This menu allows one to mutate the sequence of a molecule. The molecule must exist in the data base. The commands may/will make use of the side chain and main chain databases and must be correctly specified via the Lego_setup command.
mutate_replace <molecule> <residue_name new_residue_type>i
Any number of residues can be mutated until a blank line is entered. All atom properties of the specified molecule are changed in size to accommodate the new sequence. Certain properties are assigned special values, others are given default values.
_atom_z is changed to reflect the elemental type of the new atom
_atom_b new atoms have a temperature factor of 20.Å2
_atom_name new atom names are taken from the contents of the file specified in the last Connect_file command.
_atom_wt new atoms have weights of 1.0
_atom_colour all atoms in a mutated residue are coloured magenta
The default values for all other properties are 0,0.0 and ' ' for integer, real and character properties.
The new residue type must exist as an entry in the contents of the file specified in the last Connect_file command.
Because molecular objects are described in the database as link lists, their pointers are to the OLD positions in the molecule. All objects of the changed molecule must be re-made by the user. Mutated residues will appear coloured magenta.
Side chain confirmations are from the most frequent side chain rotamer. The database must therefore be correctly defined with Lego_setup
mutate_delete <molecule> <residue_name>i
Any number of residues are deleted. Input is terminated by a blank input.
This command would usually leave non-standard stereochemistry. This can be corrected with refi_zone, lego_loop or Manip commands.
mutate_insert <molecule> <residue_name>
<new_residue_name new_residue_type>i
Adds new residues after a specified place in the molecule. Terminated by a blank line. The new residue names should be unique to the molecule.
This command merely makes space in the database for new residues. The user must place them. This could be done in a number of ways, but recommend lego_loop to start with
E.g. The following will insert an alanine residue after residue 102 in molecule A26.
mut_insert a26 102 102a ala ;
sel_off a26 102 103
lego_loop a100 a105
If the new residue had a longer side chain e.g. PHE it would also need to be constructed with lego_side and identify an atom.
menu_mutate.o
This distributed file shows you how to make a menu that makes it easier to mutate a structure. This is an O file that must be read into the user's database. For each amino acid, there is a macro which when activated will mutate the the residue containing the next Id'ed atom and make an object sph centred on this atom. To mutate a residue into a tryptophan, you would hit the @trp macro on the menu. This macro contains
cen_id wait_id
mut_repl $.id_m $.id_r trp ;
mol $.id_m obj sph sph 10 end