GRASP - MORASS 2.1 FILES AND SAMPLE OUTPUT
This directory contains two GRASP files -
o defcol.dat - contains the color coding information for GRASP to
color the MORASS generated NOESY constraint differences
by range. RED is hot, that is, bad and GREEN is cool, good.
Progression is RED, ORANGE, YELLOW, WHITE, CYAN, GREEN.
Note that exact fits don't show at all so there is a virtual
7th color - transparent. The idea is if it isn't a problem
why show it and clutter up the display. The user can change
these to suit their own intuition by using the ^P (control P)
function in GRASP to redo the color palette.
o morass_macro1 - tells GRASP how to read the MORASS output file.
This directory also contains sample output in .rgb format. On our SGI Indigo
we can view these with the 'imgview filename' command. They show the
convergence of an A-DNA model with the NOESY constraints into its final(B-like)
structure over several MORASS iterations -
o grasp0.rgb - Initial model .pdb file and initial NOESY constraints. Notice
the large red ones showing very poor agreement between the
model structure and the NOESY defined structure.
o grasp1.rgb - DNA after one MORASS - restrained MD iteration. Note how many
fewer red constraints there are already.
o grasp2.rgb - One more iteration. Structure is cleaning up quite well.
o grasp3.rdb - Last iteration. Fairly good agreement of the NOESY constraints
with the rMD structure. Note that the remaining bad (red)
constraints are very few and are surrounded by many good
constraints suggesting that the bad constraint is internally
inconsistent with the rest of the NOESY defined structure.
Could be experimental error of some sort.
Note that these data represent actual structures from our laboratory and
as such are copyright protected and all rights are reserved. Please do
not use or distribute without our permission or without proper reference