[chimerax-users] Colour residues by local resolution estimation map

[Ioannis Skalidis]

Good morning!

Thanks a lot to everybody for their suggestions and especially to Tom for
implementing the feature directly!

Cheers,

Yiannis
On 20.05.21 04:25, Tom Goddard wrote:

Hi Yiannis,

  I added a "measure mapvalues" command to ChimeraX, in tonight's
build (dated May 20) that allows you to interpolate a local resolution
map at atom positions and assign the interpolated value to each atom.
Then the "color byattribute" command can do the coloring you want.
For example, if your local resolution map is #2 and your atomic model
is #1

	measure mapvalues #2 atoms #1 attribute "resolution"
	color byattribute "resolution" #1 palette 3,blue:4.5,white:6,red key true

The color command will color the atoms and each residue in a ribbon
using the average resolution value for that residue's atoms.  See the
color command documentation for more details

	https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute

  Tom



On May 19, 2021, at 10:22 AM, Tom Goddard <goddard at sonic.net>
<goddard at sonic.net> wrote:

Hi Yiannis,

 I'll see if I can add that today to the ChimeraX daily build.

	Tom



On May 19, 2021, at 6:22 AM, Ioannis Skalidis <johnskalidis at gmail.com>
<johnskalidis at gmail.com> wrote:

Dear all,

I am trying to color a protein model based on the local resolution of
the corresponding map. I can color the overall surface of the model,
but not the residues themselves. Is there a way to do this, e.g, color
the model backbone somehow?

Thanks a lot for your help!

Cheers,
Yiannis

-- 



Skalidis Ioannis, MSc
Biochemistry & Cryo-EM Scientist
PhD Candidate
Kastritis Laboratory for Biomolecular Research
Cryo-Electron Microscopy & Computational Structural Biology

________________________________________________
Martin-Luther-Universität Halle-Wittenberg
Biozentrum, Room A.2.21
IWE ZIK HALOmem NWG III
"Kryo-Elektronenmikroskopie an Membranproteinkomplexen"
Weinbergweg 22, 06120 Halle
tel: +49 345 5524986
web (Lab): https://blogs.urz.uni-halle.de/kastritislab/
web (HALOmem): https://www.halomem.de/en/

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-- 



Skalidis Ioannis, MSc
Biochemistry & Cryo-EM Scientist
PhD Candidate
Kastritis Laboratory for Biomolecular Research
Cryo-Electron Microscopy & Computational Structural Biology

________________________________________________
Martin-Luther-Universität Halle-Wittenberg
Biozentrum, Room A.2.21
IWE ZIK HALOmem NWG III
"Kryo-Elektronenmikroskopie an Membranproteinkomplexen"
Weinbergweg 22, 06120 Halle
tel: +49 345 5524986
web (Lab): https://blogs.urz.uni-halle.de/kastritislab/
web (HALOmem): https://www.halomem.de/en/
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