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PyRosetta

Calling SnugDock from PyRosetta

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! 

 

Post Situation: 

Segfault when loading scorefxn() and load_from_pdb()

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. 

 

Post Situation: 

Best Way to Append/Insert Residue

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.

Post Situation: 

PyRosetta Setup

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.

Post Situation: 

Python3.8 release for Mac download is a dead link

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.

Post Situation: 

Availability of PyRosetta compiled with Python3.8

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

Post Situation: 

can't install ipython + all tests fail

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:

Post Situation: 

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