[Chimera-users] Wire thickness

Hernando J Sosa hernando.sosa at einstein.yu.edu
Tue May 9 16:12:59 PDT 2017

Dear Chimera
How do you set the thickness of the backbone and side chains independently to produce figures like the ones below (sorry  I hijacked the picture used in blurred-display discussion).



From: Chimera-users [mailto:chimera-users-bounces at cgl.ucsf.edu] On Behalf Of Tom Goddard
Sent: Tuesday, May 09, 2017 2:02 PM
To: UCSF Chimera Mailing List
Subject: Re: [Chimera-users] Gaussian blur depth cueing? (ChimeraX)

Before/after pair - at large size, I think the blur is helpful, but YMMV

[cid:image001.jpg at 01D2C8F6.BEA06B60][cid:image002.jpg at 01D2C8F6.BEA06B60]
On May 9, 2017, at 12:09 PM, Oliver Clarke <olibclarke at gmail.com<mailto:olibclarke at gmail.com>> wrote:

Perhaps a better example:

On May 8, 2017, at 10:07 PM, Tom Goddard <goddard at sonic.net<mailto:goddard at sonic.net>> wrote:

Hi Oliver,

 The depth of field blur images I have seen of maps and molecules have all struck me as cool looking and less useful then conventional brightness based depth cuing.  Brightness depth cue allows you to include more of the structure in back while reducing the obscuring effect it has on stuff in front.  Blurring depth cue interferes much more with the stuff you want to be in focus.  Your image minimizes the badness by not having any blurring in the central region of the image, but the periphery where there is blurring may be artistically nice, but I hope you are not looking at the structure there.

 That said the technique could be done using the depth buffer that assigns depth to each pixel — it can’t be done really well that way because that depth only gives the front-most object and if transparency is present the pixel shows multiple objects at different depths.  I think it would require a compelling mock-up image to make it worth spending effort on this effect.  It is relatively easy to make a mock-up image by using clip planes to save several images representing slabs at different depths, then blur each slab image differently depending on depth in a photo editor and composite.


On May 5, 2017, at 6:42 AM, Oliver Clarke <olibclarke at gmail.com<mailto:olibclarke at gmail.com>> wrote:


I was wondering if you have thought about implementing depth-dependent gaussian blur as a depth cueing mechanism in ChimeraX?

The idea would be to blur the image in a manner dependent on the distance from the plane intersecting with the center of rotation, to mimick depth of field in a camera.

Mocked up in the attached using a tilt/shift effect, but without access to real depth information - I wonder if it might better convey depth information than distance-dependent changes in brightness/contrast under some circumstances?


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