Thanks a lot for the response, I can send data if necessary, but it likely has to do with options / resolution

The higher resolution of map2 is, the sharper the subtraction. I tried using a finer gridSpacing but it doesn't change much!

Does the map threshold factor into the subtraction?

On Tue, Sep 29, 2020 at 10:05 AM Elaine Meng <meng@cgl.ucsf.edu> wrote:

Hi Ahmad,
To my knowledge the map subtraction is precise. But if you think there is a problem, you will need to give a precise and detailed description of exactly what you did, including the data files and all the steps needed to show the problem, and why you believe there is a problem (and possibly use menu: Help... Report a Bug, instead of sending e-mail here). If we can't reproduce a problem, we can't fix it!

It may be that you need to create the molmaps with smaller grid spacing to give a more precise result.

molmap details and options:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html>

vop subtract details and options:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#subtract>

Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Sep 29, 2020, at 9:55 AM, Ahmad Khalifa <underoath006@gmail.com> wrote:
>
> I'm trying to subtract two overlapping molmaps: map1-map2, but the subtraction ends up removing too much of map1 where map2 doesn't overlap with map1!
>
> how can I get precise subtraction?