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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: 

Resfile Error

Category: 
PyRosetta

Hello everyone,

 

I am trying to perform RosettaDesign, and I have a script that uses pyrosetta.rosetta.core.pack.task.parse_resfile()

In the past this worked just fine, but now with the new update it seems it doesn't work, I get this error:

RuntimeError:
File: /scratch/benchmark/W.glass/rosetta.Glass/_commits_$ main/source/src/core/pack/task/ResfileReader.cc:1582 [ ERROR ] UtilityExitException ERROR:

I am not sure how to fix this issue, following is two codes that break:

Post Situation: 

Pyrosetta: restrict repack (and minimization) to specific region

Category: 
PyRosetta

Hi everyone,

I am trying to restrict repacking around a residue . I have written a script with PreventRepacking() and RestrictToRepacking but I am still confised about the result. Here is the code I am using:

Post Situation: 

Residue is not compatible with cutpoints

Category: 
PyRosetta

Hi all,

I'm currently trying to run the CCDLoopClosureMover function in order to attach two protein domains together. 

When I try to add a single cutpoint variant around my jump point, I repeatedly get a warning that says:

"Residue 126 is not compatible with cutpoints; variant type not changed." 

Residue 126 is the Cterminus

This warning also shows up for residue 127 (the Nterminus of the other protein domain). And thus, I cannot apply CCD to my pose because I don't have a cutpoint variant....

Post Situation: 

Question about the error when using pyrosetta.distributed.io

Category: 
PyRosetta

I have tried the latest version of Pyrosetta Anaconda python3.6 (PyRosetta4.Release.python36.mac 2019.19+release 5adc612fd9dee20f808a07e761610d95698b0f35) and previous version, PyRosetta4.Release.python36.mac 2019.18+release on MacOS, but run into the same errors when I do, for example,

Post Situation: 

Need help figuring out the meaning and cause of an error

Category: 
PyRosetta

I run into this problem when trying to use prepend_polymer_residue_before_seqpos and I can't understand what it really means and, most importantly, what its cause is and how to prevent it from happening. There's a screenshot of the error in the attached pic.

Assertion `moving_connection.icoor().is_internal() && fixed_connection.icoor().is_internal()` failed
Post Situation: 

Installation files not found

Category: 
PyRosetta

I'm currently installing PyRosetta on windows (anaconda) using the linux tar file with the installation instructions from

http://www.pyrosetta.org/dow

I've reached step 6:

From within the new PyRosetta directory, type cd setup && python setup.py install into the command line to set up the PyRosetta.

I've run the installation and received the following output:

Post Situation: 

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