Posts by antu

1) Message boards : Rosetta@home Science : Viewing structure predictions (Message 76335)
Posted 8 Jan 2014 by antu
Post:

Hey,

I just tried to view the predicted proteins from rosetta@home following this tutorial:

http://boinc.bakerlab.org/rosetta/rah_view_predictions.php

But it didn't work, the rosetta command failed with the following errors:

[2014- 1- 8 21:50:14:] :: BOINC:: Initializing ... ok.
Can't open init data file - running in standalone mode
[2014- 1- 8 21:50:14:] :: BOINC :: boinc_init()
BOINC:: Setting up shared resources ... ok.
BOINC:: Setting up semaphores ... ok.
semget failure! Cannot create semaphore!
BOINC:: Updating status ... ok.
BOINC:: Registering timer callback... ok.
BOINC:: Worker initialized successfully.
command: ./minirosetta_3.48_x86_64-pc-linux-gnu -extract -all -s chk_S_00000005_ClassicAbinitio__stage_2.out
Registering options..
Registered extra options.
Initializing broker options ...
Registered extra options.
Initializing core...
Initializing options.... ok
Options::initialize()
Options::adding_options()
Options::initialize() Check specs.
Options::initialize()  End reached
ERROR: Option matching -extract not found in command line top-level context

The command I used was:

./minirosetta_3.48_x86_64-pc-linux-gnu -extract -all -s chk_S_00000005_ClassicAbinitio__stage_2.out

I already googled the errors and found some people saying that the tutorial was outdated but I didn't find newer instructions.

How can I extract a .pdb file from the .out files?

It would be really nice if someone could update the tutorial/answer that question. I'm curious what those proteins look like that we are computing all the time. :-)

Regards,

antu