I am trying to compile the vienna source code and am going to use elnando888’s hack. Does anyone know how to compile it so that I can use it in Windows? It looks like it is in Linux.
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So i’m downloading MSYS2 to see if that will work. Wish me luck.
My advice would be to use a VM. The Vienna team didn’t bother making their package compilable on Windows, and it’s quite difficult to build it on that platform, or even on Mac OSX (when I tried, all I could get were crashes).
If you manage to build it, then you will need
Progs/RNAfold -p
to compute the basepairs probabilities in the normal case, without FMN (btw, -d2 is implied), and
Progs/RNAfold -p --ligand FMN:200
to fold simulating a solution that contains 200 μM FMN
I just got it to compile in Windows using cygwin64 and I had to do alot of installing things. I had just asked Rhiju for files from Stanford because I couldn’t make it work and dont have access to VM right now, should have waited. I can generate the dot.ps and rna.ps now but the lbox data looks like the pairing is off. Do you know if it is supposed to be like that? If not how do I know how much FMN is in the design? How do I know the code compiled correctly? I would appreciate any help you can give me.
Here is a link to your compiled code with necessary libraries from cygwin64 that will run on Windows 8.1.
https://dl.dropboxusercontent.com/u/87351147/ViennaFold_with_Nando-FMN-Hack.zip
Here are all the programs with the librarys needed
https://dl.dropboxusercontent.com/u/87351147/Vienna_With_Nando_FMN_Hack_Progs.zip
That was fun and challenging!
Jennifer
Something you need to know about this hack of mine: as it is, it contains a hard-coded parameter-tuning that diverges a bit from the standard Turner parameter set. The change is strictly limited to the FMN aptamer motif and stems from observations dating back from the Cloud Lab. Brourd ran at least one FMN chemical footprint lab, and a pattern of protection within the aptamer loop was observed in the absence of FMN in the solution, suggesting that the loop could be intrinsically more stable than the model predicts. The free energy value for a 6-5 loop is an extrapolation that ignores and/or averages the potential for additional (on top of the predicted mismatches) non-canonical interactions. Subsequently, I tried to roughly evaluate what this intrinsic ‘bonus’ could be and derived some value from the R91 experimental dataset.
In the code, it is the -60 value that you can see on lines 40 and 41 of the file lib/motifs.c
If you’d rather work without that possibly dubious hypothesis of mine, change to 0 and recompile.
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@Jennifer: what do you mean with “pairing is off”?
It has in the lower box say a pairing of nts 9 and 36 but in eterna it is 9 and 30.
EteRNA started off with Vienna 1.8.x which uses the Turner 1999 parameter set. Current versions of the Vienna package use the Turner 2004 parameter set, and this makes for numerous differences… In the lab, there’s now a button you can click to fold under the Vienna2 model.
ah, another thing I forgot: I made some other changes you may want to revert:
https://github.com/ElNando888/vrna-hack/commit/ff06d0ae520708a875db0eafd92de78452c35bee
The above tunings are linked to the idea that the Turner 2004 parameters still seem to be a little overoptimistic when it comes to the stability of junctions. I went to check the actual parameters on http://rna.urmc.rochester.edu/NNDB/turner04/index.html and proceeded to adjust some hard-coded values while staying within the error range.
So if you want this hack to behave exactly like the original Vienna2 (with the exception of FMN binding handling), you should revert the changes from that commit too.
I finished it. I had to skip the perl and Kinfold since it wasn’t compiling correctly but everything else did. I made a GetSat post about it and gave a link to your compiled code.
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Sounds great Jennifer, thanks for this!
Would it be possible that you document briefly how you did it?
Glad you like it. It was fun to do, let me know if you come across anything this hard again I would love a challenge.
I edited the thread to include the documentation. Here is the link as well to teh procedure on how to do it.
https://dl.dropboxusercontent.com/u/87351147/How%20to%20compile%20Vienna%20Source%20code%20for%20use…
For the record wrt the Mac, there is now documentation on what flags to specify in order to build ViennaRNA under OSX. I had no problems.
For the record wrt the Mac, there is now documentation on what flags to specify in order to build ViennaRNA under OSX. I had no problems.