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antibody.py

Submitted by franfdez on Mon, 2016-08-01 08:12
Category: 
Loop Modeling
PyRosetta

Dear all,

I am using the antibody.py script that comes with PyRosetta (rosetta_src_2016.13.58602_bundle, v3.6) and associated software to generate structural models for VH/VL sequences. For most of the sequences that I am using as input, the script terminates at the antibody_graft step with an error (pasted below):

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PyRosetta - Applications

PyRosetta memory footprint

Submitted by LiorZ on Thu, 2016-06-16 04:36
Category: 
PyRosetta

Hi All,

I have a design protocol implemented in PyRosetta that has a very large memory footprint ~ 4Gb. I ran a python memory profiler on the design script and discovered that the sharp memory consumption increase occurs upon the initialization of PackRotamerMover (I presume this is where the rotamer library is instantiated). I have taken the following measures to reduce the memory consumption with no success:

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PyRosetta - General

PyRosetta init() error (Linux)

Submitted by FRiemer on Mon, 2016-04-25 01:21
Category: 
PyRosetta

Dear all,

I've been trying (and failing) to build PyRosetta (monolith release 95) for a couple of days now.

I'm running Kubuntu 15.10 64bit.

I've tried running PyRosetta with Python 2.6, 2.6.6 and python 2.7 (ipython & regular).

I never get complaints for from rosetta import * or import rosetta, but when I try to init() I get

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PyRosetta - Build/Install

Install PyRosetta 101?

Submitted by anelutt on Thu, 2016-02-11 09:21
Category: 
PyRosetta

Dear Reader!

I'm doing computational redesign as the project for my  bachelor degree and my supervisor told me to use Rosetta/PyRosetta. I've been trying to install this thing on my computer for about three weeks now and I haven't gotten anywhere. Can somebody please explain how to do for a person who never have been programming or used the command tool in the computer before? I have installed it in my PC through a  .exe-file, but when I click on the shortcut nothing happens. 

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PyRosetta - Build/Install

ClassicRelax: how to block the backbone

Submitted by oppopomoz on Fri, 2015-11-27 08:17
Category: 
PyRosetta

hello! isnt the following command meant to keep the backbone fixed? cos i obtain a model with a RMSD of about 1A from the initial model.

movemap=MoveMap()    
movemap.set_bb(False)
relax=ClassicRelax()
relax.set_scorefxn(scorefxn_tala)
relax.set_movemap(movemap)
relax.apply(sample_pose)

Thanks :)

 

 

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PyRosetta - General

How to determine interface residues

Submitted by rbehan on Wed, 2015-10-14 11:25
Category: 
Scoring
PyRosetta

Hi,

I have a couple questions about fold-trees and how interfaces are calculated in pyrosetta (or rosetta).  I have a structure of an antibody-antigen that I have prepared using rosetta (attached).  A visual inspection shows that residue B:TYR210 is making a number of close contacts with residues in Chain C (the antigen).  However, when I construct an Interface object in pyrosetta, this residue is not identified as being in the interface (using a cutoff of 5.0A):

 

from rosetta import *

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PyMOL did not work from a remote machine with PyRosetta

Submitted by Jeremy1990 on Sat, 2015-08-08 21:25
Category: 
PyRosetta

Hi all,

I want to show the structures by PyMOL_mover to PyMOL in another computer,so according to the tutorial by setting pymover.link.udp_ip = #IP(where PyMOL is running) and pymover.link.udp_port = 65000,but after pymover.apply(pose),the pymol did't show anything,(if PyRosetta and PyMOL run in the same computer,it works),have anyone met this problem,thanks a lot if you can help me!

Thanks,
Jeremy

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