Hello everyone, recently I've been trying to make a homology model with a protein chain along with a nucleotide chain within it based on an existing template, but .
post-partial threading Rosetta dislocates the nucleotides nearly 1000 angstrom away from the structure. .
In principal, I'm suspecting this to be a result of an unwanted interaction between the nucleotide parameters and the protein which makes me wonder if their is a way to make cm_rosetta treat a specific chain/s as a rigid body ? In a sense, like I would with a ligand ?
My flags are these :
Thanks in advance to all the helpers !
As nobody has answered I thought I'd give my two penny's worth.
The movement is the hybridiser's doing, not clashes from Lenard-Jones r^12 term —which I assume cut off after a given distance.
There are a few threading movers in Rosetta, including ThreadingMover which fills gaps if asked to do. I have not used with it scripts, only with PyRosetta (example):
I am sure it would work in scripts too...
Thanks matteoferla, i tried applying the simplethread mover to my model but I can't seem to get the xml format right. I also tried looking online for an example of it but couldn't find it, perhaps you can refer me to a relevant example of an xml file that applies it ?
Thanks in advance,
As mentioned, I don't know how to use Rosetta Scripts, so am of little help...
thanks a lot for your response matteoferla, I believe I have resolved it using the backbone motions flag. so I consider this topic closed.
All the best,