosetta - General

Cannot run binaries after successful compilation

Submitted by ac.research on Mon, 2017-08-14 02:56
Category: 
Compilation

Dear all,

I have been trying to compile rosetta 3.8 for a while now without success (meathod worked will with 3.7). I have a 17.04 Ubuntu Gnome Operating System.

Compile Commands:

sudo apt install zlib1g-dev scons build-essential -y
tar -xvzf rosetta_src_3.8_bundle.tgz
cd {ROSETTA}/main/source
./scons.py mode=release bin

 

Result:

Successfully compiles everything, no errors printed.

 

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Rosetta 3 - General

Getting error with Rosetta "antibody.linuxgccrelease" command

Submitted by Sunyp_IM on Mon, 2017-08-07 19:40
Category: 
Structure prediction

Dear all, 

I installed ROSETTA3 (rosetta_src_2017.08.59291_bundle) on my centos 7 system. The install process seemed ok without error.

when I use the antibody.linuxgccrelease to prediction antibody structure according to the tutorial in the Nature Protocol 2017, 12(2),401 paper with the follow commad:

antibody.linuxgccrelease -fasta antibody.fasta -exclude_homologs -exclude_homologs_cdr_cutoff 95 -exclude_homologs_fr_cutoff 90 -antibody::grafting_database $ROSETTA/tools/antibody | tee grafting.log
 

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Rosetta 3 - Applications

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