Is there a Rosetta script/scenario to perform a partial ab initio model? I mean, I am working with a protein sequence which has two structural subdomains already solved and available in two separate PDB's. The sequence I'm working on spans the two subdomains and has additional parts, which have not been solved and have poor SS predictions. I was thinking of using a Rosetta scenario/script to model the C- and N-terminal of the sequence and the linker between these two subdomains while keeping their original structures. The problem is, the relative position between these structural subdomains is unknown.
Does the script "thread_pdb_from_alignment.py" support a multiple sequence alignments and multiple pdb templates?
Please, could someone shed some light on this problem?
You have a ton of options, most of which don't do quite what you want or aren't documented properly.
If your two domains are known well, FloppyTail functions as a domain assembler. I am its author and am currently working with a collaborator doing this exact experiment via FloppyTail. 3.3 FloppyTail is newly fully compatible with internal linker regions; 3.4 will be compatible with multiple separate linker regions (caveat: hasn't been fully tested). If you want to try 3.3 FloppyTail, or get a patch for the multilinker functionality, I can get it to you. http://www.rosettacommons.org/manuals/archive/rosetta3.3_user_guide/app_...
We haven't yet released the tutorials, but there is a tarball for "homology modeling with end extension" that might be useful to you. Unfortunately it has fragments files so it's 11 MB. Would you like me to email it to the address to which your forum account is registered, or some other address? (I can also strip the frags files, which means you'd need to regenerate them to actually run the tutorial, but the instructions would all be intact).
Thank your for your replay. I'll go for your FloppyTail approach and would be very nice if we could keep in touch. Please, send your tarball including frags to my account's e-mail. I'm afraid that my e-mail couldn't handle such a big file. So, let me know if you receive any warning. Otherwise, I can send you instructions for a ssh login here.
It may not have been entirely clear - the tarball and FloppyTail describe entirely different methods. I am happy to provide further support on FloppyTail (just ask here!), but I don't know much more about the tarball than what's in it.
I am unable to attach the tarball to the forum posts like I should be able to due to a disk quota issue; I've emailed it to you instead (a safe no-frags and a large with-frags version). I can pass that out to others who need it; we plan on officially releasing the tutorials soon anyway.