[Chimera-users] Surface/Cap colouring

Healey, Joe J.R.J.Healey at warwick.ac.uk
Sun Feb 11 03:00:56 PST 2018


Hi again Elaine,


The process you described seems to work nicely - redrawing the surfaces looks to have worked and 'reset' the cap behaviour.


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<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
________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: 09 February 2018 17:00:17
To: Healey, Joe
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Surface/Cap colouring

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

[cid:1B1E0633-82E7-438C-911B-57D70E7967E3 at gateway.sonic.net]


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


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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