How to make a resfile

[Anonymous]

Hello,

I am new to using Rosetta. I would like to make a res file to mutate through all 20 amino acids in a Protein-protein interface and predict binding energy using RosettaDesign.  This might be a stupid question but how to you make a resfile? Do you write it in text edit? Is the file extention .res?

I have found the refile syntax page from Rosettas website but it does not say where you type any of the commands into or how to save it.

[Anonymous]

A resfile is a flat text file.  You’ll have the easiest time making it in emacs or vi, perhaps gedit or TextEdit if you want something more visual.

The extension is irrelevant – Rosetta just looks for the file at the specified path and ignores the extension.  (Extensions are useful for users and for the operating system to classify files, but has no effect on the file itself).  

Writing them “from scratch” is admittely laborious.  Generally I would do something like write a quick-and-dirty python script to write my resfile for me, or paste a column of just the residue numbers at my interface in and then use a rectangle-editing mode to fill the rest in quickly.  Nobody’s ever written a sufficiently generic “resfile writing tool” to make it simpler, and most of the developers and users end up knowing enough text editing tricks to make it easy.

[Anonymous]

Thank you for the reply.  

So I am trying to write a simple resfile for using RosettaDesign server for protein design. I upload the PDB file and I’ve selected 2 residue positions that I would like to allow all 20 amino acids and determine the binding energy.  From the RosettaDesign server (http://rosettadesign.med.unc.edu/login.php) they have a link to a format shown here:

NATAA

EX 1

USE_INPUT_SC

start

6 A ALLAAwc EX 1 EX 2

21 A ALLAA EX 1 EX 2

29 A PIKAA DEKR EX 1 EX 2 EX 3

16 A POLAR EX 1 EX 2

18 A NATRO

 

To make a practice run and figure out the resfile I essentially entered this same format into TextEdit on my mac as:

NATAA

EX 1

USE_INPUT_SC

start

9 B ALLAAwc EX 1 EX 2

Then saved and uploaded this as the resfile in the server and submitted the job. The job fails.  In the midst of all the text that is spit out for the log I see core.pack.task.ResfileReader: RESFILE WARNING: reached the end of resfile without finding a ‘start’ token.

core.pack.task.ResfileReader: RESFILE WARNING: No residue-specific behavior specified in resfile

core.pack.task.ResfileReader: The default  command 

I just want a simple resfile that I can edit to cyce through mutations on one of my chains since the PDB is more than 200 amino acids….

[Anonymous]

If you are getting “no start token” errors, it’s probably a file format encoding problem.  On command line, cat the file (`cat myfile`) – does it look right?  If it’s garbled it probably was not saved as a flat text file, but instead a fancier format.

I assume from TextEdit you are on mac, so the windows vs unix end line encoding issue is unlikely to be the problem, but if that’s the problem, here’s how you can convert windows endlines to unix endlines:

tr -d '15' <old-file >new-file

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