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Foldtree setup, jump problem in PyRosetta 2.0

Submitted by msellers on Thu, 2011-07-21 12:00

For some reason, PyRosetta is only identifying two jumps in my Pose, where in version 1.0 I had three. Using jump=3 with the following gives me an error when I try to randomize or dock.

Here is my chain layout: AB_X

Here are the foldree commands I am issuing:


jumpVec = rosetta.Vector1([3])
rosetta.protocols.docking.DockingProtocol.setup_foldtree(pose,'AB_X',jumpVec)
print pose.fold_tree()
print str(pose.num_jump())+" jumps."

which prints:

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PyRosetta - General

rosetta building "zlib1g-dev" error

Submitted by AG88 on Wed, 2011-07-20 23:24

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.

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Rosetta 3 - Build/Install

keep crystal structure hydrogens

Submitted by gw on Wed, 2011-07-20 03:54

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.

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Rosetta 3 - General

Unable to run Rosetta LoopModeling application

Submitted by BDBorrillo on Tue, 2011-07-19 14:06

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: =================================================

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Rosetta 3 - Applications

ligand.py script problem

Submitted by almeida on Tue, 2011-07-19 10:02

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

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PyRosetta - Scripts

computer shuts down during autobulding with rosetta

Submitted by intekhab on Tue, 2011-07-19 01:07

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

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Rosetta 3 - General

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