Monte Carlo usage?

Hmm…well I installed 3.4 onto an older redhat Linux build, but it’s on a remote cluster, and I’m not proficient enough at linux command line to even begin to figure out how to actually execute stuff on it. I picked PyRosetta simply because it seemed more accessible, though I knew the hardware risks that came with it…and apparently, that’s come back to bite me in the rear. Anyway, basically, yeah…I’m trying to run vanilla ab initio…with all the crap that comes with. My sequence is 55aa long…I suppose with the number of iterations needed per residue, that’d still require a lot more processing power than I have on my Windows machine. Perhaps you could advise my next step to take? If necessary we could move this thread to the Rosetta 3.4 forum if you think it’d be more likely to be executed there. I have considerably more processing power on that Linux cluster, but again, it’s only via remote access, and I might as well have the skill of an infant when it comes to that…not that I’m much better with Python. My programming background is mainly in java, so the horizontal transition is ordinarily simple, but this is…on a different level for me.

I had actually stumbled across that exact file while rummaging through the Scripts list, but I was confused by “fragment insertion”. Then again, I’m new at this (not just Linux/Rosetta, but computational modeling in general…this would be my first foray into the actual craziness, and not straightforward webapps like SWISS-MODEL, etc.), so perhaps it’s a related concept after all. Thanks for the clarification though. I suppose I could try it on my desktop, and if it takes too long, try it (or an analogue…which I assume is also buried in the folders somewhere?) on the Linux cluster, I suppose. Is there a built-in overflow warning? Or is it just going to busy-loop? How will I know if my computer is unable to perform the calculation?

Edit: In the comments, it states that 2 fragment files must be provided…is that not indicative of homology modeling? I only have one file to use (since it has no homology with anything else). Is there something else going on here that I’m not understanding? Sorry if I’m seeming a bit…inept; I definitely feel it.

Hmm…okay, I guess I’ll just see what it spits out and judge from there.

What about that second file in the Gray lab script? Am I just misunderstanding the instructions or something?

At the very top in the block comment:

“This script performs fragment insertion for an input protein sequence. The
sequence may be explicit, in a FASTA file, or in a PDB file. Two fragment files,
preferably one longer than the other, must also be provided. Fragment insertion
is accompanied by a Monte Carlo assessment allowing the conformation to escape
local minima. Output structures from this protocol are intended to proceed into
a refinement step (such as that in refinement.py) to produce reasonable
estimates of the protein conformation.”

But directly below that, in the instructions section, it only requires one pdb. Am I misunderstanding the meaning of “fragment file”?

Apologies for going off the grid for a month; I just started classes up, and took a brief break from this project.

I’ve finally gotten around to trying D060_Folding.py in PyRosetta, but it appears that I’m raising an exception. My full output is below:

—

In [12]: run D060_Folding.py
PYROSETTA_DATABASE environment variable was set to: C:Program Files (x86)PyRos
ettarosetta_database… using it…
PyRosetta 2.011 [r48543:49680M] retrieved from: https://svn.rosettacommons.org/s
ource/trunk/rosetta/rosetta_source
(C) Copyright Rosetta Commons Member Institutions.
Created in JHU by Sergey Lyskov and PyRosetta Team.

core.init: Mini-Rosetta version 48543:49680M from https://svn.rosettacommons.org
/source/trunk/rosetta/rosetta_source
core.init: command: app -database C:Program Files (x86)PyRosettarosetta_datab
ase -ex1 -ex2aro -constant_seed
core.init: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111
core.init.random: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt1993
7
core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set
. Created 6225 residue types
core.import_pose.import_pose: PDB File:test/data/test_in.pdb not found!

ERROR: Cannot open PDB file “test/data/test_in.pdb”
ERROR:: Exit from: core/import_pose/import_pose.cc line: 184

---

PyRosettaException Traceback (most recent call last)
C:Python27libsite-packagesipython-0.13-py2.7.eggIPythonutilspy3compat.pyc
in execfile(fname, glob, loc)
169 else:
170 filename = fname
–> 171 exec compile(scripttext, filename, ‘exec’) in glob, loc
172 else:
173 def execfile(fname, *where):

C:UsersAlex TruongDropboxAlex Truong – iPLA2Rosetta Input FilesD060_Foldin
g.py in ()
435 pdb_filename = options.pdb_filename
436 if pdb_filename: # the default behavior or if you use a PDB file
–> 437 pose_from_pdb(pose, pdb_filename)
438 sequence = pose.sequence()
439 # Fasta file option

