PyRosetta

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Is a personal PC feasible to run PyRosetta?

Submitted by lanselibai on Wed, 2014-08-13 07:49

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PyRosetta

Dear Sir or Madam,
Recently I encountered some problems (e.g. Runtime error, memory error) when running PyRosetta. I am not sure whether it is due to my old PC or my incorrect code. Can I ask do you think it is feasible to install

PyRosetta.Windows.64Bit.monolith.mode=release.branch=release-r10.exe

on a PC of

AMD Athlon(tm) II P360 Dual-Core Processor 2.30 GHz
4.00 GB
64-bit OS
Win 7 Ultimate, Service Pack 1
?

Or do you run your PyRosetta work on a cluster?

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Calculating sasa per atom and atomid_map

Submitted by ioannis.f on Wed, 2014-08-13 05:26

Category:

PyRosetta

Hi,

I am trying to calculate the sasa for each atom but I cannot get the arguments correct for rosetta.core.scoring.calc_per_atom_sasa.

I guess for "utility::vector1< Real > & rsd_sasa" I can use rosetta.utility.vector1_Real().

However, I have trouble with "id::AtomID_Map< Real > & atom_sasa". I tried rosetta.core.id.AtomID_Map_AtomID() but it doesn't match the C++ signature.

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Bug in the BuildBindings.py with Linux kernel version

Submitted by Cyril Cros on Mon, 2014-07-28 12:07

Category:

Compilation

PyRosetta

Hi,
I think I have found a rather minor bug. It happens only with Linux. I don't know if there is a report system for this, so I am posting it on the forum.
Thanks for your work with Rosetta, it is really amazing.
Cyril

Context:
I am building pyrosetta from source, using the BuildPyRosetta.sh generated by rosetta/tools/PyRosetta.develop/DeployPyRosetta.py.

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64 bit windows version of PyRosetta does not include rosetta.dll?

Submitted by pepfolder on Tue, 2014-07-22 10:45

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PyRosetta

I was trying to download and use the 64 bit windows versions of PyRosetta, but when I tried to run "from rosetta import *" it can't find the rosetta.dll Any suggestions on how to get the 64 bit version of PyRosetta running on windows?

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Argument error when running D120_Ligand_interface.py

Submitted by piladam on Wed, 2014-07-09 10:43

Category:

Docking

PyRosetta

Hi,

I am trying to run D120_Ligand_interface.py sample script with the provided test_lig.pdb and ATP.params. I have placed the ATP.params file into (in PyRosetta main directory) /rosetta_database/chemical/residue_type_sets/fa_standard/residue_types and added the path of the ATP.params file to the file /rosetta_database/chemical/residue_type_sets/fa_standard/residue_types.txt. When I run the script (in ipython - run D120_Ligand_interface.py) I get the following error message.

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Problems when inserting spin-label R1A

Submitted by ajasja on Fri, 2014-06-27 04:14

Category:

Non-Canonical Peptides

PyRosetta

Dear all,

I would like to use the spin-lable R1A (implemented as part of Rosetta EPR).
In database/chemical/residue_type_sets/fa_standard/residue_types.txt I activated the needed lines

## Spin label types
# kills my unit tests???
residue_types/spin_labels/R1A.params

Although the “kills my unit tests???” comment is not very encouraging:=)

The problem is:

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pose_from_sequence with modified residue

Submitted by nawsad on Wed, 2014-06-25 02:59

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PyRosetta

How can I create a pose from sequence containing acetylated lysine?
Using p = pose_from_sequence("VSK[LYS_p:N_acetylated]GPF","fa_standard") and then dumping it gives a pdb with two chains and the K residue is not modified.
thanks!

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Capturing the output of scorefxn.show(pose)

Submitted by ajasja on Fri, 2014-06-20 05:30

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PyRosetta

I'm using PyRosetta-r21 on Ubuntu togather with IPython 2.0.0 notebooks. This works extremly well, with one small problem:
Some output is redirected to the console in which "ipython notebook" command was started instead of the notebook cell.
So the question is: is it possible to capture the output of scorefxn.show(pose)?

I have tried to use the example in "test/T007_TracerIO.py"

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Possible minor mistakes in SetPyRosettaEnvironment.sh (in r21 for Ubuntu)

Submitted by ajasja on Fri, 2014-06-20 05:10

Category:

PyRosetta

Dear all,
There may be some minor mistakes in the SetPyRosettaEnvironment.sh in the r21 release of PyRosetta:

On line 34 "export LD_LIBRARY_PATH=$PYROSETTA/rosetta${LD_LIBRARY_PATH+:$LD_LIBRARY_PATH}"
$PYROSETTA is not added to the LD_LIBRARY_PATH and "libboost_python.so.1.55.0.so" is consequently not found.
Corrected: "export LD_LIBRARY_PATH=$PYROSETTA:$PYROSETTA/rosetta${LD_LIBRARY_PATH+:$LD_LIBRARY_PATH}"
(Or just move the offending so to rosseta subdir)

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