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Error of building abinitiorelax on macOS 14

Submitted by ylwang on Tue, 2020-03-10 05:33
Category: 
Compilation

Undefined symbols for architecture x86_64:

  "protocols::abinitio::ResolutionSwitcher::ResolutionSwitcher(core::pose::Pose const&, bool, bool, bool)", referenced from:

      protocols::moves::MonteCarlo::boltzmann(core::pose::Pose&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, double, double) in MonteCarlo.os

  "vtable for protocols::abinitio::ResolutionSwitcher", referenced from:

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Rosetta 3 - Build/Install

Comparative Modeling Templates for Protein with Multiple Domains

Submitted by Morrian_Lynn on Wed, 2020-03-04 10:42
Category: 
Structure prediction

I want to build the structure of a protein that consists of multiple chains. One of my templates is homologous to the entire protein, but the other templates are only homologous to portions of the protein. I found an early post that suggests manually merging different structures into a sequence that's homologous to the entire protein. Since this answer was posted in 2012, I wonder if is there any new approach to deal with structures that are homologous to different parts of the target?

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Rosetta 3 - Applications

Rosetta changing Atom Name in PDB ATOM record?

Submitted by chrisHKL on Tue, 2020-03-03 20:50
Category: 
Design

Looking at an output PDB file from Rosetta Design, I've noticed that some of the hydrogens have a numeric prefix attached to their atom name in the ATOM record of the PDB file (picture attached).

Does anybody know what this prefix indicates? According to the PDB website, that particular column (column 12) should just be empty, so it is surprising to see a numeric value there.

I believe this is also causing errors for me trying to use another software which analyzes PDB files, by not recognizing the atom name.

 

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Rosetta 3 - General

Pyrosetta conda install not accessing Rosetta features

Submitted by drewaight on Tue, 2020-03-03 14:22
Category: 
Compilation

Hey yall, 

 Im not really sure how this all works so I'll just describe my phenomenon. Im running Ubuntu18.04. I switched using the conda installer to install the latest build of Pyrosetta4, but then I noticed I was missing some of the features which are pulled from Rosetta. The specific example I am working with is the ShapeComplimentarityCalculator example. When I install from the conda so that the latest Pyrosetta is running from :

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PyRosetta - Build/Install

nstruct vs. trials?

Submitted by chrisHKL on Mon, 2020-03-02 13:22
Category: 
Design

In RosettaScripts,

we can specific the number of target structures for the script to design via the

-jd2: ntrials X 

flag where X is the number.

However, in the GenericMonteCarlo mover used for iterative design, we can also specify the number of iterations via the "trials" argument.

My question is, are there any advantages/disadvantages to setting the nstruct number low but setting the trials number high, and vice versa? 

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Rosetta 3 - Applications

Pyrosetta imported after rdkit

Submitted by matteoferla on Sun, 2020-03-01 02:38
Category: 
Small Molecules

I have encountered a curious issue. If I import rdkit before pyrosetta, the latter will not work properly. Rdkit after pyrosetta works fine —so I am basically reporting it here (right place?). Both use Boost wrapping C++ IIRC, so I'm guessing Rdkit changes some setting or imports some library. This code block misbehaves:

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PyRosetta - General

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