Electron Density Map Tests - X-PLOR format
Jmol 11.9.19
Eric Martz, January 17, 2010.
This page is obsolete. Problems described on this page have been fixed. Please see THIS UPDATE.

DOWNLOAD THIS FILESET jmol-edm-test2.zip

The map file, 3hyd_map.xplor, was generated using the unix utility mapman from the Uppsala Software Factory. I used mapman to convert 3hyd_map.ccp4 to X-PLOR format. This produced a 2 megabyte file in plain text (for a small protein domain, it was 25 MB), which looked like this snapshot. In contrast, the CCP4 format file was compressed, and I don't know how to decompress it. (Click on thumbnails for full-sized images.)

The putatively X-PLOR format map can be loaded into PyMOL and is automatically aligned with the molecule. If the map filename ends .xplor, double-clicking on it loads it into MacPyMOL. If the map filename has no filetype, PyMOL still loads it correctly but only if the load command ends with "format=xplor". If the map is gzipped (.xplor.gz), PyMOL doesn't interpret it as a map even if loaded with "format=xplor".

When I tried to use Bob's command to load this file into Jmol 11.9.19, nothing appeared. There was no error message.

When I loaded the putative xplor-format file with a simple isosurface command, the surface did not surround the atoms in the molecule. (The menu in the snapshot was a botched attempt to show the Jmol version number. It was 11.9.19, really!)