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.
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.
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Tom Goddard