You are an expert in writing code in many different languages. Your goal is to perform code completion for the following code, keeping in mind the rest of the code and the file meta data.
    Metadata details:
    filename: meanstructure.m
    path of file: ./repos/mdtoolbox/mdtoolbox
    
    the code of the file until where you have to start completion: function [crd, trj, vel] = meanstructure(trj, index, mass, tolerance, vel)
%% meanstructure
% calc average structure by iterative superimpose
%
%% Syntax
%# crd = meanstructure(trj);
%# crd = meanstructure(trj);
%# [crd, trj] = meanstructure(trj);
%# [crd, trj] = meanstructure(trj, index_atom);
%# [crd, trj] = meanstructure(trj, index_atom, mass);
%# [crd, trj] = meanstructure(trj, index_atom, mass, tolerance);
%# [crd, trj] = meanstructure(trj, index_atom, mass, tolerance, vel);

    
function [crd, trj, vel] = meanstructure(trj, index, mass, tolerance, vel)
%% meanstructure
% calc average structure by iterative superimpose
%
%% Syntax
%# crd = meanstructure(trj);
%# crd = meanstructure(trj);
%# [crd, trj] = meanstructure(trj);
%# [crd, trj] = meanstructure(trj, index_atom);
%# [crd, trj] = meanstructure(trj, index_atom, mass);
%# [crd, trj] = meanstructure(trj, index_atom, mass, tolerance);
%# [crd, trj] = meanstructure(trj, index_atom, mass, tolerance, vel);
%# [crd, trj, vel] = meanstructure(trj, [], [], [], vel);
%
%% Description
% This routine calculates the average structure from given
% trajectory. The algorithm superimposes the trajectories to a
% plausible average structure, then updates the average structrue.
% This process is repeated until some convergence is achieved in
% the RMSD between the average structures.
% This routine may be useful for a preprocess
% for the subsequent structure-analysis routines, such as Principal
% Component Analysis. 
%
%% Example
%# trj = readnetcdf('ak.nc');
%# [crd, trj] = meanstructure(trj);
%
%% See also
% superimpose
%

%% initialization
ref = trj(1, :);
rmsd = realmax;

if ~exist('index', 'var')
  index = [];
end