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why two packing setting return different energy?

Submitted by zhangying1990 on Wed, 2019-01-30 00:18
Category: 
PyRosetta

Hello everyone, 

recently, i doing the Exercises of workshop6, but i found i was confused about the packing and design in rosetta...

Anybody can help to figure out why the two setting method of PACK （def pack1 and def pack2) return different energy？it should be the same as i think！

if i run pack1 followed by pack2, then it return the same(lower) energy. it seens that the design energy is not optimized. so should i set another packing after the design? 

thanks if anyone can help.

 

MY CODE: 

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PyRosetta - General

about deNovoProteinMimeticsGen2

Submitted by zhangying1990 on Mon, 2019-01-14 17:09
Category: 
PyRosetta

Good morning everyone~ 

Recently, I had read the paper entitled "De novo design of potent and selective mimics of IL-2 and IL-15”

And I am very interesting in it, and I want to learning how to performing it in using pyrosetta. 

However, in the Code availability section, I can not find any information about the submodule 

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PyRosetta - Scripts

pyrosetta source

Submitted by scdantu on Mon, 2018-09-17 08:02
Category: 
Compilation
PyRosetta

Hi,

I have GLIBC issue with the compiled PyRosetta4.Release.python35.linux.release-191 on a Suse Linux cluster. So I would like to compile it from the source but I cannot find the download link and cannot download it from github using my login details. Kindly suggest the link to download the source code for PyRosetta4.


Regards,


Sarath

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PyRosetta - Build/Install

Introducing N/C-terminal residues to a pose

Submitted by MNP1986 on Thu, 2018-08-23 06:09
Category: 
PyRosetta

Hello everyone,

I work with a protein where the crystal structure does not include the first 14 amino acids, which are intrinsically disordered.

I would like to add the missing 14 residues using PyRosetta, and I have therefore looked into the FAQ and tried to find the relevant methods in the documentation.  After some considerations I have come up with strategy:

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PyRosetta - Applications

How to make FastRelax use smaller number of rotamers from PyRosetta app?

Submitted by sn on Tue, 2018-08-21 15:55
Category: 
PyRosetta

I am using FastRelax from PyRosetta. When I run it from PyRosetta, the number of rotamers built are way more than the number of rotamers when I run it with C++ relax binary. For instance: I use the following to relax a pdb with movemap in PyRosetta as follows:

def relax_pdb_with_movemap(self, pose, movemap):
        relax = FastRelax()
        relax.set_scorefxn(get_fa_scorefxn())
        relax.set_movemap(movemap)
        relax.apply(pose)
        return pose

In C++ I give the following command:

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PyRosetta - Applications

Alternative to MinMover

Submitted by MNP1986 on Tue, 2018-07-31 02:18
Category: 
PyRosetta

Hello everyone,

I have checked the D070_Refinement.py* script provided by the Graylab, and I would like to make my own little refinement script based on it and the other guides and tutorials available.

I have, however, run into problems as the ‘MinMover’ method is not available under pyrosetta.rosetta.protocols.simple_moves which prevents me from using the approach outlined in D070_refinement.py to minimize the pose score.

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PyRosetta - General

installation / python versions

Submitted by rta on Thu, 2018-06-07 00:43
Category: 
PyRosetta

Hi,

I would like to install PyRosetta4 for python 3.6 on Ubuntu 16.04 64bit. For this I installed python3.6, as deafault python version was 2.7. According the installation instruction I have to use smth like

cd setup && sudo python setup.py install

Will it call python 2.7? should I expect any errors? How should I install PyRosetta properly?

Thanks!

 

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