map file specification

From: Pascal
Date: 15 September 2011 08:30


Hi,

I am looking at the specifications of the ccp4 map file format and I am
confused with the number of columns and the number of intervals.

I assume that the number of columns is the grid size but what is the
number of intervals (elements 8-9 in the header)?

Regards,
Pascal

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From: David Waterman


Hi Pascal,

The map data is a three dimensional array with dimensions [NC, NR, NS]. On its own, this gives you no information about the grid pitch in the three (crystallographic, not Cartesian) directions, which is determined in fractional coordinates by the number of intervals. That is, along the X direction the sampling interval has size 1/NX. Of course, you need the X, Y and Z lengths (elements 11-13) to convert the fractional coordinate sizes to real space units. There is a further conversion to take into account too: the correspondence between X, Y, Z and C, R, S is not fixed by the format, but is file dependent and described by MAPC, MAPR and MAPS (elements 11-13). 

Hope this helps,
-- David

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From: David Waterman


typo: MAPC, MAPR and MAPS are elements 17-19 of the header, but you can see that anyway from the specification.

Cheers

-- David

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From: Pascal


Thanks for all the answers. I can almost write a map file.

Only one problem remain: what is the machine stamp (element 54)?
What should I put there? A small fortran program is used to write the file.

Pascal

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From: David Waterman


Hi Pascal,

This document makes an attempt at an explanation, but in a somewhat obtuse way: http://conventions.cnb.uam.es/References/maplib.html. The important point is that the machine stamp is 4 bytes that are specific for the architecture that wrote the file. For little endian hardware the stamp is 0x44, 0x41, 0x00, 0x00 while the big endian stamp is 0x11, 0x11, 0x00, 0x00.

Cheers

-- David