RANDMARDI RANDMARDI

RANDMARDI

randmardi is a C Shell script which does random noise mardigras 
calculations and generates the average distances and distance bounds. 
To run the program, type:

randmardi parm_file

parm_file is a normal mardigras PARM file with the lines, for example:

PDB FILE test.pdb
INT FILE test.INT.1
OUT FILE testout 
MINITN 2
NOISE ABSOLUTE NORMALIZED 0.002
NORMALIZE ALL 
METHYL JUMP 3

The noise type should be consistant with you intensity file, i.e. if the 
intensities are not normalized (using corma), the noise level should be 
unnormalized, for example:

NOISE ABSOLUTE UNNORMALIZED 11000

Unnormalized noise should be about the size of your smallest intensities.
But make sure the smallest intensities are reasonable. In some situations
the integration tools do not handle very weak intensities well,       
especially when there is phase or baseline problem.


"randmardi" calls program "addrand" to add random noises to the intensity
file. Random noise will be added to the intensity file N times (default is 30) 
and mardigras is run for each randomly varied intensity set. N may be changed 
by adding the following line to the PARM file, for example:  
(where to add the line in the PARM file is not important.)

NUMBER OF RUNS 20

"randmardi" over writes mardigras criterion for rejecting a distance (which is 
over 5.0A). Instead, a script "strip.a" is called to strip off very long 
distances. The maximum distances allowed for different type of spins may be 
changed by editing "strip.a". The default now is (see strip.a):

#maximum distance between inter-residue methyl-methyl groups: 
interMM=8.5
#maximum distance between intra-residue methyl-methyl groups:
intraMM=8.0
#maximum distance between inter-residue proton-methyl group:
interMH=8.0
#maximum distance between intra-residue proton-methyl group:
intraMH=7.5
#maximum distance between inter-residue proton-proton:
interHH=7.0
#maximum distance between intra-residue proton-proton:
intraHH=6.0
#maximum distance between sugar protons:
insugar=5.0

Finally, "calsd2" is called to calculate the average distances and bounds.
Output files include:
        .bnds  - average distances and bounds of N mardigras runs. 
                 Also included are model distances, and distances and bounds 
                 of one mardigras run on the original intensity file. 
        .run10 - distances of the first 10 runs. noise is not added to the 
                 first run. 
        .run20 - distances of the 11-20 runs. 
        .run30 - distances of the 21-30 runs. 
        .REJ   - rejected distances for each run.
        .out   - mardigras message normally written on the screen and .OUT file.
If "randmardi" is run for more than one mixing time and starting structures,
the results may be averaged by "avgbnds". "avgbnds" allows you to select among 
3 different bounds from the .bnds files: min_d/max_d, avg+/-SD, and bounds of a single mardigras run. It also allows you to choose how the final bounds should 
be generated. You may choose to average the bounds of different randmardi runs, or take the maximum and minimum of the runs, or add SD to the averaged upper 
bounds and subtract SD from the averaged lower bounds.
Type "avgbnds" and hit return to find out how to use the options.