The Yup.vlat program is an implementation of the VLAT method found in Yammp version 1, with some small improvements. The command syntax is: Yup.vlat [ options ] PARTMAP SCXFILE Documentation for the program is available by typing the following command (and you probably want to pipe the large volume of output from this command to a pager): Yup.vlat --help The full replacement for the VLAT method is the SCX method implemented in Yup.scx. If you must use Yup.vlat, please make sure you do not use the all-atom partition map generated by Yup.scx, or vice-versa.
With Yup.vlat, a reduced representation model is broken into a number of rigid bodies which are then fitted into the volume map using Simulated Annealing based on the Monte Carlo method. The partition map describes how the model is broken into rigid bodies. The map generated by Yup.vlat contains a default partitioning scheme which is not likely to be useful but it provides a useful starting point. In the default scheme, each chain is divided into interleaved residue triplets. This provides for a softer hinge (19 November 2007).	YUP.SCX INTRODUCTION TUTORIAL YUP.SCX YUP.VLAT EMMENTAL
The output from the Monte Carlo method consists of transformation matrices, one for each rigid body. These are then applied to the starting coordinates to create the final model. This is correct only if each rigid body is large enough (at least three atoms) and the atoms are not colinear. If the starting coordinates are of an all-atom model, the output from Yup.vlat is also an all-atom model.