[chimerax-users] Displaying silhouette around specific visual elements

Wed Mar 31 18:36:56 PDT 2021

 Thank you very much, Tom.
Likewise, my images looked great with this alternative approach.
One small caveat with this, though, is that when you have solvent exposed,
flexible side chains, which are not fully explained by the x-ray map (which
is one of my cases), they may look artificial crossing the transparent map
boundary. This can be overcomed with the method described by Elaine.
Thank you both again for helping.
All the best,
Andre.

Em qua., 31 de mar. de 2021 às 19:03, Tom Goddard <goddard at sonic.net>
escreveu:

> Hi Gustavo,
>
>   Glad you noticed the smoothness of the surface.  I made it smoother than
> the default.  The surface came from the molmap command which computes a
> density map from the atomic model. That command uses a density map grid
> spacing of 1/3 the requested resolution by default, but I specified an
> extra option that used a grid spacing 1/8 of the resolution:
>
> open 2gbp
> molmap #1 8 gridSpacing 1
>
> Also if you are doing this with a big molecule (100,000 atoms) the density
> map created may be very large and may be shown subsampled so the surface
> looks coarser.  Make sure to set the "step" to 1 in the Volume Viewer panel
> so that it uses the full resolution of the computed map instead of step 2
> which would use only every other grid point.
>
>   One more pro tip about that image composition example.  It only worked
> nicely because the atomic structure was completely behind the surface, so I
> could layer the surface on top.  If part of the atomic model was behind and
> part in front (for example with a cryoEM map surface), then the layering
> would not work well -- the composite image would have the surface in front
> everywhere.  Elaine's selection highlight approach can handle that
> situation with correct occlusions but the edging is not as nice as
> silhouettes.
>
>   Tom
>
>
> On Mar 31, 2021, at 1:00 PM, de Miranda Seabra, Gustavo <
> seabra at cop.ufl.edu> wrote:
>
> Hi Tom,
>
> This looks beautiful! Just one tangential question: How do you get such a
> smooth surface? Can you share the exact commands you gave?
>
> Thanks!
>
> --
> *Gustavo Seabra*
> Assistant Scientist
> Center for Natural Products, Drug Discovery and Development (CNPD3)
> Department of Medicinal Chemistry
> College of Pharmacy
> University of Florida, Gainesville, FL, USA
> ------------------------------
> *From:* ChimeraX-users <chimerax-users-bounces at cgl.ucsf.edu> on behalf of
> Tom Goddard <goddard at sonic.net>
> *Sent:* Tuesday, March 30, 2021 8:55 PM
> *To:* Andre LB Ambrosio <andre at ifsc.usp.br>
> *Cc:* ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>
> *Subject:* Re: [chimerax-users] Displaying silhouette around specific
> visual elements
>
> *[External Email]*
> Hi Andre,
>
>   If you are willing to go to a little trouble you can get silhouettes on
> an atomic model beneath a transparent surface that has no silhouettes.  You
> first save an image of the atomic model with silhouettes with no surface,
> then save an image of the transparent surface with no atomic model and no
> silhouettes, then overlay the second image on the first in a photo editor
> like Gimp.  Below is Elaine's example done this way.  The command to save
> the surface image with transparency for overlaying is "save transpsurf.png
> transparentBackground true".
>
> Tom
>
> Overlay of two images.
>
> Atomic model image
>
> Transparent surface image
>
>
> On Mar 30, 2021, at 3:11 PM, Andre LB Ambrosio <andre at ifsc.usp.br> wrote:
>
> Dear Elaine, that is excellent! It is the visual effect I was looking for
> indeed.
> Thank you very much for this and thank you Tom for the very detailed
> response and for the feature request ticket.
> Andre.
>
> Em ter., 30 de mar. de 2021 às 15:59, Elaine Meng <meng at cgl.ucsf.edu>
> escreveu:
>
> Hi Andre,
> Sometimes you can approximately "fake" this effect by using the selection
> outline.  It is not the same, however, as silhouettes; it will only go
> around the outside perimeter of the selected item(s).  For example, if I
> have a molecule inside a map surface, I can make the surface transparent,
> select the atomic structure, and make the selection outline color black
> etc. as in these commands, resulting in the appearance in the attached
> image.
>
> open 2gbp
> molmap protein 8
> trans 70
> view
> set bgColor white
> select @*
> graphics selection color black
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
>
>
> On Mar 25, 2021, at 8:23 PM, Tom Goddard <goddard at sonic.net> wrote:
>
> Hi Andre,
>
>  It is not currently possible to display silhouettes on some models and
> not others.
>
>  Several people have wanted this but I think it is complex to achieve.
> The silhouettes show boundaries where the depth in the entire scene changes
> abruptly.  In order to have per-model silhouettes the ChimeraX GPU shader
> programs would need to compute an additional depth buffer separately for
> each model.  Also the silhouette edges are not currently drawn at a
> specific depth.  If per-model silhouettes were supported a stick model with
> silhouettes beneath a transparent surface needs to draw the silhouettes
> under the transparent surface so knowing the depth of the silhouette edge
> becomes important.  When not using silhouettes the shader programs need to
> not compute the extra per-model depth buffers otherwise it would slow
> down rendering even when not being used.  Adding these additional
> complexities to already complex graphics rendering shader programs have so
> far made this feature out of reach for our one graphics rendering
> developer (me).
>
>  I made a feature request for per-model silhouette edges and perhaps in
> the future we will find a simpler way to implement it that makes it
> feasible.
>
> https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/4420
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.rbvi.ucsf.edu_trac_ChimeraX_ticket_4420&d=DwMFaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=IFgzc8_Vdkz-B7UF2uxuBCj87hyWuUEjWI2N297ETz4&m=buIaGFiuOEg93LpD7JBCYgWU_w9PFNqzQcrtEu3dwS4&s=4rNagowyowqf-kDt4FSpoXKb-pTc5iJJptB8I4YexpU&e=>
>
>  Tom
>
> On Mar 25, 2021, at 10:09 PM, Andre LB Ambrosio <andre at ifsc.usp.br> wrote:
>
> Dear all,
>
> I wonder if it's possible to display silhouettes selectively in the same
> figure; for instance, displaying silhouettes only on structure
> representation (around sticks, spheres, cartoons and so on), but not around
> the maps or volumes that surround them.
> Many thanks in advance,
>
> Andre
> _
>
>
>
> --
> Andre LB Ambrosio
> Associate Professor, IFSC/USP - Brazil
> www.ifsc.usp.br/alba
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ifsc.usp.br_alba&d=DwMFaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=IFgzc8_Vdkz-B7UF2uxuBCj87hyWuUEjWI2N297ETz4&m=buIaGFiuOEg93LpD7JBCYgWU_w9PFNqzQcrtEu3dwS4&s=ySFDlzFgm5R9qi6-4q_NIK-FlZAlewimOtx8sOwInfA&e=>
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-- 
Andre LB Ambrosio
Associate Professor, IFSC/USP - Brazil
www.ifsc.usp.br/alba
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