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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
and identification.
                                                        B.A.Luxon 5/94

Modified: Fri May 13 16:00:00 1994 GMT
Page accessed 4625 times since Sat Apr 17 21:34:57 1999 GMT