This command allows the user to change the details of the MCMC mechanism that updates the state of the chain. The useage is:
props
On typing "props", you will get a list of parameters to change. The program works as follows: On typing "mcmc", MrBayes figures out which model parameters need to be updated. For example, if you include a transition/transversion rate parameter, then the program needs to update this parameter along with others, such as the tree and branch lengths. Once MrBayes figures out which moves are needed, it figures out the probability of making each move on every cycle of the chain. MrBayes updates parameters in blocks; it decides which parameter to update, changes the parameter, and then accepts or rejects the move according to the Metropolis-Hastings equation. The probability of making a move is calculated as the proposal rate for the move divided by the sum of the proposal rates for all of the other parameters that need to be updated. This command also allows you to change the details of each proposal mechanism. Many of the moves change parameters using sliding windows centered on the current value of the parameter. If you increase or decrease the window size, you will respectively decrease or increase the acceptance rate of the move. Some of the other moves update using a dirichlet or beta distribution, centered on the current values. You can change the variance parameter of the dirichlet or beta distribution. Finally, a few of the topology moves have a tuning parameter which influences the degree to which branch lengths are modified. If you increase this tuning parameter, you will make more radical changes to the branch lengths.
One word of warning: You should be extremely careful when modifying any of the chain parameters using "props". It is quite possible to completely wreck any hope of achieving convergence by inappropriately setting the chain parameters. Please exercise this command with caution.