YUP.SCX: Introduction
|
|||||||||||
|
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version of the VLAT procedure (unpublished) in Yammp 1.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. |
||||||||||
|
|||||||||||