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@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@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@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@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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