Re: [Chimera-users] vop subtract removing too much of my map

Correction. vop subtract does not use the map threshold levels unless the minRMS option is given. As described in the vop subtract documentation: "the minRMS option can be used to scale othermap automatically to minimize the root-mean-square sum of the resulting (subtracted) values at grid points within the lowest contour of othermap." https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#subtract https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#subtract Tom

On Sep 29, 2020, at 11:41 AM, Tom Goddard wrote:

Correct, vop subtract does not use displayed threshold levels in any way.

Tom

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On Sep 29, 2020, at 11:23 AM, Elaine Meng wrote:

I don't see anything about map threshold in the "vop subtract" link I sent you earlier, so I don't think it has an effect.

So the factors you can control are the molmap resolution (as you said) and molmap grid spacing. The resolution of results from map interpolation (which is part of subtraction and several other map calculations) depend on input map resolution, grid spacing, bumpiness, and the shift between their grids, as discussed here:

http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#notes

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On Sep 29, 2020, at 10:53 AM, Ahmad Khalifa wrote:

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 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

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On Sep 29, 2020, at 9:55 AM, Ahmad Khalifa 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?

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