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AbinitioRelax of RCSB PDB structures

Submitted by ac.research on Tue, 2019-09-03 02:35
Category: 
Structure prediction

When I try to model a protein from the PDB (4WYH) I follow the abintio protocol correctly and generate fragments from Robetta. Yet I do not get a funnel shaped plot after 25,000 decoys.

Though it’s sequence clearly folds into this particular structure (as proved by the crystal structure) why can’t abinitio performs a successful simulation and result in a funnel shaped plot?

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Rosetta 3 - General

"make" error in "pdb2vall/structure_profile_scripts/DEPTH-CLONE-2.8.7"

Submitted by Danielsebas on Mon, 2019-09-02 08:14
Category: 
Structure prediction

Dear friends,

 

I am trying to run "make" in "pdb2vall/structure_profile_scripts/DEPTH-CLONE-2.8.7", follwing the installation instructions in "pdb2vall.README"; however, when running "make", I get this error (error is very long, so I have pasted the first and last lines of STDOUT) :

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Rosetta 3 - Applications

ipython can't find PyRosetta files

Submitted by dukeuser on Thu, 2019-08-29 17:48
Category: 
PyRosetta

I'm trying to get interactive rosetta to work on a linux virtual machine. I have zero experience coding so I've been struggling royally. I first tried Ubuntu 18.04, but after having some difficulty I decided to switch to as close of a setup as what is in the interactive rosetta install video as I could. I tried Ubuntu 12.04 64 bit with python 2.7.3 and PyRosetta 3 release 104. When I try to import rosetta into ipython this appears:

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PyRosetta - Build/Install

Rosetta fragment tools installation error

Submitted by Danielsebas on Thu, 2019-08-29 02:17
Category: 
Structure prediction

Dear Friends,

 

I am trying to install rosetta on my local system, but facing issues because of CSBLAST. The latest rosetta bunble I downloaded from rosetta website is : rosetta_src_2019.31.60840_bundle.

After that, since I want to perform "ab initio structure prediction", I am following this tutorial:

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Rosetta 3 - Applications

can anyone help me correct this script to do alanine scanning

Submitted by xinmiaohe on Mon, 2019-08-26 17:23
Category: 
Structure prediction

HI,

I want to do alanine scanning. I just started learning to use Rosetta. I really do not know how to fix this rosettascripts. I am wondering anyone coul please help me out. I would much appreciated.

Thank you very much.

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Rosetta 3 - Applications

how to find help informations on rosetta_scripts in rosetta3.10

Submitted by xinmiaohe on Mon, 2019-08-26 14:48
Category: 
Compilation

Hi,

I am just learning how to use rosetta_scripts and I do not know how to find some descriptions on example xml and its contents in rosetta suit. I am wondering whether anyone can help out. I would much appreciated.

I want to find some help information on the alanine_scan.xml. 

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Rosetta 3 - Applications

how to run ala_scan.xml

Submitted by xinmiaohe on Mon, 2019-08-26 09:38
Category: 
Structure prediction

HI,

I am running ala_scan.xml. it looks like that it calculated the difference of binding energy but not scan the interface. and I am wondering why the process was stopped in the middle. Could someone please help me. I just started learning to use Rosetta. I would very much appreciated.

 

rosetta_scripts.default.linuxgccrelease -s my.pdb -parser:protocol ala_scan.xml -database ~/rosettadatabase -ex1 -ex2 -use_input_sc

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Rosetta 3 - Applications

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