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Re: [cnsbb] ncs restrain mentioning segid and atom name

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  • Joe Krahn
    CNS currently does not allow restraints with non-matching residue names. It is easy to modify the source code to turn these from errors into just warnings, but
    Message 1 of 3 , Mar 7, 2010
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      CNS currently does not allow restraints with non-matching residue names.
      It is easy to modify the source code to turn these from errors into just
      warnings, but it is normally much better NOT to mutant to alanine. In
      some older software, that was the only way to delete side-chain atoms,
      but most software now supports truncated side chains. It is much easier
      to work with tht structure when the sequence is correct, and those
      alanines have to be converted back to deposit the correct structure to
      the PDB.

      Some programs don't like the CNS 9999 missing-coordinate value, so
      you may want to put a "delete select=(unknown) end" in your script, or
      enter the following command editing the file in vim:
      :%g/0009999/del

      If you are an O user, here is a macro to delete the side chain:
      ---------------------
      print identify a residue to truncate
      message identify a residue to truncate
      wait_id

      sel_on $.ID_M ;
      sel_off $.ID_M $.ID_R $.ID_R
      sel_prop atom_name = N on
      sel_prop atom_name = CA on
      sel_prop atom_name = CB on
      sel_prop atom_name = C on
      sel_prop atom_name = O on

      pdb_write temp.pdb $.ID_M ; ; yes ; ;


      pdb_read temp.pdb $.ID_M ; ;

      mol $.ID_M
      obj ${.ID_M}ALL zone ; end
      ---------------------


      Venkataraman wrote:
      >
      >
      > Hi
      >
      > I wanted to do ncs restrain for only main chain. I do have six monomer
      > and wanted to do the ncs restrain for main chain.
      >
      > I mutated many residues to alanine cause of lack of density, so again
      > if I wanted to ncs restrain, I do have to mutate back all to keep the
      > same in order ncs to work in cns.
      >
      > Please let me know what is the syntax for mentioning segid ID and atom name.
      >
      > Thanks
      >
      > venakt
      >
      >
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