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trans-ACPC

Category: 
PyRosetta

Hello!

I've been trying to create a pose with trans-ACPC, but when I use the X[TAC] in the sequence, it doesn't seem to know what residue it is. I know there's a params file for it... I tried loading a pdb structure with ACPC in it as my pose to see what'd happen and it says that:

"ERROR: Error in core::scoring::methods::RamaPreProEnergy::residue_pair_energy(): The RamaPrePro term is incompatible with cyclic dipeptides (as is most of the rest of Rosetta)."

Post Situation: 

Rosetta get_fa_scorefxn()

Category: 
PyRosetta

I am using PyRosetta to minimize several complexes and obtain the rosetta calculated energy values. In order to obtain all the rosetta scoring terms, I am using the get_fa_scorefxn function. Whereas I want to retain all the scoring terms, the only option that seems available to see all of them is with the following lines:

scorefxn = get_fa_scorefxn()

pose = pose_from_pdb(<minimized_complex_pdb>)

scorefxn.show(pose)

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how to download "GUIs/pyrosetta_toolkit/documentation" ?

Category: 
PyRosetta

Hello,

      I need GUIs/pyrosetta_toolkit/ documentation from http://www.pyrosetta.org/documentation#TOC-1.-The-PyRosetta-Toolkit. However the linkage to this documentation is forbidden now. Can someone do me a favour to provide this documentation by email ? My email address is liuhui@qibebt.ac.cn

      Thank you very much!

best wishes

Hui Liu

Post Situation: 

ipython can't find PyRosetta files

Category: 
PyRosetta

I'm trying to get interactive rosetta to work on a linux virtual machine. I have zero experience coding so I've been struggling royally. I first tried Ubuntu 18.04, but after having some difficulty I decided to switch to as close of a setup as what is in the interactive rosetta install video as I could. I tried Ubuntu 12.04 64 bit with python 2.7.3 and PyRosetta 3 release 104. When I try to import rosetta into ipython this appears:

Post Situation: 

Incomplete Error message

Category: 
PyRosetta

So, I have a code that is supposed to design an enzyme with constraints taken into account. I started it once, looping through a folder of pdb files (that one is still running, takes a while to design 375 pdb files), then just changed which folder and pdb files it would work with. Unfortunately, I then got an error message that cuts off before actually giving the error:

RuntimeError: 

Post Situation: 

PyMOLMover object has no attribute 'link'

Category: 
PyRosetta

Hi Guys,

I am trying to set up the PyMOLMover object to view structure manipulations. We have PyRosetta set up on a compter cluster, and I was going to have it run scripts and send structure info to another PyMOL instance on a separate computer on the same network - however it errors out when trying to assign an IP address to the link.udp_ip attribute. The code is simple and pulled straight from the following documentation/tutorial: http://www.pyrosetta.org/pymol_mover-tutorial

Post Situation: 

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