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"Server Could Not Be Reached" although I have an Internet connection

Category: 
PyRosetta

I am a new user of Interactive Rosetta, I use the software as guided in the tutorial. But when I want to "Thread" my protein, it came up with the message "Server Could Not Be Reached". I have already tried with several different Internet connection, but it still came up with this message. May I know how can I solve this problem? Thank you! 

 

Description of the message: 

The comparative modeling job could not sent to the server! Verify that you have an Internet connection and that the server is running.

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trRosetta modelling with a ligand

Category: 
PyRosetta

Hi all,

 

I am trying to modify the trRosetta scripts to run it with a ligand (heme; I added few distance constraints between the protein residues and atoms in the ligand).

I ran molfile2params with the -c flag and have both centroid and full atom params and pdb files of the ligand. I inserted the ligand to the pose and converted it to centroid mode for the initial folding calculations. When I add my ligand constraints prior to the minimization stage, after all the network constraints are read, I get the following error:

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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! 

 

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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. 

 

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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.

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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.

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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.

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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

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