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

[Ahmad Khalifa]

Well I'm trying to make a mask for a part of my molecule, my strategy for
this is to create a molmap of 60 A (map1) and another of 5 A (map2) and
subtract map1 - map2

Usually people would suggest using volume eraser for this, but I want to go
with the lazy approach of subtraction!!!

Is there a way I can tweak the molmap / vop subtract settings to give me
what I want?

On Tue, Sep 29, 2020 at 11:41 AM Tom Goddard <goddard at sonic.net> wrote:

> Correct, vop subtract does not use displayed threshold levels in any way.
>
>         Tom
>
> > On Sep 29, 2020, at 11:23 AM, Elaine Meng <meng at cgl.ucsf.edu> 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>
> >
> >> On Sep 29, 2020, at 10:53 AM, Ahmad Khalifa <underoath006 at gmail.com>
> 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 <meng at 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 at 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?
> >>
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