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ProteinInterfaceDesign algorithm questions

Submitted by tsztain on Mon, 2019-02-18 14:10
Category: 
Design

Hello, I am using the following protocol, modified from the design raf-rac interface demo, to design a protien protein interface. I ran 2 designs in parallel using nstruct = 1,000 and ran SequenceProfile.py to analyze and found that the results were the same for each. Therefore I wondering exactly how the sequence space is "randomly" searched to identify mutations and how likely these mutations will be to give a more favorable interface in vitro.  Thanks in advance

        </SCOREFXNS>

        <FILTERS>

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Rosetta 3 - Applications

Error msg while compiling on a new cluster

Submitted by jharamesh on Fri, 2019-02-15 20:55
Category: 
Compilation

Not sure why scons is failing on a new cluster

>./scons.py bin -j16 mode=release extras=mpi

I see en error:

scons: *** Do not know how to make File target `bin' (/usr/projects/xyz/shared/rosetta_3.10_release/main/source/bin). Stop.

rosetta_3.10_release could be easily compiled on my local machine.

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Rosetta 3 - Build/Install

Rosetta_CM error unrecognized atom 'CS' this atom is not in PDB

Submitted by rlwoltz on Thu, 2019-01-24 19:43
Category: 
Structure prediction

Hi all,

 

       I'm sorry if this is an old thread, I did find other forums dealing with unrecognized atoms but in those threads my problem was not resolved.  I am trying to follow the rosetta_CM tutorial and I got through the setup_rosetta_CM.py script and it generated the .xml file which I checked and it looked good. However, when I run the hybridized steps using rosetta scripts I get this error:

 

ERROR: unrecognized atom_type_name 'CS'

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Rosetta 3 - Applications

Rosetta3.10 on macOS segmentation fault 11

Submitted by G Mustafa on Thu, 2019-01-24 08:40
Category: 
Structure prediction

 

I have tried several times to install Rosetta3.10 for macOS version 10.14.2. My system info is:

Model Name: MacBook Pro

  Model Identifier: MacBookPro15,2

  Processor Name: Intel Core i7

  Processor Speed: 2,7 GHz

  Number of Processors: 1

  Total Number of Cores: 4

  L2 Cache (per Core): 256 KB

  L3 Cache: 8 MB

  Memory: 8 GB

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Rosetta 3 - Build/Install

RosettaMP: issue with generating .lips4 file

Submitted by ksy141 on Mon, 2019-01-21 17:17
Category: 
Structure prediction

Hi Rosetta users,

I am experiencing trouble using RosettaMP to predict membrane protein structures. I am currently following the RosettaMP tutorial, which can be found here (https://www.rosettacommons.org/docs/latest/application_documentation/structure_prediction/membrane-abinitio).

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Rosetta 3 - Applications

Build problem "Never include <bits/libio.h> directly; use <stdio.h> instead."

Submitted by Martin Floor on Mon, 2019-01-21 00:48
Category: 
Compilation

Hi everyone,

I am trying to build Pyrosetta from source in Ubuntu 18.04 x64, but  I am having a compilation error, as indicated in the title.

Does anyone have a clue about what could be the issue or has a better idea to compile it?

I am using python 2.7.15, rosetta build 2018.33.60351, ninja 1.8.2, cmake 3.12.1 and gcc 4.8, specified with the global variables: CC=gcc-4.8 and CXX=g++-4.8. The error log is:

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PyRosetta - Build/Install

Problems when working with PTMs - cannot make sugar poses

Submitted by MNP1986 on Thu, 2019-01-10 07:44
Category: 
Chemically Modified Residues

Hello everyone,

I have a protein which has a few PTMs in the form of sugars, and I have therefore started experimenting with sugars in PyRosetta. I have found a very nice guide:

https://graylab.jhu.edu/pyrosetta/downloads/documentation/RosettaCarbohydrate_Tutorial-Demo.pdf

which I have used as a starting point together with the documentation e.g.

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PyRosetta - Applications

pyrosetta with Parallel Studio XE

Submitted by psteinb on Mon, 2019-01-07 02:42
Category: 
Compilation

Hi,

I'd like to build pyrosetta with the intel compiler and potentially link against the Intel MKL for use on HPC infrastructure. I saw in the rosetta docs, that rosetta can already be used with the intel compiler on TACC resources:

 https://www.rosettacommons.org/docs/latest/build_documentation/TACC

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PyRosetta - Build/Install

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