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PyRosetta

newbie question re pose syntax

Category: 
PyRosetta

Hello :

I am learning the basics of pyrosetta from this tutorial 

https://graylab.jhu.edu/pyrosetta/downloads/documentation/PyRosetta_Manual.pdf

but when I enter the code verbatim I get an error.

is  something wrong with the syntax they give?  trying to do this:

 

Post Situation: 

Motif Graft Mover error

Category: 
PyRosetta

hello everyone,

I was using a script i wrote last year regarding motif grafting, but it no longer works, i suspect a pyrosetta update issue.

anyway, i am looking through the errors and it seemed the pyrosetta.rosetta.protocols.motif_grafting.movers.MotifGraftMover's init_parameters() have some additional arguments that is must have.

my code is as follows:

Post Situation: 

Adding Custom AtomTypes to Pyrosetta

Category: 
PyRosetta

 

Hello everyone,

 

Does anyone have experience adding custom atom types to Pyrosetta? I have tried creating my own `atom_properties.txt` file, shown below.

```

NAME  ATOM LJ_RADIUS LJ_WDEPTH LK_DGFREE LK_LAMBDA LK_VOLUME
A1     X 2.0000         0.0486       1.0000           3.5000 23.7000
A2     X 2.0000        0.2000  1.0000 5.0000           23.7000
VIRT    VIRT 0.0000         0.0000 0.0000            3.5000 0.0000 VIRTUAL

Post Situation: 

why two packing setting return different energy?

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: 

Post Situation: 

about deNovoProteinMimeticsGen2

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 

Post Situation: 

pyrosetta source

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

Post Situation: 

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