[chimerax-users] Surface Coloring

[Juliana Glavina]

This is great, thank you so much!
I've been all day trying to do something like that.

Yeah, I know it is an artifact, but it looks much more natural for me,
since it is more like a continuous characteristic (in contrast to sequence
conservation which is discrete in all sense).

And yes! I'm using kd because I want to compare fix values (and everything
I have done in the past is with this scale, I've just begun migrating my
work to chimeraX)

I was exploring mlp today and I will propose it soon to my advisor, I
really like the results.

Thanks again for everything !

Juliana



El lun., 7 jun. 2021 19:04, Elaine Meng <meng at cgl.ucsf.edu> escribió:

> Hi Juliana,
> The appearance in ChimeraX is actually a more accurate representation of
> coloring by Kyte-Doolittle hydrophobicity values.  In both Chimera and
> ChimeraX, there is a simple lookup table by amino acid type (e.g. leucine
> always gets the same number), and then the surface for each amino acid is
> colored to show that value.  Chimera shows a more blurry edge because some
> of the surface triangles cross between different residues, but it's really
> an artifact.  ChimeraX shows a sharp edge because the surface triangles are
> drawn so that they only belong to one atom instead of crossing between more
> than one atom.
>
> Two thoughts:
>
> (1) MLP is different and actually varies in space on a 3D grid, so you
> will get gradual changes in color.  So my first thought is why not use
> MLP?  If you don't like the coloring scheme you can use other colors, e.g.
> command
>
> mlp palette dodgerblue:white:orangered range -20,20
>
> (2) If you really want to just use a simple lookup table that always gives
> the same value for the same type of amino acid but try to make it look more
> like the result in Chimera, you would have to force the surface creation to
> make triangles that cross between atoms, then color the atoms by attribute,
> and then use yet another color command to make the surface colors match
> nearby atoms.  You can't color the surface in a single command because this
> type of surface (with triangles that go with more than one atom) isn't
> directly associated with the atoms/residues or their attributes.
>
> Sounds like you already found the ChimeraX command file to assign
> Kyte-Doolittle hydrophobicities and color by attribute:
> <
> https://rbvi.ucsf.edu/chimerax/docs/user/kyte-doolittle_hydrophobicity.cxc
> >
>
> The last two commands in that file are:
>
> surf protein; hide protein atoms
> color byattribute kdh protein target rs palette dodgerblue:white:orangered
> novalue gray
>
> To get jagged boundaries you would need replace those with something like
> the following, where #1 is the surface model (change that as needed if your
> surface is a different model number):
>
> surf protein sharp false; hide protein atoms
> color byattribute kdh protein target a palette dodgerblue:white:orangered
> novalue gray
> color zone #1 near protein distance 3
>
> It still doesn't look exactly like it does in Chimera, but again, how it
> looks in Chimera is really an artifact anyway.
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Jun 7, 2021, at 11:27 AM, Juliana Glavina via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
> >
> > Dear All,
> > I am moving from Chimera to ChimeraX and I am trying to reproduce some
> of things that I used to do in Chimera.
> > I managed to colour the surface by the kdHydrophobicity scale. However,
> the coloring is discrete with sharp edges between the residues. I was
> wondering if it was possible to smooth the edge between two different
> colors on the surface - similar to mlp but with customized attributes.
> > Thank you very much in advance
> >
> > UCSF ChimeraX version: 1.2.3 (2021-05-13)
> > Ubuntu 20.04
> >
> > Juliana
>
>
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