[Chimera-users] Surface/Cap colouring

Healey, Joe J.R.J.Healey at warwick.ac.uk
Sat Feb 10 08:51:43 PST 2018


Hi Elaine,

I thought it might be slightly buggy yeah, I encountered the same thing with the caps not responding to commands/toggled etc. There was also some strange clipping and disappearance of the caps as the models were moved (even with an offset).

I’ll try redrawing the surfaces as you suggest - thanks!

Joe


M.Sc. B.Sc. (Hons) MSRB
PhD Student
MOAC CDT, Senate House
University of Warwick
Coventry
CV47AL
Mob: +44 (0) 7536 042620<tel:+44%207536%20042620>  |  Email: J.R.J.Healey at warwick.ac.uk<mailto:J.R.J.Healey at warwick.ac.uk>

Jointly working in:
Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/> (WMS Microbiology and Infection Unit)
and the Gibson Lab<http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry)

Twitter: @JRJHealey<https://twitter.com/JRJHealey>  |  Website: MOAC Page<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> | ORCID: orcid.org/0000-0002-9569-6738<http://orcid.org/0000-0002-9569-6738>

On 9 Feb 2018, at 17:00, Elaine Meng <meng at cgl.ucsf.edu<mailto:meng at cgl.ucsf.edu>> wrote:

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
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

<caps.png>


On Feb 9, 2018, at 4:39 AM, Healey, Joe <J.R.J.Healey at warwick.ac.uk<mailto: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<http://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<mailto: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<http://orcid.org/0000-0002-9569-6738>
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