[Chimera-users] Problem with volumetric data in XPLOR format

[Tom Goddard]

Hi Matthias,

   The problem is the line of your example file

      30       4      12      15       5      10      16       2      12

which corresponds to NA,AMIN,AMAX,NB,BMIN,BMAX,NC,CMIN,CMAX.  It says 
the dimensions of the original map were 30 by 15 by 16, but only slices 
4-12 along the x-axis, slices 5-10 along y-axis and 2-12 along the 
z-axis are in this file.

   Here's some XPLOR Fortran code that illustrates this (hard to find 
actual file format documentation).

     http://nmr.cit.nih.gov/xplor-nih/xplorMan/node333.html

The Chimera Python code that reads the xplor file is in your Chimera 
distribution

     chimera/share/VolumeData/xplor/xplor_format.py

and says the number of data files in the file is

      (amax - amin + 1) * (bmax - bmin + 1) * (cmax - cmin + 1)

Only axis order ZYX where z varies slowest in reading the array values 
is handled by Chimera.

Here's an example file:

This line is ignored
        1
Sean generated grid density
       40     -19      20      40     -19      20      40     -19      20
       40.000      40.000      40.000      90.000      90.000      90.000
XYZ
      -19
      0.00000     0.00000     0.00000     0.00000     0.00000     2.00000
      0.00000     1.00000     0.00000     0.00000     0.00000     0.00000
      0.00000     0.00000     0.00000     0.00000     0.00000     0.00000
...
      0.00000     0.00000     0.00000     0.00000     0.00000     0.00000
      1.00000     0.00000     0.00000     0.00000


   Tom



> Dear all,
>
>                 I'm trying to write volumetric data in XPLOR format in 
> order to import it into
>
> Chimera for displaying. The volumetric data set is a general volume 
> data set, not necessarily
>
> an electron density map. However, it keeps on failing as Chimera keeps 
> on thinking there
>
> are only 262 data values, whilst expecting 90601 numbers (which is the 
> correct number).
>
> I'm trying to write the XPLOR file in the format given on the CNS web 
> page:
>
> Format of CNS maps
>
> The grid size of the map is determined by the GRID parameter in the 
> FFT statement.
>
> The following lines show the beginning of a typical electron density 
> map file:
>
>        2 !NTITLE
>
>  REMARKS FILENAME=""
>
>  REMARKS DATE:18-Jun-98  12:24:08       created by user:
>
>      30       4      12      15       5      10      16       2      12
>
> 0.40960E+02 0.18650E+02 0.22520E+02 0.90000E+02 0.90770E+02 0.90000E+02
>
> ZYX
>
>       0
>
> -0.97086E+00-0.49927E+00-0.82774E+00-0.13491E+01-0.57034E+00-0.71253E-01
>
> -0.19491E+00 0.61017E+00 0.10064E+01-0.22888E+01-0.94020E+00 0.77451E+00
>
>  0.57539E+00-0.31211E-01-0.27430E+00-0.36526E+00 0.34772E+00 0.81884E+00
>
> -0.19954E+01-0.10117E+01 0.18038E+01 0.19008E+01 0.11886E+00-0.41646E+00
>
>  0.47560E-01 0.48855E+00 0.57606E+00-0.22320E+00-0.12787E+01 0.47590E+00
>
> ....
>
>    -9999
>
>   0.2044E-09  0.9999E+00
>
> Is this correct or is Chimera expecting a different format?
>
> Looking forward to your replies!
>
> Many thanks and best wishes,
>
> Matthias
>
> ----------------------------------------------------------------------------------------------
>
> Matthias Gutmann                                          Instrument 
> Scientist SXD
>
> Rutherford Appleton Laboratory              Phone: +44 (0)1235 44 6397
>
> ISIS Facility                                                          
> Fax: +44 (0)1235 44 5200
>
> Chilton Didcot                                                    
> Office : R3, 1.28
>
> Oxfordshire OX11 0QX                                   Email: 
> Matthias.Gutmann at stfc.ac.uk
>
> UNITED KINGDOM
>
>
> -- 
> Scanned by iCritical.
>
>
>
>
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