Chain specific flags

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  • This topic has 5 replies, 2 voices, and was last updated 4 years ago by Anonymous.
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    • October 19, 2020 at 10:31 am #3605
      Anonymous

        Hi all,

        It is possible to apply options in relaxation and cartesian, only for specific chains? How? I am working with hla*02:01

      • October 19, 2020 at 2:23 pm #15565
        Anonymous

          It depends a bit on which options you want to apply. If you want to control the movement of protein, the rotameric sampling is controlled by a resfile (https://www.rosettacommons.org/docs/latest/rosetta_basics/file_types/resfiles) and the minimization behavior is controlled by a MoveMap (https://www.rosettacommons.org/docs/latest/rosetta_basics/file_types/movemap-file). You can specify residue/chain level behavior with those, using the command line relax application. You can have a bit more flexibility/control in specification if you use the FastRelax mover within RosettaScripts.

        • November 3, 2020 at 12:32 pm #15580
          Anonymous

            Thanks! I am playing with and I have tried to write “*C ex1” and similar expressions. But it does not work  


            
* <CHAIN> <COMMANDS>

            • November 4, 2020 at 2:37 pm #15583
              Anonymous

                The ex1 option won’t do much for relax. While it will add in addition rotamers for chi1 (the rotatable bond around the Calpha-Cbeta bond), those tend not to have all that great of an effect in a full relax run. With relax, the resfile is more useful in turning off packing entirely (with NATRO).

                 

                Past that, it would help to clarify “not working”. What effect were you hoping for, what commands did you try, and what undesired effect did you see?

            • November 5, 2020 at 2:10 pm #15585
              Anonymous

                Yes. I am sorry, I should have specified that. I have not managed to run any commands. I get errors, one of them being “ERROR: Unused “free” argument specified: C”as Rosetta don’t understand what I want to do . I want to apply specific options to chain c . 

                • November 6, 2020 at 4:04 pm #15588
                  Anonymous

                    That message about unused free arguments comes from the command line option parsing code, not the resfile parsing code.

                    How are you specifying your resfile? The resfile is a separate file on-disk, the name of which you pass to the -in:file:resfile option (or other similar location). If you instead are putting the commands directly onto the command line it won’t work and you’ll possibly get a message like the one you’re seeing.

                     

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