Dear Kai, I don't know anything about the Pymol end, but in Chimera you can control how the map grid indices relate to Cartesian coordinates. In the Volume Viewer "Features" menu, choose to show the Coordinates options in the dialog. The settings include "Origin index" and are described here: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#coordinates> Maybe in Pymol you can look up the corresponding settings for your map, then change the settings in Chimera to match them before fitting the PDB. Or possibly the converse, changing the settings in Pymol to match those in Chimera. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 4, 2014, at 5:15 AM, Kai Zhang <kzhang@mrc-lmb.cam.ac.uk> wrote:

Dear Chimera users, I found the pdb files fitted to mrc maps in Chimera do not always fit the same map opened by Pymol. It seems that the origins are calculated differently between Chimera and Pymol. I can easily handle an entire map of mrc file. But if the map has been cut, it's very difficult to find out what really needs to be modified to fit both chimera and pymol. Does anyone know an easy way to deal with this issue? Best wishes Kai

Hi Kai, MRC map files have two header fields for specifying the origin in two different ways. This problem with the format comes from the fact that the original origin specification was only for x-ray maps and could only handle integer grid points as the origin. For electron microscopy it is sometimes necessary to specify an origin that is between grid points, for example when a symmetry axis of the map does not pass through a grid point but it is desired to make the origin lie on the symmetry axis. So the MRC 2000 format added a floating point origin to handle electron microscopy maps. Chimera reads and writes both origin fields and has been extensively tested that it follows the conventions for these fields. Other software doesn’t always handle the origin header values, sometimes just ignoring them. I don’t know what PyMol does. It is a clue that you say it works if you use the entire map but not if you have cropped the map. When you crop it changes the origin fields. Software that ignores the origin header values will then not align such a map correctly with the original full map. At any rate, I believe Chimera is handling the origin values correctly and I don’t know any tricks to make other software correctly respect the origin specified in the file. Glad to hear that your export to BRIX format gave proper alignment in PyMol. That is probably the way to go. The only drawback might be that BRIX has only 8-bit data values while MRC maps are most often 32-bit floating point values. The detectors used to acquire EM data are typically 10-16 bits I think but there is a good bit of noise so 8-bits is probably ok. Tom On Sep 4, 2014, at 5:15 AM, Kai Zhang wrote:

Dear Chimera users,

I found the pdb files fitted to mrc maps in Chimera do not always fit the same map opened by Pymol. It seems that the origins are calculated differently between Chimera and Pymol. I can easily handle an entire map of mrc file. But if the map has been cut, it's very difficult to find out what really needs to be modified to fit both chimera and pymol. Does anyone know an easy way to deal with this issue?

Best wishes Kai

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