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Hi Matthias,<br>
<br>
The problem is the line of your example file<br>
<br>
30 4 12 15 5 10 16 2
12
<br>
<br>
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.<br>
<br>
Here's some XPLOR Fortran code that illustrates this (hard to find
actual file format documentation).<br>
<br>
<a class="moz-txt-link-freetext" href="http://nmr.cit.nih.gov/xplor-nih/xplorMan/node333.html">http://nmr.cit.nih.gov/xplor-nih/xplorMan/node333.html</a><br>
<br>
The Chimera Python code that reads the xplor file is in your Chimera
distribution<br>
<br>
chimera/share/VolumeData/xplor/xplor_format.py<br>
<br>
and says the number of data files in the file is<br>
<br>
(amax - amin + 1) * (bmax - bmin + 1) * (cmax - cmin + 1)<br>
<br>
Only axis order ZYX where z varies slowest in reading the array
values is handled by Chimera.<br>
<br>
Here's an example file:<br>
<br>
This line is ignored<br>
1<br>
Sean generated grid density<br>
40 -19 20 40 -19 20 40
-19 20<br>
40.000 40.000 40.000 90.000 90.000
90.000<br>
XYZ<br>
-19<br>
0.00000 0.00000 0.00000 0.00000 0.00000
2.00000<br>
0.00000 1.00000 0.00000 0.00000 0.00000
0.00000<br>
0.00000 0.00000 0.00000 0.00000 0.00000
0.00000<br>
...<br>
0.00000 0.00000 0.00000 0.00000 0.00000
0.00000<br>
1.00000 0.00000 0.00000 0.00000<br>
<br>
<br>
Tom<br>
<br>
<br>
<br>
<blockquote
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<div class="WordSection1">
<p class="MsoNormal">Dear all,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"> I’m trying to write
volumetric data in XPLOR format in order to import it into<o:p></o:p></p>
<p class="MsoNormal">Chimera for displaying. The volumetric data
set is a general volume data set, not necessarily<o:p></o:p></p>
<p class="MsoNormal">an electron density map. However, it keeps
on failing as Chimera keeps on thinking there<o:p></o:p></p>
<p class="MsoNormal">are only 262 data values, whilst expecting
90601 numbers (which is the correct number).<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I’m trying to write the XPLOR file in the
format given on the CNS web page:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Format of CNS maps<o:p></o:p></p>
<p class="MsoNormal">The grid size of the map is determined by
the GRID parameter in the FFT statement.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">The following lines show the beginning of a
typical electron density map file:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"> 2 !NTITLE <o:p></o:p></p>
<p class="MsoNormal"> REMARKS
FILENAME="" <o:p></o:p></p>
<p class="MsoNormal"> REMARKS DATE:18-Jun-98 12:24:08
created by
user: <o:p></o:p></p>
<p class="MsoNormal"> 30 4 12 15
5 10 16 2 12
<o:p></o:p></p>
<p class="MsoNormal">0.40960E+02 0.18650E+02 0.22520E+02
0.90000E+02 0.90770E+02 0.90000E+02
<o:p></o:p></p>
<p class="MsoNormal">ZYX <o:p></o:p></p>
<p class="MsoNormal"> 0 <o:p></o:p></p>
<p class="MsoNormal">-0.97086E+00-0.49927E+00-0.82774E+00-0.13491E+01-0.57034E+00-0.71253E-01
<o:p></o:p></p>
<p class="MsoNormal">-0.19491E+00 0.61017E+00
0.10064E+01-0.22888E+01-0.94020E+00 0.77451E+00
<o:p></o:p></p>
<p class="MsoNormal"> 0.57539E+00-0.31211E-01-0.27430E+00-0.36526E+00
0.34772E+00 0.81884E+00
<o:p></o:p></p>
<p class="MsoNormal">-0.19954E+01-0.10117E+01 0.18038E+01
0.19008E+01 0.11886E+00-0.41646E+00
<o:p></o:p></p>
<p class="MsoNormal"> 0.47560E-01 0.48855E+00
0.57606E+00-0.22320E+00-0.12787E+01 0.47590E+00<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">....<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"> -9999<o:p></o:p></p>
<p class="MsoNormal"> 0.2044E-09 0.9999E+00<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Is this correct or is Chimera expecting a
different format?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Looking forward to your replies!<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Many thanks and best wishes,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Matthias<o:p></o:p></p>
<p class="MsoNormal">----------------------------------------------------------------------------------------------<o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-GB">Matthias
Gutmann Instrument
Scientist SXD<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">Rutherford Appleton
Laboratory Phone: +44 (0)1235 44 6397<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">ISIS
Facility
Fax: +44 (0)1235 44 5200<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">Chilton
Didcot
Office : R3, 1.28<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">Oxfordshire OX11
0QX Email:
<a class="moz-txt-link-abbreviated" href="mailto:Matthias.Gutmann@stfc.ac.uk">Matthias.Gutmann@stfc.ac.uk</a><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB">UNITED KINGDOM<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<br>
<p>-- <br>
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