Member Site Forums Rosetta 3 Rosetta 3 – Applications a trouble during floppytail modeling Reply To: a trouble during floppytail modeling


    “So if possible and at your conveinence, could you share with us your method to change pdb chain id?”

    I meant to move the lines of text in the PDB around, not re-letter the chains. The order in which the domains appear in the PDB file is relevant; their chain IDs are not. (That the chain ID matches what you pass to -flexible_chain does matter, of course). To answer the question you asked, the easiest way is sed, awk, or a basic text editor like emacs or vim. There are many tutorials floating around the internet on “regular expressions”, which is how you’d do the regular-expression search-and-replace to change the chains.

    As for the patched code – I tested that it compiles this time (against developer trunk, not 3.2, but it should be ok). I tried to get fancy and do all the changes on one line, but the compiler reminds me I have to make a local copy of the FoldTree to modify it. Here’s code that will compile; let me know if it works:

    //for nonterminal sections, this fold tree might help (or might make it worse...)
    if( stop_ != pose.total_residue() ){
    TR << "non-terminal floppy section, using a linear fold tree to try to ensure downstream residues follown"
    << "Old tree: " << pose.fold_tree();
    core::kinematics::FoldTree ft(pose.fold_tree());
    TR << pose.fold_tree();