C:Program Files (x86)PyRosettarosetta__init__.py in exit_callback(self)
1129 class PythonPyExitCallback(utility.PyExitCallback):
1130 def exit_callback(self):
-> 1131 raise PyRosettaException()
1132
1133 def __init__(self): utility.PyExitCallback.__init__(self)

PyRosettaException: PyRosettaException

In [13]:

—

What confused me is the section with the test_in.pdb part, and I’m not sure how that applies to my job. I tried looking through the code in the script, but I didn’t see any indication. I ran the script while in the working directory comtaining the fasta file and the 2 fragment files. Could you possibly spot where I went wrong? The example given at the bottom of the script seems to imply that I need to name the files a certain way, but there’s no indication (based on the output above) that I even made it that far to raise the error.

The thing is, I’m not trying to run a test. When I was browsing the code, there was a section that said “All of the default variables and parameters used above are specific to the example with “test_in.pdb””. Now, since my query file is not named “test_in.pdb”, do I just go through the script and rename all instances to my file name? Because that file call doesn’t seem to be in the actual meat of the script…I’m also not sure whether that test is just a precursor to the actual job run, and the test file will be accessed each time I run the script, regardless of whether it is for testing or for my own file.

It also appears that I’m raising a couple of exceptions…one related to the test file, and one related to mine; the query is in fasta form, but the output took the pdb route as shown.

There’s a line of code in the script that when exectuted, simulates a real example; I’ve tried pasting the entire line and editing it to my needs:

python D060_folding.py –fasta_filename pin.fasta –long_frag_filename pin.frag9 –long_frag_length 9 –short_frag_filename pin.frag3 –short_frag_length 3 –jobs 100 –job_output pin_folding_output –kT 1.0 –long_inserts 1 –short_inserts 3 –cycles 200 –disulfides 1

However, when I run the script from the working directory, it says I have a syntax error; what is the error? At first, there is a carat under the disulfides flag, but when I delete the entire thing, the carat stays out in the middle of nowhere.

So should I put the input files in the PyRosetta directory as well? From the output given above, it seemed like it was automatically switching directories depending on where I executed the script from. I had just put the script in the same directory as my inputs, and ran it like that. Should I just move everything there? Because I don’t want to run Folding.py as a “test”, I want to run it with my own files.

I just cd’d the location of the script, then ran it with the command you can see above. That’s it. I’m still getting the same error as pasted earlier.

I could try the new file…if it doesn’t work, it’s probably something wrong with the input files or something as referenced in the script itself.

Oh, okay. So I have my fragment files and PSIPRED file (all from ROBETTA). Stupid question: where do I put these files to load them? The root rosetta directory? Or in the same directory as the /../../rosetta_source/src/apps/public folder that contains the AbinitioRelax.cc executable?

Also, I think I’m going to revisit Rosetta 3.4 for this project, so feel free to move this thread if you’d like.

How do I specify the paths for Rosetta to access? I know how to change directories and the like; I’m not sure I know how to operate within one while grabbing information from another though.

So to specify my input file directory, I slap the entire path in in front, like

-in:file:fasta /../../blah.fasta

or something like that? Based on the flags you’ve specified (and that I was reading on the link you provided that I’d actually stumbled upon just a little while earlier), it only specifies the file name. The flags look different from the database call, which was how I was expecting it to look. Is that how I’d do it?

I tried running the script with the full flags (as typed above): when specifying the file names, I used the full path for each file. However, I still get a syntax error with the carat being in a completely unhelpful place. Is there a different way to execute the script?

EDIT: I fixed the syntax error (it was something really stupid with the execution…I had to use “run” instead of “python” since I was already operating in the iPython shell). However, even with the full paths specified, I’m raising the same exceptions and errors with test_in.pdb. Should I go in and change the instances anyway just in case? It appears the flags are not related to the problem I’m having.

Okay, it works (I had to drop the disulfides flag because apparently that’s not a real parameter…). However, I have…100 pdb files. Is there an optimization step I can take using these output files, similar to AbinitioRelax for Rosetta (which I’m also currently trying)? I know in general, I just pick the output file with the lowest centroid score as given by the script, but is there a more comprehensive way to test all the pdb files?