Hello everyone,
I am trying to run the rosettaDNA application program to change the specificity of a transcription factor protein towards a novel DNA sequence. I have tried to run the XML script file by referring to Prof Thyme's book named "Redesigning the Specificity of Protein–DNA Interactions with Rosetta" https://link.springer.com/protocol/10.1007/978-1-62703-968-0_17/figures/3. However, even when I am trying the default XML script, there is an error stating that the XML script is wrong. Can you please assist me with the XML script issue?
| Attachment | Size |
|---|---|
 Here is the XML script file i am using with very few modifications | 321.79 KB |
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It's probably an old version of the XML syntax. (Quotes are needed now etc...).
Also, have a look at this paper for the latest methods of what you want to do
Glasscock Baker bioRxiv 2023 Computational design of sequence specific DNA binding proteins.pdf
https://www.biorxiv.org/content/10.1101/2023.09.20.558720v1
It's a bit hard to say without the exact error message you're seeing, but I believe the issue is that the precise format of RosettaScripts XML has changed slightly since that paper was published.
We have a script which can convert most old-format XML files into the new-format ones. It should be availible at rosetta/tools/xsd_xrw/rewrite_rosetta_script.py This script takes -input and -output parameters which specify the input (old format) xml file and the output (new format) xml file names.
Note that this won't necessarily fix all the issues the script has -- other things may have changed since as well. But it should fix the immediate issue.