The problem hasn't been solved
Dear all,
I have a membrane protein which is a dimer. I want to fold the monomer and to assemble it to a dimer.
Can Rosetta3.2 or 3.2.1 do it?
If yes, please give some advice on option setup.
Thank you!
-Justin
Hello
I am trying to build rosetta upon unbuntu (Oracle VM Virtual Box) with gcc (4.4.5) g++ (4.4.5) python (2.2.6). While trying to build rosetta with the command "scons bin" I got an error "usr/bin/Id: -lz not found". I tried to install this library with command "sudo apt-get install zlib-dev" but got the following error.
jamil@jamil-VirtualBox:~/rosetta/rosetta_source$ sudo apt-get install zlib-dev
Reading package lists... Done
Building dependency tree
Reading state information... Done
Package zlib-dev is not available, but is referred to by another package.
I have a pdb with the hydrogens already in it. I would like to keep the some specific hydrogens (on the amide nitrogen of a n terminal residue) in the same orientation as the crystal structure. The -no_optH flag doesn't seem to do anything (same output weather set as true or false).
I am aware of the possibility to work in constraints, but this is less desirable than keeping the native structure as it is.
I am a new Rosetta user trying to run the LoopModel application demo.
but I get the following print out with the command line:'loopmodel.linuxgccrelease @flags -database'
core.init: command: loopmodel.linuxgccrelease @flags -database
core.init: 'RNG device' seed mode, using '/dev/urandom', seed=-683210121 seed_offset=0 real_seed=-683210121
core.init.random: RandomGenerator:init: Normal mode, seed=-683210121 RG_type=mt19937
core.init: ROSETTA3_DB not defined
protocols::loopbuild: ==== Loop protocol: =================================================
Hello all...
I'm new in PyRosetta and I'm doing the tutorial by the tutorial scripts. There's a problem with the ligand.py script in the ligand_docking section.
File "ligand.py", line 22, in
slide_into_contact = FaDockingSlideTogether( dock_jump )
NameError: name 'FaDockingSlideTogether' is not defined
Any suggestion???
Thanks in advance
Yasser
Could someone please clarify the examples of angle constraints mentioned here:
http://www.rosettacommons.org/manuals/archive/rosetta3.2.1_user_guide/co...
Specifically, in the example below, is 1.95 in radians or degrees?
Angle CB 5 SG 5 ZN 32 HARMONIC 1.95 0.35
Hi
i tried to run rosetta on a unix machine (ubuntu 9.04) for my data. Upto MR step everything goes fine , but during the rebuilding step after 20 cycles the computer shuts down.
i have attached the log file for the autobuilding run of rosetta. i am using phenix 1.7.1-743 version.
i will be grateful if some one helps me out
the error message is as folows
Parameters taken from: /home/khkim/kjcho/ros_st4/MR_ROSETTA_2/GROUP_OF_ROSETTA_REBUILD_1/PARAMS_1.eff
# mr_rosetta
#
# Run automr/autobuild/rosetta together
# Type phenix.doc for help
I'm am unsure of how to do this. AtomID() does not fit any of the standard types in __init__.Vector1().
For a double, you can do:
vec1 = rosetta.utility.vector1_double()
vec1.append(doubleX)
from rosetta import *
import sys
init()
pose = Pose()
scorefxn = create_score_function_ws_patch('standard','score12')
pose_from_pdb(pose,'config.pdb')
scorePose = scorefxn(pose)
print scorePose
coord = pose.residue(740).atom('N').xyz()
print coord
coord.x = 100.0
print coord
scorePose = scorefxn(pose)
print scorePose
Returns:
...
core.pack.task: Packer task: initialize from command line()
core.scoring.dunbrack: Dunbrack library took 0.01 seconds to load from binary
-1347.47520146
Similar to the Rosetta simulations done in Kidd, Baker,Thomas "Computation of Conformational Coupling in Allosteric Proteins", PLoS Computational Biology , 2009, 5(8), I would like to generate structure ensembles for allosteric regulated proteins using PyRosetta. Starting from crystal or homology structure with/without a bound allosteric effector molecule I want to generate new conformations to analyze the effect of different compounds.
