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Calling SnugDock from PyRosetta

Submitted by shruthi.murali on Wed, 2020-07-29 15:10
Category: 
Docking
PyRosetta

I am very new to the PyRosetta platform and was hoping to get some guidance on how I can do a SnugDock run from the PyRosetta interface with an antibody pdb and antigen pdb, as I know that the ROSIE queue can be quite long. I've seen the PyRosetta 4.0 documentation for SnugDock but am a little bit overwhelmed as I'm not too well versed in Python. Any level of guidance would be greatly appreciated! 

 

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PyRosetta - General

Segfault when loading scorefxn() and load_from_pdb()

Submitted by mm on Wed, 2020-07-22 03:00
Category: 
Scoring
PyRosetta

Hi,

I am trying to load a structure from PDB and then calculate pairwise residue energies between residues in the structure. For this, I want to first load the scorefxn and then the structure (or viceversa), but whenever I try, either of them gives me a segfault, i.e. if I do scorefxn = get_fa_scorefxn(); pose_from_pdb() the latter crashes and if I do the opposite, get_fa_scorefxn() crashes. 

 

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PyRosetta - General

Best Way to Append/Insert Residue

Submitted by jaulicino on Tue, 2020-07-21 10:24
Category: 
PyRosetta

 

Hello everyone,

I am an undergraduate student researching with Pyrosetta for my lab this summer, and I am having difficulties appending/inserting residues into a pose. I would love some help.

I have tried using the grafting protocols (insert_pose_into_pose) but I just realized that there are methods such as append_polymer_residue_after_seqpos which seem to do what I want, perhaps more accurately.

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PyRosetta - General

PyRosetta Setup

Submitted by CathedralEP on Thu, 2020-07-02 15:01
Category: 
PyRosetta

Mac OS Catalina 10.15.5

Python 3.7

MinSizeRel.python37-258

Hello, I am having trouble setting up PyRosetta after it is installed on my computer. I have unpacked it but when I try to do - cd setup && sudo python setup.py install - in command line it asks for a password. The password I was given with my academic license does not work. Any help or guidance would be much appreciated.

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PyRosetta - Build/Install

Python3.8 release for Mac download is a dead link

Submitted by noahC_noahDo on Fri, 2020-06-26 18:20
Category: 
PyRosetta

I saw there was a release that's compatible with py3.8 but the links for Mac versions lead to a "Not Found" page and there aren't any links for this version in the archive either. Not sure if that's an issue on my end or there was an upload issue.

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PyRosetta - General

Availability of PyRosetta compiled with Python3.8

Submitted by SenyorDrew on Wed, 2020-06-24 13:47
Category: 
PyRosetta

Hi,

I have a commercial licence for PyRosetta.  I recently upgraded to Ubuntu20.04, which comes with Python3.8.  I understand that you're planning on releasing PyRosetta compiled with Python3.8 and was wondering when that might be available.  I tried compiling PyRosetta myself (and have been previously sucessful with python3.6 on ubuntu18.04), but ran into issues compiling under stock Ubuntu20.04.

 

Thanks

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PyRosetta - Build/Install

can't install ipython + all tests fail

Submitted by Itai on Wed, 2020-06-24 09:20
Category: 
PyRosetta

Hi all,

  I am trying to install ipython to eventually install pyrosetta as instructed by this guide:

http://www.pyrosetta.org/documentation/windows

However, I can't install iphyton (enable to locate package error) 

I tried many solutions that I found online, but all failed to solve it

Moreover, when I try to continue without solving it, all the tests fail. I checked the python version as recommanded here:

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Rosetta 3 - Build/Install

How to fold-and-dock in PyRosetta?

Submitted by sarah_b on Thu, 2020-05-14 02:37
Category: 
Structure prediction
Docking
Symmetry
PyRosetta

I'd like to do something similar to regular Rosetta fold-and-dock but in PyRosetta.  I've looked at D060_Folding.py and D100_Docking.py examples and while I (mostly) understand what each is doing, I have no idea how to combine them.

How to get a foldtree with symmetry? (in my case it's just simple C3) 

How to combine folding and docking?  Just alternate calls to folding.apply(test_pose) and dock_prot.apply(test_pose)?  (It can't be that simple...)

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