Installing rna_denovo

[Anonymous]

Hi,

I tried using the Rosetta RNA tertiary structure modeling pipeline as described in your article “Modeling complex RNA tertiary folds with Rosetta.”

My build is correct.

But every time I try to run

helix_preassemble_setup.py -secstruct sec.txt -fasta fasta.fasta

I am getting error as

subprocess.check_call([str(elem) for elem in cmdline.split()])

  File “/usr/lib/python2.7/subprocess.py”, line 185, in check_call

    retcode = call(*popenargs, **kwargs)

  File “/usr/lib/python2.7/subprocess.py”, line 172, in call

    return Popen(*popenargs, **kwargs).wait()

  File “/usr/lib/python2.7/subprocess.py”, line 394, in __init__

    errread, errwrite)

  File “/usr/lib/python2.7/subprocess.py”, line 1047, in _execute_child

    raise child_exception

OSError: [Errno 2] No such file or directory

going back to the code, in line 75,

“rna_denovo -score:weights stepwise/rna/rna_res_level_energy4.wts -minimize_rna true -use_legacy_job_distributor true -restore_talaris_behavior true “

this rna_denovo is called.

But, in rosetta bin there is no .exe called rna_denovo, instead I found,

rna_denovo.default.linuxgccrelease

rna_denovo.linuxgccrelease

rna_denovo.static.linuxgccrelease

not sure, why is name mismatch and how to call rna_denovo.

So my pipeline is not working.

Can you help me resolving this issue?

Thanks,

Tanusree

[Anonymous]

Hi, Tanusree — 

If you just change all occurrences of “rna_denovo” to the specific version you want (“rna_denovo.default.linuxgccrelease” for the dynamically linked version, “rna_denovo.static.linuxgccrelease” for the static version) you should be okay.

For a little technical detail, although Rosetta is typically built with scons (that’s probably the build you used!) we can also build with cmake (you may notice main/source/cmake), which had long been traditional in our lab. The cmake build generates executable symlinks with no suffixes attached, and it looks like this script improperly assumed that you were using that build system. Sorry!

[Author]

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