[Chimera-users] Fwd: Re: Density display with CHIMERA

F.Xavier Gomis-Rüth fxgr at ibmb.csic.es
Wed Apr 13 09:58:05 PDT 2016

Dear Elaine,
thanks a lot for your prompt answer and sorry for not using the . The 
coordinates are regular PDB coordinates coming from a crystallographic
refinement program such as PHENIX, BUSTER/TNT, REFMAC5, and the map file 
was likewise generated by these
programs. It's the regular pair of coordinates and map one uses to 
perform subsequent model building with COOT and, in this program, everything
is fine as to the matching of coordinates and map. In this case, should 
I really change the origin of the map?
Best wishes,

-------- Forwarded Message --------
Subject: 	Re: Density display with CHIMERA
Date: 	Wed, 13 Apr 2016 09:52:07 -0700
From: 	Elaine Meng <meng at cgl.ucsf.edu>
Reply-To: 	Chimera User Forum <chimera-users at cgl.ucsf.edu>
To: 	fxgr at ibmb.csic.es
CC: 	Chimera User Forum <chimera-users at cgl.ucsf.edu>

On Apr 13, 2016, at 9:27 AM, F.Xavier Gomis-Rüth <fxgr at ibmb.csic.es> wrote:

> Dear Elaine,
> I am encountering problems while trying to display a fragment of a structure from a PDB file superimposed
> with its Fourier map. When I load the latter, it is presented displaced from the model and I cannot get it centered
> onto it. All other features (contouring, mesh/solid style, etc.) work fine, it's just that atoms and density do not superimpose.
> I've tried it with different space groups, just for the case it was a problem in a particular library, but without success.
> I am working on a Mac, I don´t know if there is a problem, and I am using CCP4 maps.
> Any suggestions would be very welcomed!
> Best wishes,
> Xavier
> --
> <fxgr_signanew.jpg>

Dear Xavier,
I don’t know where or from what program these files came frome, so it is hard to say why the coordinates don’t match up.  In some cases the map file does not include information that aligns its coordinates with the corresponding atomic structure, or maybe the map file header does have this information but it is not in a format understood by Chimera.

You can change the offset of the map in Chimera, if you know what it should be.  After opening the map, in the Volume Viewer dialog choose Features… Coordinates, and in the resulting options you can change origin index, spacing, etc.  However, I don’t know how to figure out what values are needed, if you don’t already have that information.  The options are explained here:


It is generally recommended to send Chimera questions to chimera-users at cgl.ucsf.edu  (CC’d here), especially in certain areas where others know more than I do.  I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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