Index of /mardigras/utilities/mardi2xplor

 Name                    Last modified       Size  Description

 Parent Directory        24-Jan-2001 11:24      -  
 Examples/               24-Jan-2001 11:22      -  
 mardi2xplor.f           24-Jan-2001 11:22     8k  

    mardi2xplor - version 1.0 - March 2000

						
The program mardi2xplor changes the format and the 
nomenclature of atoms and pseudoatoms from an 
input constraint file to the NOE table accepted by 
X-PLOR.

mardi2xplor can read as input:

the old prefix.BNDS file generated by MARDIGRAS 
(see the example files).
or 
any free format file of the type :

atom1 residue1 atom2 residue2 data data data data data 

e.g.

HA   12 HN   12   4.63   5.45   4.63   5.45   4.63
HA   12 HN   13   3.65   4.37   3.56   4.26   3.81
HA   14 HN   15   3.66   4.21   3.35   3.64   4.10

where the data columns contain information about the 
lower, upper bounds and/or distances.

mardi2xplor will first attempt reading the input file
as if it were the output file of MARDIGRAS, prefix.BNDS
(old format, changed with newer version of MARDIGRAS). 
If it fails it will then try to read the input file
as a free format file. In such a case, mardi2xplor 
will prompt the user for the position of the columns 
that contain the upper, lower bounds and distances. 

NOTE: The first data column is column number 1 (rather
 than 5).

If the distance column is not specified  (or set to 0), 
the distances will be set to the average of upper and 
lower bounds:

    distance = (upper bound + lower bound) / 2.0

This is the option to use if the input file does not
contain a column with distances, i.e. set its value
to 0.

If the lower bound and the upper bound columns are set
to the same number, the value in this column and the 
distance will be used to set the upper and lower bounds:

  lower bound = distance - value in specified column 
  upper bound = distance + value in specified column

This is the option to use if the input file does 
contain the distance and standard deviation, but NOT
the lower and upper bounds (that will be then calculated
using the distance and standard deviation).

NOTE: If the width of the bounds in the input file is 
smaller than 0.1 Angstroms (e.g. 0.04), the program will
write down 0.0 in the 2nd and 3rd data columns of the 
output file in XPLOR format (I am not sure how to 'solve' 
this problem).


INSTALLATION

To compile the program type the following command at 
the prompt :

f77 -o mardi2xplor mardi2xplor.f

(a fortran compiler is required)
This program was written on a SGI workstation running
IRIX 6.5 and it may not compile properly on other 
platforms.

RUNNING mardi2xplor

mardi2xplor is an interactive program. 
To run type, at the prompt:

mardi2xplor 

The program will ask for the name of the input and output
files.
If the input file is NOT the default prefix.BNDS generated
by MARDIGRAS, mardi2xplor will then ask for the position 
of the columns containing the lower, upper bounds and the
distances.

THE FIRST DATA COLUMN IS COLUMN NUMBER 1 (RATHER THAN 5).


BUGS

I am sure there are , if you find any or if you would like 
some modification to this program please contact me at 
tonelli@picasso.nmr.ucsf.edu .


AUTHOR

Marco Tonelli - UCSF - March 2000

Questions and comments are welcome. Send them to: 
tonelli@picasso.nmr.cusf.edu

Last update - 1/23/01