Hi all,
I'm getting the following error when trying to run my script with pypy. I can run the script fine with python 2.7.9.
Is there a way to directly manipulate ligand dihedrals in PyRosetta? If so, which mover does this?
Thanks!
I seem to be having an issue with getting the binary version of the Dunbrack library to load properly in PyRosetta on Windows and I was wondering if anyone knows if there is a fix for it. Obviously it takes about 30 seconds or so to load the Dunbrack libraries from text so it can turn into a rate-limiting step if you have to read these files a lot.
I was wondering of there are any PyRosetta people based in London? Does the forum know of any research people or groups in London? I have a little project in mind....
Thanks
Mark
I am following this tutorial:
http://graylab.jhu.edu/pyrosetta/downloads/documentation/Workshop2_PyRos...
When I get to the line:
pose = pose_from_pdb("1YY8.clean.pdb")
it results in an error:
RuntimeError Traceback (most recent call last)
<ipython-input-9-755d9c16f3f1> in <module>()
----> 1 pose = pose_from_pdb("1YY8.clean.pdb")
RuntimeError: unidentifiable C++ exception
I have downloaded PyRosetta (64-bit, Scientific/Red-Hat linux) for a Fedora 18 OS. I have on this machine python2.7 (64-bit) and a libpython2.7.so.1.0 in my /usr/lib64 directory. When I run ipython.py I get:
When I load a PDB file the coordinates for residue 18 (R1A) reported by pyrosetta do not match those found in the PDB. An example notebook is attached.
What is the reason for this mismatch and how could I fix it? Is it connected to the internal coordinates of R1A.params?
The CB atoms of the other residues (ALA) are correct.
Thank you for your help and best regards,
Ajasja
Hello,
I'm developing a new protocol using PyRosetta. I hoped to use Rosetta's built-in random functions (numeric::random::gaussian for example) but couldn't find them in PyRosetta under numeric (numeric.random does not exist)
Is there a way to access them?
I remember reading that having a good random generator for stochastic highly-parallelized application is quite important. Does it make sense to use Python's built-in random class in case it did not work with Rosetta's?
Thank you!
I’m really happy with my PyRosetta prototype script, so it’s time for a production run!
But there is a problem. My nodes have 4GB of memory and 8 cores. But PyRosetta needs ~1.5GB of memory to run.
