Hi Elena, I'm afraid mr_rosetta is not well-equipped to handle this case where two molecules have the same sequence but do not have NCS. Can you possibly try this work-around: 1. Do any sequence edits of your model before starting (using phenix.sculptor for example). 2. assuming you have chains A and B, rename all the residues in chain B to "A" and renumber everything so that you don't have duplicate residue numbers. Now you have one twice-as-long chain A. 3. create a sequence file that matches your new PDB and that has "GGGGGG" or something like that separating the (old) A and B chains: seq.dat:
sequence of chain A then GGGGG then chain B: AYVESAAEFLVFCIDYQRHATINPDVQADFTELTLIGAVDSGIMAQN GGGGG AYVESAAEFLVFCIDYQRHATINPDVQADFTELTLIGAVDSGIMAQN
4. no need for any alignment file. Then run without ncs. With luck this may do what you want it to! Let me know if additional problems arise! All the best, Tom T ________________________________________ From: [email protected] [[email protected]] on behalf of Elena Seiradake [[email protected]] Sent: Thursday, February 23, 2012 6:51 AM To: PHENIX user mailing list Subject: [phenixbb] question about phenix rosetta with two chains Dear Phenixians, I would like to use mr_rosetta to re-build a model with two copies per AU. Although the two copies have the same sequence, they adopt different conformations and one is partially disordered. So I don't want to impose NCS. Could someone please send me an example input file for running mr_rosetta with phenix for multiple chains of the same protein? I think this probably would have to contain "fragment_files_chain_list" and "fragment_files_3_mer_by_chain" etc. (?) I have tried including the above keys in my script, in various ways, but I always get the error: "Sorry, the file path/test_1.pdb representing group 1 has no atoms? This could indicate a problem with sequence alignment in rebuilding" When I run it with just one of the two chains in my pdb (using simple "fragment_file ="), it rebuilds happily. Also, when use both chains and impose NCS=2 it works, but then one of the two chains is forced into the wrong conformation. Any advice on how to change my script would be welcome! Below is part of my simple script, the one that runs ok, using "fragment_file =". seq_file= Seq.dat \ data=test.mtz \ search_models=test.pdb \ already_placed=True \ fragment_files= frag_A_3.gz \ fragment_files= frag_A_9.gz \ rescore_mr.relax=False \ rosetta_models=20 \ ncs_copies= 1\ Cheers Elena _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb