[Chimera-users] Origin issue of mrc file from chimera to pymol

[Elaine Meng]

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 at 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