[Chimera-users] Color by height from surface?

[Tom Goddard]

Hi Oliver,

  Yes, the fake ambient occlusion method can be applied to a molecular surface.  In that case you use the molmap command to create the low resolution map whose values determine the coloring.  Then use the Surface Color dialog or scolor command on the molecular surface.

	Tom


> From: Oliver Clarke 
> Subject: Re: [Chimera-users] Color by height from surface?
> Date: June 25, 2014 at 9:12:51 AM PDT
> To: Tom Goddard 
> 
> Yes, that is exactly what I want, thank you!
> 
> But is it possible to employ the fake ambient occlusion technique for molecular surfaces, that is, derived from a model? 
> 
> Doesn’t seem intuitively that they will behave in the same way…
> 
> Oliver

On Jun 25, 2014, at 8:52 AM, Tom Goddard <goddard at sonic.net> wrote:

> Hi Oliver,
> 
>   Sounds like you want “ambient occlusion” lighting.  This is where recesses in a structure appear darker because not as much light reaches them.  It greatly improves the sense of depth.  Chimera doesn’t have this lighting mode, but it does have shadows which have a similar effect.  I’ve attached 4 images of ribosome map EMDB 1303 to illustrate this.  The first image is normal Chimera lighting and it is hard to see the recess in the structure, the second adds silhouette edges, the third image adds shadows, and the fourth is a fake ambient occlusion.
> 
> 
> <emd_1303_default.jpg><emd_1303_silhouette.jpg><emd_1303_shadows.jpg><emd_1303_ambient.jpg>
> 
> The fake ambient occlusion version was done with a Gaussian smoothed copy of the map and the scolor command.  A smoothed map gives higher density in the recesses and lower density at the extremities of the original map and then I color the original map by the smooth map value, high density dark gray, low density light gray, (Surface Color dialog color by “volume data value” mode, or equivalent scolor command).
> 
>   The fake ambient occlusion technique is a pain to set up while the shadows are easy, so usually I settle for using shadows.  To turn on shadows use menu Tools / Viewing Controls / Effects, or command “set shadow”.  If you want darker shadows you can adjust the “key-fill ratio ratio” using menu Tools / Viewing Controls / Lighting to a higher value.  In the following shadow image I increased it from 1.25 to 2.5.
> 
> <emd_1303_shadows2.jpg>
> 
> Chimera uses two lights, the “key” light is the main one shining from the upper right, and the “fill” light is weaker and shines from the right and intended to give some light to surfaces that are parallel to the key light.  Only the key light casts shadows.  If you reduce the fill you get darker shadows.  With any setting shadows gives harsher dark/light edges than ambient occlusion.
> 
>   Here’s a description of the fake ambient occlusion method from the Chimera volume data guide
> 
> 	http://www.cgl.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html#ambient
> 
>   Tom
> 
> 
> On Jun 25, 2014, at 5:18 AM, Oliver Clarke wrote:
> 
>> Hi all,
>> 
>> I’m wondering if there is any way to use scolor to color by height from another surface rather than from a plane, axis or point?
>> 
>> Specifically, I’d like to color a molecular surface by distance from the surface of the low-res model generated using multi-scale models, in order to highlight cavities in the surface of the protein.
>> 
>> Best,
>> Oliver.
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> 
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