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pose_from_pdb gives RuntimeError: unidentifiable C++ exception?

Submitted by cossio on Thu, 2014-11-27 14:43
Category: 
PyRosetta

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

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PyRosetta - General

Error installing rosetta2014.35 on Ubuntu14.04

Submitted by annalisa on Fri, 2014-10-31 12:25
Category: 
Compilation

Hello,

I am trying to install rosetta2014.35 on ubuntu14.04.
I installed the last versions of gcc and clang compilers, namely gcc-4.8 and clang-3.5

I installed the following packages and libraries as reccommanded

sudo apt-get install build-essential
sudo apt-get install zlib1g-dev
sudo apt-get update

and executed the commands

cd main/source/
scons bin mode=release

but unsuccessfully!! I always receive the same error (see below)

Also I updated g++ compilers on tools/build/site.setting. topsail file

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Rosetta 3 - Build/Install

Coordinates in pose do not match those in PDB

Submitted by ajasja on Tue, 2014-10-28 12:29
Category: 
PyRosetta

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

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PyRosetta - General

Generating random number using numeric.random

Submitted by resiros on Thu, 2014-10-23 09:25
Category: 
PyRosetta

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!

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PyRosetta - General

Memory leak? Memory consumption rises quickly when using JD2 app(s)

Submitted by yuvals on Mon, 2014-10-06 11:35
Category: 
Scoring

Hey!

I don't know if this is a known issue or not, but when I run score_jd2 with a -in:list:l I get increasing memory consumption, which passes 1.4g (RES column untop `top`) within a minute. Using score with same flags has constant memory usage. I did this check because a JD2 app I'm developing also showed increasingly high memory usage, so I suspect it's a JD2 issue (?)

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Rosetta 3 - General

Syntax to extract PDB files from a silent file

Submitted by lanselibai on Fri, 2014-09-26 13:48
Category: 
Structure prediction

Dear friends,
I think there is nothing incorrect in my command line to extract PDB files from a silent file:

~/Cheng/rosetta_2014.30.57114_bundle/main/source/bin/score_jd2.linuxgccrelease -database ~/Cheng/rosetta_2014.30.57114_bundle/main/database -in:file:silent /mnt/hgfs/Downloads/silent.out -in:file:fullatom -in:file:silent_optH -out:output

The prompt goes well and completes successfully:

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Rosetta 3 - Applications

clean_pdb.py of Rosetta VS cleanATOM of PyRosetta

Submitted by lanselibai on Wed, 2014-09-24 03:02
Category: 
Structure prediction

Dear friends,
I am dealing with a PDB file missing some residues. I think I should clean it by clean_pdb.py of Rosetta or cleanATOM of PyRosetta.

In Rosetta, the clean_pdb ignores the missing positions and renumber all the residues from 1 to the end regardless of the missing gap.

In PyRosetta, the missing gap can still be remained.

Can I ask can I get the result similar to cleanATOM by using Rosetta's clean_pdb.py? I think I should clean the PDB first, then do loop modeling for the missing residues. Is that correct?

Thank you very much.

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Rosetta 3 - Applications

Iterating over graph edges in PyRosetta.

Submitted by ajasja on Mon, 2014-09-22 07:21
Category: 
PyRosetta

I would like to get all residues that are close to any chosen residue in my pose. (I need a list of all residues whose side chains could potentially interact with the side chain of my chosen residue.)

I’m guessing the information is available in `pose.energies().tenA_neighbor_graph()`, but I can’t seem to access it in PyRosetta.

calling:

    for l in pose.energies().tenA_neighbor_graph().get_node(1).edge_list_begin():
        pass

returns:

    TypeError: 'EdgeListIterator' object is not iterable

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