[Chimera-users] Surface/Cap colouring

Elaine Meng meng at cgl.ucsf.edu
Fri Feb 9 09:00:17 PST 2018

Hi Joe,
There may be some bugginess/hysteresis going on, because at first I also had the same problem when I tried a simple example of two models, each with molecular surfaces.

According to the documentation, if in Surface Capping, the “Use cap color” option is turned off, then each model will be capped with its own model color, as in your image.

However, when I turned this option off when it had previously been on, both caps remained the color in that option instead of turning into the separate model colors, even when I moved the clipping plane or unclipped and reclipped.  I was able to get the separate model-color caps by showing Model Panel, closing the surface models, making sure the “Use cap color” option was turned off, and re-creating the surfaces.  (image attached below)

I hope this helps (and sorry for the rigmarole),
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Feb 9, 2018, at 4:39 AM, Healey, Joe <J.R.J.Healey at warwick.ac.uk> wrote:
> Hi chimera team,
> Is there an easy way to control the transparency of a surface and its clipping cap separately?
> I managed to do this in one session where the caps are solid, but the rest of the surface is transparent (e.g. see this link: https://drive.google.com/file/d/1-WQtUdYWbITetPl2RgRtU96eXKUj3_v5/view?usp=sharing )
> 3J9Q_wholetier_sliced_colcap.tif
> drive.google.com
> However in a different session I'm struggling to figure out how I achieved this. If I alter the surface colour in the Inspect dialog, it sets the surface and cap transparency to be the same. If I change the suface cap colour in the Effects > Side View dialogue, it gives the desired differential transparency, but colours ALL the surface endcaps identically which isn't what I want.
> Help me unpick what I did!
> Many thanks
> Joe Healey
> M.Sc. B.Sc. (Hons) MSRB
> PhD Student
> MOAC CDT, Senate House
> University of Warwick
> Coventry
> CV47AL
> Mob: +44 (0) 7536 042620  |  Email: J.R.J.Healey at warwick.ac.uk
> Jointly working in:
> Waterfield Lab (WMS Microbiology and Infection Unit)
> and the Gibson Lab (Warwick Chemistry)
> Twitter: @JRJHealey  |  Website: MOAC Page | ORCID: orcid.org/0000-0002-9569-6738
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