YUP.SCX: Introduction

YUP.SCX
INTRODUCTION
TUTORIAL
YUP.SCX
YUP.VLAT
EMMENTAL


YUP.SCX is a method of refining high-resolution atomic structures to fit optimally into intermediate-resolution electron density maps. This is not a search procedure; the initial structure must first be positioned approximately into the target map. YUP.SCX makes use of the simulated annealing procedure, a global optimization method.

This procedure is implemented in an easy-to-use program Yup.scx which is available as part of YUP, a general-purpose molecular mechanics program (download link at the bottom of the page). More detailed information can be reached through the link table on the left.
Citation If you publish work that makes use of this program, please cite:

Tan, R.K.-Z.; Devkota, B. and Harvey S.C.
YUP.SCX: Coaxing Atomic Models into Medium Resolution Electron Density Maps.
J. Struct. Biol. 163, 163-174 (2008)
doi: 10.1016/j.jsb.2008.05.01

The current version of Yup.scx contains some improvements over the version described in the paper [1] Chiral constraints can now be imposed (but this has not been fully parameterized and tested); [2] The starting structure can be minimized before annealing.
Tutorial
(Link above). This is based on the paper cited above. The commands to carry out the calculations discussed in the paper are listed.
Yup.scx
To make use of the YUP.SCX procedure, you only need to run one program: Yup.scx. Some help is available from the link table (top left). Or, simply type the command: Yup.scx --help. The output is 142 lines, so it is a good idea to pipe it to a pager like more.
Yup.vlat
This is an updated version of the VLAT procedure (unpublished) in Yammp 1. Although Yammp 1 is still available (IRIX only), we encourage people to switch to YUP and to use the revised version. Yup.vlat is much easier to use, more complete and more convergent than VLAT. Even so, we feel that Yup.scx is a superior program. Usage help can be obtained by typing the command: Yup.vlat --help.
Emmental
Yup.scx is a command-line procedure that makes use of the Emmental module at the lowest level. Yup.scx hides the details of this module from the user, but as a result only a small portion of the module is accessible to the user. If you know how to write Python programs, you can use this module directly and gain access to many other options and even different refinement methods.
Home
Information
News
User
Technical
Programmer
iYup
Download
Showcase
ETC