Hey,

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

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I already googled the errors and found some people saying that the tutorial was outdated but I didn't find newer instructions.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

Hi antu,

Not sure if this is the easiest way to do it... but you can give minirosetta a rosettascript (an xml file that defines a job), but instead of making it do anything you can simply give it a empty xml file

make an empty rosettascripts file called it "xml", paste the following:









then pass the following flags

-run:protocol jd2_scripting
-parser:protocol xml
-in:file:silent *.out (the silent file that contains the compressed job output)
-out:pdb
-nstruct 1 (number of structures you want to extract, the silent file may contain multiple outputs)

Tell me if it works, depending on the stage of the protocol we may need to add additional flags.
-Krypton

Hey,

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

https://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

Hi antu,

Not sure if this is the easiest way to do it... but you can give minirosetta a rosettascript (an xml file that defines a job), but instead of making it do anything you can simply give it a empty xml file

make an empty rosettascripts file called it "xml", paste the following:
<ROSETTASCRIPTS>
<SCOREFXNS></SCOREFXNS>
<TASKOPERATIONS></TASKOPERATIONS>
<FILTERS></FILTERS>
<MOVERS></MOVERS>
<APPLY_TO_POSE></APPLY_TO_POSE>
<PROTOCOLS></PROTOCOLS>
</ROSETTASCRIPTS>

then pass the following flags

-run:protocol jd2_scripting
-parser:protocol xml
-in:file:silent *.out (the silent file that contains the compressed job output)
-out:pdb
-nstruct 1 (number of structures you want to extract, the silent file may contain multiple outputs)

Tell me if it works, depending on the stage of the protocol we may need to add additional flags.
-Krypton

hi krypton

i tried the instructions unfortunately i'm not knowledgeable about rosetta in general and do not know how to play with the protocol file :)

the instructions did generate/extract a PDB file.

however a PDB file extracted has the following contents:
FAILURE_FAILURE_input_dummy_0063_0001.pdb
---------------------
TER
# All scores below are weighted scores, not raw scores.
#BEGIN_POSE_ENERGIES_TABLE FAILURE_FAILURE_input_dummy_0063_0001.pdb
label total
weights NA
pose#END_POSE_ENERGIES_TABLE FAILURE_FAILURE_input_dummy_0063_0001.pdb
---------------------

i think it is basically an empty pdb file.

i later found some additional instructions and i've also tried using extract_pdb
as given in this thread
https://boinc.bakerlab.org/rosetta/forum_thread.php?id=5611&nowrap=true#69429

unfortunately i think those binaries may be some what old and i got an error saying something to the extent of aromatic symbol is not recognized

i guess we'd just need to await updates e.g. new extract pdb etc but i guess most people are tied up with work to work on this. hence, i guess we'd make do without the extracts for now

Hi sgaboinc,

Can you send me the .out or .silent file? my mail: krypton [] uw [] edu

I'll test it.

Thanks,
krypton