[Chimera-users] molmap and origin index

Catalin Buiu cbuiu at yahoo.com
Sun Jul 14 07:26:01 PDT 2013

Hi Tom,

thanks for your reply.

Now the both maps (molmap and Matlab) have the same origin index, the same voxel size and still the Matlab map is shifted away from the other map (and atomic structure). Can you tell me a possible reason for that?

Thanks again,


 From: Tom Goddard <goddard at sonic.net>
To: Catalin Buiu <cbuiu at yahoo.com> 
Cc: "chimera-users at cgl.ucsf.edu" <chimera-users at cgl.ucsf.edu> 
Sent: Monday, July 8, 2013 11:46 PM
Subject: Re: [Chimera-users] molmap and origin index

Hi Catalin,

  The Chimera molmap command creates a density map for a molecule using a grid that has its 3 axes aligned with the x, y, and z axes of the molecular data (atom coordinates) with padding 3 times the requested map resolution.  This is described in the molmap documentation

The origin of the grid equals the x,y,z coordinates of the grid point at grid index 0,0,0.  That origin position (floating point values) is saved in an MRC 2000 file in the xorigin, yorigin, zorigin header fields. 


It cannot be saved in the nxstart,nystart,nzstart header fields since those are integer values and can't accomodate the exact floating point origin.  Here's the Chimera Python source code that reads MRC files if you want more details of how  that is handled.



On Jul 8, 2013, at 1:08 PM, Catalin Buiu wrote:

Hello all,
>I have the following problem: when I use molmap to generate 
>a map from an atomic structure, the result is fine: both align.
>When I use another (Matlab) program to generate the map, the two,
>when opened in Chimera do not align anymore.
>My question is how molmap generates an origin index such that
>both the map and the structure do align and how Chimera reads (and converts)
>the xyz origin data from the MRC file?
>Thank you.
>Catalin Buiu
>University of Bucharest, Romania_______________________________________________
>Chimera-users mailing list
>Chimera-users at cgl.ucsf.edu
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20130714/a21d5af2/attachment.html>

More information about the Chimera-users mailing list