[chimerax-users] Showing waters changes lighting

[Daniel Asarnow]

Thanks, exactly right about the water molecule! One of them slipped away
from me and I didn't notice. I can spend the rest of the weekend wondering
which peak it belonged to...

Best,
-da

On Fri, Dec 18, 2020 at 5:46 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Daniel,
> Other than specific hiding, it might also work to show the Side View and
> move the far clipping plane closer to the viewer.
>
> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sideview.html>
>
> Elaine
>
>
> > On Dec 18, 2020, at 5:24 PM, Tom Goddard <goddard at sonic.net> wrote:
> >
> > The sensible solution if there is a far away water is to just hide or
> delete distant waters.  A model refinement could easily send a water into
> deep space.  How do you find them?  You could select a close water then use
> menu Select / Zone to select all atoms more than 500 Angstroms away, then
> hide those.  I see that logs the command "select sel @>500" so you could
> use that if you prefer commands to using the zone panel.
> >
> >       # select nearby atom with mouse, then
> >       select sel @>500
> >       hide sel
> >
> > Ambient lighting is hard to do well and entails lots of approximations
> since in the real world it is achieved by the massive parallel processing
> of photons flying around.  So aberrations in ChimeraX ambient lighting are
> to be expected and judicious use of the lighting command  multi-shadow
> options can sometimes improve appearance even in a case without distant
> atoms.
> >
> >   Tom
> >
> >> On Dec 18, 2020, at 5:06 PM, Tom Goddard <goddard at sonic.net> wrote:
> >>
> >> Hi DA,
> >>
> >> Elaine is right that if you have a water very far away from the map it
> would likely cause what you observe.  The reason is that the water out in
> deep space has to also cast a shadow, so the "shadow maps" which are two
> dimensional images of lights cast from 64 different directions have to
> extend to cover that distant water and your surface.  Then they don't have
> enough resolution and it causes it to look as if no shadows are cast at all.
> >>
> >> The other possibility is that it is a bug and the shadow recomputation
> just went astray and we would want a bug report.
> >>
> >> If you really want to try to tweak the parameters of the lighting to
> cover a very distant water and still look good by using huge shadow map
> images look at the ChimeraX lighting command msMapSize and msDepthBias
> options
> >>
> >>
> https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/lighting.html#shadows
> >>
> >> That probably cannot work because the shadow map size is limited by the
> graphics driver and current graphics drivers only support 16384 as a max
> texture size for the highest end graphics cards.  The default msMapSize is
> 1024 so at most you can get 16x larger coverage of the shadows.
> >>
> >>      Tom
> >>
> >>> On Dec 18, 2020, at 3:41 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> >>>
> >>> Hi Daniel,
> >>> After showing waters, can you restore the desired appearance with
> "light soft shad f" or "light full shad f"?  I'm guessing no...
> >>>
> >>> Other guesses are that it's either a graphics bug or some of the
> waters are extremely far away in the back making the visible scene
> dimensions change drastically, changing the position of the depth-cueing
> ramp and other lighting-related calculations.
> >>>
> >>> One reason I thought of scene-depth change is that the silhouettes are
> shown when the objects are some fraction of the total depth apart, and in
> your after-water pictures, there are many fewer silhouettes, suggesting the
> overall depth is now huge.  See "graphics silhouette"
> >>> <
> https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#silhouettes
> >
> >>>
> >>> However to really figure it out we would probably need to you use
> Help... Report a Bug and attach a session that exhibits the problem.
> >>>
> >>> I hope this helps,
> >>> Elaine
> >>> -----
> >>> Elaine C. Meng, Ph.D.
> >>> UCSF Chimera(X) team
> >>> Department of Pharmaceutical Chemistry
> >>> University of California, San Francisco
> >>>
> >>>> On Dec 18, 2020, at 2:44 PM, Daniel Asarnow <asarnow at msg.ucsf.edu>
> wrote:
> >>>>
> >>>> Hi all,
> >>>> I have a few maps and models loaded, which have a couple hundred
> water molecules. When I display all the waters using 'show :HOH' the
> lighting changes. It makes "soft" look like "flat" and creates what looks
> like more ambient reflection in "full" or "simple." I embedded some
> screenshots below.
> >>>>
> >>>> My guess is something about a depth or lighting calculation is
> affected by all the waters, does anyone recognize what setting would need
> to change to correct this?
> >>>>
> >>>> Soft, shadows false:
> >>>> <image.png>
> >>>> Same after show :HOH
> >>>> <image.png>
> >>>> Full, shadows false
> >>>> <image.png>
> >>>> Same after show :HOH
> >>>> <image.png>
> >>>>
> >>>> Best,
> >>>> -da
> >>>
> >>>
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> >>>
> >>
> >
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