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@stfc.ac.uk

UNITED KINGDOM

--
Scanned by iCritical.
_______________________________________________
Chimera-users mailing list
Chimera-users@cgl.ucsf.edu
http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users