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collected and edited by
Randal R. Ketchem
last updated
Wed Aug 28 19:44:33 PDT 1996
For a much better explanation of DDM's, see Melanie Nelson's DISCOM wisdom.
This is a collection of a few hints that I discovered while running DISCOM recently on four structure families. I had to run DISCOM and the other helper programs six separate times to cover all possible family pairs, so I wrote a few simple scripts to help me. I'll show the scripts and how I used them in hopes that they will help you. In the interest of space I will only show the comparison of two familes.
Generally, DISCOM creates ad.mtx and dd.mtx files. DISCOM helper programs strip the labels from these files and merge them into full matrices. The dd.mtx matrix contains the average distance differences in the upper triangle and the RMS distance differences in the lower triangle. The ad.mtx matrix contains the absolute values of the distance differences.
The manual is a good place to start. It is located at:
/nmr/dg/bin/src/gap/help/discom.help
First I created a shell script to run discom and discom.strip:
----- #!/bin/sh discom -sf1 mol1 -sf2 mol2 -for PDB -sub N,CA,C,H,O -mat 0 discom.strip dd.mtx > dd.strip -----discom.strip strips away the atom identifiers.
Next comes Mathematica. From within Mathematica load the math script:
math: <<math.inp
where math.inp is:
-----
disdif = ReadList["dd.strip", Number, RecordLists -> True] ;
disdifplt = Raster[disdif, ColorFunction -> (RGBColor[If[#<0,-#,0],If[#>0,#,0],1]&)] ;
Display["dd.rawps", Show[Graphics[disdifplt, AspectRatio -> 1, Frame -> True, Ticks -> Automatic, PlotRegion -> {{0.1,0.9},{0.1,0.9}}, DisplayFunction -> Identity]]]
-----
This creates a Mathematica PostScript file that does not have all of the
necessary macros. Mathematica supplies a fixer program called psfix. Run it
as:
/tsri/math/Bin.SPARC/Display/psfix dd.rawps > dd.psThis PostScript file can then be viewed or sent to a printer. If you want to view the image directly from Mathematica without saving the raw PostScript, change the Display line to read:
Show[Graphics[disdifplt, AspectRatio -> 1, Frame -> True, Ticks -> Automatic, PlotRegion -> {{0.1,0.9},{0.1,0.9}}]]
That is all there is to creating the matrix plots. Pretty easy unless you
want to change the color scale. Mathematica understands 0-1.
Next comes Grasp. Grasp will display the molecule and lines connected the distance difference atoms. These lines can be color coded and size coded to represent the distance differences. Take a look at the file HOWTO.ddm_in_grasp. It will explain the things I leave out. Well, perhaps it will just confuse you more.
First create a resmap file. One line for each residue. Capitalized 3 letter codes. This file should list all of the residues in the pdb file(s) in their correct order. You can grab them with awk or something. You only need a single list, not one for each file.
Next generate the pairwise interactions.
unix> discom2grasp dd.strip resmap 0.5 > discom2grasp.outwhere 0.5 is the cutoff value.
Get the max and min for the color mapping.
unix> discom.pos_neg discom.strip.outNow the color macro has to be edited. It looks like:
Macro Name: color_ddm line :ic=11,ip=(1.0,10.0) line :ic=12,ip=(0.8,1.0) line :ic=13,ip=(0.6,0.8) line :ic=14,ip=(0.4,0.6) line :ic=16,ip=(0.0,0.4) Macro EndAlso, the colors have to be set in the Grasp file defcol.dat. Grasp can output this file, you can edit it so that the corresponding lines in defcol.dat match the required ic lines in color_ddm macro, and then quit and run Grasp again to read in the new colors.
In Grasp, read the pdb file and the pairwise interaction file discom2grasp.out. If the colors are set in the color macro, read the macro and execute the macro.
Here is a Grasp history file that can be read and executed with little modification:
----- GRASP HISTORY FILE Fri Aug 16 12:01:36 1996 Key :Control X Menu Cascade Begin menu :GRASP | Read menu :Read Submenu | PDB File menu :Enter/List | Enter File Name line :avgref_iupac.pdb Menu Cascade End Menu Cascade Begin menu :GRASP | Read menu :Read Submenu | Pair Wise Interactions menu :Name of File | Let me Enter It line :discom2grasp.out Menu Cascade End Menu Cascade Begin menu: GRASP | Read menu :Read Submenu | Grasp Macro File line :color_ddm.graspmac Menu Cascade End Menu Cascade Begin menu :GRASP | Macros menu :Macrolisting | color_ddm Menu Cascade End ROT: X= -90.0 Key :Control R DRAW -----That's it.