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Error src/core/scoring/ line: 139

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Error src/core/scoring/ line: 139

Hello, following the tutorial for Comparative Modelling on under the Support section I ran the command /home/dhall/Rosetta/main/source/bin/rosetta_scripts.default.linuxgccdebug @rosetta_cm.options I know this is not the command shown in the tutorial. After editting the following files; Rosetta_cm.xml and rosetta_cm.options to suit my files i get the following error src/core/ line: 139 , this is what is shown on line 139 in the MembraneTopology file if ( total_tmhelix_==0 ) {
        utility_exit_with_message("bad format for spanfile total_tmhelix=0");

I am not sure how to fix this error also this protein is non membrane bound

Thank you for advice in advance


MembraneTopology.png198.36 KB
rosetta_cm.png206.77 KB
rosettaoptions.png143.23 KB
Post Situation: 
Thu, 2017-07-13 04:58
Daniel Hall

That error means that there is something wrong with your span file. What does the TDP-43.span file look like? See for an example of what a properly formatted span file looks like.

In particular, you want to pay attention to the second line of the file, the one with two numbers. The first number is the number of TM helicies in the protein and the second line is the number of residues in the protein. The error message you're getting indicates there's some issue with the line, and Rosetta isn't able to figure out how many transmembrane helicies are in the file.


But you said that you're protein isn't a Membrane protein ... if that's the case, you don't need the span file. You'll want to remove all of the membrane flags from your options (everything below "#Initialize mmbrane"), and also use the non-membrane versions of all of the scoring files. 

Thu, 2017-07-13 09:22

Hello, in the rosetta_cm.xml under score function   <ScoreFunction name="stage1" weights="stage1_membrane.wts", even though the protein isnt a membrane protein do i still include the stage1_membrane weight files.


**EDIT** Just read the last part of the message saying to use the non-membrane scoring, silly me

Mon, 2017-07-17 07:42
Daniel Hall

The comment I got from one of the membrane developers:

"I'm not sure what tutorial this person is referring to. I'm currently looking at the membrane homology modeling tutorial in demos/public and I don't see the rosetta_cm.options file. I'm not familiar with this specific protocol. Based on the error, I suspect the person has a poorly formatted or missing span file. I recommend directing them to the other tutorial for examples. "

Fri, 2017-07-14 14:39

Thank you for the replys. I will look over these files on Monday, then get back in touch to see if this works 

Sat, 2017-07-15 10:35
Daniel Hall

Hello, it appears i am getting these errors now,

core.optimization.AtomTreeMinimizer: (17) ***************************************************************
core.optimization.AtomTreeMinimizer: (17) ** WARNING: Non-ideal minimization used with a ScoreFunction **
core.optimization.AtomTreeMinimizer: (17) ** which isn't set up for non-ideal minimization **
core.optimization.AtomTreeMinimizer: (17) ***************************************************************

but i am not sure why as i have removed all of the membrane weight files and set the options to non_weight files

Kind regards



Mon, 2017-07-17 09:20
Daniel Hall

That message ("Non-ideal minimization used with a ScoreFunction which isn't set up for non-ideal minimization" occurs when you're doing either Cartesian minimization or bond length/angle minimization with a "standard" Rosetta scorefunction. Standard Rosetta minimization only occurs over torsion angles, keeping bond length and angles fixed. As such, the standard Rosetta energy functions don't really need to penalize deviations from ideal bond length/angles, so the standard energy functions don't include terms for these degrees of freedom.

What you would need to do is add the cart_bonded energy term to the scorefunction in question, as well as remove the pro_close term (to avoid double counting).

I'm not entirely sure which ScoreFunction is giving you this issue, but I'm guessing it's the fullatom scorefunction. For many of the standard scorefunctions (e.g. talaris2013, talaris2014, ref2015) there's a "_cart" version in the database which does the appropriate manipulations. I'd recommend using this in place of the plain variant, and see if that fixes things.

Tue, 2017-07-18 09:00