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D070_Refinement.py

Submitted by thorx020 on Fri, 2012-09-14 06:40

Hi,

I'm trying to understand the D070_Refinement.py code posted by the Gray lab on PyRosetta.org. In short, the code basically makes small stabilizing backbone perturbations and repacks the sidechain of random residues in your pose. However, I don't know how many residues get perturbed/repacked. What input parameter specifies the # of residues that get perturbed? The "cycles" parameter is set 9 and is fed to the RepeatMover() function and the comments say that "cycles" affects the amount of sampling, but I'm not don't think think this is what I'm looking for.

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PyRosetta - General

Folding and Docking using Symmetry

Submitted by danielles on Wed, 2012-09-12 11:32

Recently I was trying out the modes of Docking and Fold and Dock using symmetry, but I found that when I got the structures out, none of them were in the native form. The native structure is a dimer with 2 parallel monomers, but all of the structures had the 2 monomers in an antiparallel conformation. In order to understand where I went wrong I went back to the integration test to try it out, but I got antiparallel structures when creating this as well. I wanted to know if I was doing something wrong, had the wrong form of symmetry chosen, what it could be.

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Rosetta 3 - Applications

Send the output of PyRosetta to a PyMOLPyRosettaServer on a remote computer?

Submitted by lah435 on Mon, 2012-09-10 16:06

How can I send the output of PyRosetta to a PyMOLPyRosettaServer on another computer?

The PyMOL_Mover does not have a 'link' object to specify the ip address and port, as is suggested in the tutorial: http://www.pyrosetta.org/pymol_mover-tutorial

from rosetta import *
init()
pose = pose_from_pdb("test_in.pdb")
pymover = PyMOL_Mover()
pymover.apply(pose)
pymover.send_energy(pose)
pymover.link.udp_ip = "127.0.0.1"
AttributeError: 'PyMOL_Mover' object has no attribute 'link'
pymover.link.udp_port = 65000

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PyRosetta - General

Steps to use D-amino acids

Submitted by tevang on Mon, 2012-09-10 15:42

Greetings,

I am trying to dock a D- peptide on a protein dimer using the FlexPepDocking application. After collecting all the information I could find from tutorials and old posts I followed the steps described below:

1. I uncommented all the lines under "D-CAA TYPES" in file: rosetta_database/chemical/residue_type_sets/fa_standard/residue_types.txt
2. Downloaded the rotamer libraries from http://carl.bio.nyu.edu/%7Erenfrew/ncaa/ncaa_rotamer_libraries.tar.gz and placed the files inside

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Rosetta 3 - General

Negative design: Can a filter call a mover in rosetta scripts?

Submitted by jgans on Sat, 2012-09-08 21:28

I would like to add a filter to my XML Rosetta design script that allows me to implement negative design.

Specifically, I want a filter that can take my designed and minimized input structure, apply a symmetry operation to it (i.e. rotate & translate a domain), minimized the transformed structure and compare the energy to the unmodified input structure. Is this possible with the XML-based Rosetta scripts (I couldn't find a filter operation that allowed me to modify a structure, apply a minimization mover while "remembering" the input structure).

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Rosetta 3 - General

Does Rosetta have an app for detecting brakes and clashes in proteins

Submitted by Anatol on Sat, 2012-09-08 15:48

Hi all,

I am wondering if Rosetta has an app for detecting brakes and clashes in proteins? I have got an ensembles of protein decoys that were rebuilt from Ca and Cb traces, then idealized and relaxed. Some of the decoys have clashes, others have brakes. I would like to filter "bad" decoys out.

My other question is about the "bb_min_allowed_dev" option. Does it work with the Rosetta's relaxation? I am wondering whether or no increasing "bb_min_allowed_dev" to 0.7-1.0A would remove some severe clashes?

Thanks,

Anatoly

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Rosetta 3 - General

ERROR: Error reading in FragmentPicker::read_spine_x(): does not match size of query!

Submitted by Anonymous on Sat, 2012-09-08 09:33

I have an odd error. When I try and run make_fragments.pl for my sequences first.fa and second.fa I recieve an error about read_spine but when I run the example from make fragment's from 1elwA it works fine.
What do I need to do different?

Below is the sample error output:
Thank you
Casey
first.fa
>133862
HHHFDNIFKKIHQIIKDMDNNIKPAEHHQHMQHLINQIHQLFDDFHQQIHEVRAKQNIHKLLDKIQHMFHNFKNHLDPLWVHNQMHNFMHDMNQFMQHFDHNFK
second.fa
>137822
NHKLHHFMHDMKHLLQHFQHHFKTETIHHQMKNLINNLKKMIHNLNNDFNSVIFDQNMHQMFKDFQQMMDDIQKQLHFLPHNHNIDQLLQHLQNMMDQLHQKFQ

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Rosetta 3 - General

membrane score weights

Submitted by ytao on Sat, 2012-09-08 06:56

Dear Rosetta community,

I'm learning to make models of my membrane protein using rosetta and I have tried the "membrane_abinitio" and "membrane_relax" demos in tests directory.

Can someone tell me how the scoring weights used in the "membrane_relax" test ("membrane_highres.wts" and "membrane_highres_Menv_smooth.wts" ) were developed? Is there a reference?

Best regards,

Yisong Tao

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Rosetta 3 - Applications

Rosetta Dock with MPI / PBS

Submitted by edpryor on Wed, 2012-09-05 11:04

Hello, again.

I have another (hopefully simple) question regarding rosetta, specifically RosettaDock.

I have compiled rosetta3.4 with MPI support (thanks smlewis!), and am trying to run a test docking job to ensure it is working. This cluster uses PBS as the scheduler.

My PBS script is as follows:

------------------------

#!/bin/sh
#PBS -l select=2:mpiprocs=4:ncpus=4
#PBS -q nopreempt
#PBS -l walltime=1:00:00
#PBS -j oe

module load mpich2-intel/1.3

cd $PBS_O_WORKDIR

rbin=/home/eep3m/rosetta_source/bin
rdb=/home/eep3m/rosetta_database
pdb=1brs.pdb

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Rosetta 3 - General

AbinitioRelax with very small peptides

Submitted by jamsmad on Tue, 2012-09-04 13:45

Hello,

I've been using Rosetta Abinitio for some time as a part of a larger docking simulation program. Normally the peptides are 11 amino acids to 30 amino acids long. However, in the latest system I've been working out it is desirable to test some very small peptides of length 6 amino acids to compare to some successfully docked larger peptides. I use the following inputs for the abinitio run:

**********************************************
-database ./rosetta3.4/rosetta_database

-in:file:fasta ./APRXC.fasta

-in:file:frag3 ./aaAPRXC03_05.200_v1_3

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