[Chimera-users] Difference map

BuddySphinx yangqi.gu at yale.edu
Sat Nov 17 14:40:54 PST 2018

Hi Elaine,
Thank you for your response! I tried using the command and I have been trying two maps which looks very similar, but with different resolution (3.6 A (yellow) vs 3.2 A (grey)) and with different pixel size (1.05 vs 0.822). Will this affect the gridding? (I am not very familiar with what you mean by the same grid). 

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From: Elaine Meng
Sent: Friday, November 16, 2018 7:45 PM
To: Yangqi Gu
Cc: chimera-users
Subject: Re: [Chimera-users] Difference map

Hi Yangqi,
Yes, see command “vop subtract”:


Keep in mind that if the two aren’t on the same grid, there may be small differences due to the need to sample them at the same points to do the subtractions.
I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Nov 16, 2018, at 4:39 PM, Yangqi Gu <yangqi.gu at yale.edu> wrote:
> Dear Chimera users,
> I am trying to examine two cryo-EM maps and want to know if there is a subtle change between these two. I want to calculate the difference map, is it doable in Chimera?
> Best,
> Yangqi

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