[chimerax-users] fine tuning depthcue

[vincent Chaptal]

Hi Moritz,

thank you, it does the trick.

I thought that depthcuestart would start at 1.0 at the position of 
centering, there was my mistake.

Best
Vincent

Le 17/02/2022 à 14:38, Hunkeler, Moritz a écrit :
>
> Hi Vincent,
>
> the depthCue is in relation to your clipping planes, so you have to 
> play with these values as well.
>
> https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/lighting.html
>
> /“/*/depthCueStart/*/  start
> *depthCueEnd*  end
> Set the position of the depth-cueing ramp. Depth-cueing shading 
> increases linearly from start to end, each expressed as a position 
> relative to the front (0.0) and back (1.0) global clipping planes 
> (*0.5* to *1.0* in *simple* lighting). See also: /*/_clip_/*/”/
>
> //
>
> //
>
> By setting the clipping planes right at the ‘back’ and ‘front’ of you 
> structure, you should get a very strong ‘fog gradient’ around the 
> center with something like (if I understand your query correctly):
>
> lighting depthcue true depthCueStart 0.45 depthCueEnd 0.5
>
> Best,
>
> Moritz
>
> *From: *ChimeraX-users <chimerax-users-bounces at cgl.ucsf.edu> on behalf 
> of vincent Chaptal via ChimeraX-users <ChimeraX-users at cgl.ucsf.edu>
> *Reply-To: *vincent Chaptal <vincent.chaptal at ibcp.fr>
> *Date: *Thursday, February 17, 2022 at 03:43
> *To: *ChimeraX Users Help <ChimeraX-users at cgl.ucsf.edu>
> *Subject: *[chimerax-users] fine tuning depthcue
>
> *        External Email - Use Caution *
>
> Hi,
>
> I've been playing around a lot with depthcue-ing but I can't get it to 
> do quite what I would like.
>
> I want to display a protein structure, with a focus on one zone and a 
> "heavy" depthcue to have a strong "fog" hiding much of the background 
> (without deleting the residues in the back).
>
> my script includes:
> lighting full  #(sometimes I use soft too)
> lighting shadows true intensity 0.3
> lighting qualityOfShadows finer
> lighting depthcue true depthCueStart 0.1 depthCueEnd 1.0
>
>
> First, I have selected one residue and setting the rotation around it 
> by using "cofr sel"
>
> My max depthcue is with "depthCueStart 0.1 depthCueEnd 1.0". I've 
> tried to change these numbers in many different ways, including 
> negative or very large numbers) but I can't get it to be thicker.
>
> Could you help me please. I missed the meaning of these values, so I'm 
> blind on their use.
> Thank you
> Vincent
>
> -- 
>
> Vincent Chaptal, PhD
>
> Director of GdR APPICOM
>
> Drug Resistance and Membrane Proteins Lab
>
> MMSB -UMR5086
>
> 7 passage du Vercors
>
> 69007 LYON
>
> FRANCE
>
> +33 4 37 65 29 01
>
> http://www.appicom.cnrs.fr 
> <http://secure-web.cisco.com/1qf1gtPsaDzNiHqRz6WcUF6iazTrdll-QQ3AqpL1rr8LUg7jgg2ZFXLo_1B_Z_jUqXXttNSzQcOj8FCcso0y-TUw4q9tdalX6K89qGVBXJpJpVW7YvYztTWoohHWhZe9iQY8dV09SSM_FsKzoqtDgzYZAk8lXFoVkSE6vvV8-xwB3x4aa9igOrtnHzmRWGkdPROZCGRgyX_NZJZWopELKJRbMr5mWjIsiTGPZzbSq4NfXrWGdcjKbFpekOeieikd5BhVwjglvr6-kGJNeUVtApp5HiyYD0gt98dK2dXJfyTISwT875g50j8StKT4z1wR2Q3lR2pWjmsTO07MqLaGm9w/http%3A%2F%2Fwww.appicom.cnrs.fr>
>
> http://mmsb.cnrs.fr/en/ 
> <http://secure-web.cisco.com/12QnwPK_r_Hc1y4wRjK1vzwqR-qxCK0mBJAxlm08KLOrnuwyOx-BWNTYuprn2-dVpIqCcJ50u2257dD7TvFYDXcfweHOTQT8arH6ACrk6KE9DlteGEZsDLJUEpbaxd1wQ5ek2wjJv9b9IsIdAAM1jrSqzvkQAvfsxDfqQpnsvUr8OnkRkyIQ0crNO_hlJqX9KNRzYrIxXMRuYPDI-jjMuyQWrQblCqwKGYslMmXFMlJxl_Cnk2WmqqET6hKzm6HiVAuZrO36MYKszQsXrMk-9LTzO08T_CHGCYHDwbvKv6ff9JCVtdRQT-uBLekSULjAXjM7ektOF2tM8PMTHV4cQRg/http%3A%2F%2Fmmsb.cnrs.fr%2Fen%2F>
>

-- 

Vincent Chaptal, PhD

Director of GdR APPICOM

Drug Resistance and Membrane Proteins Lab


MMSB -UMR5086

7 passage du Vercors

69007 LYON

FRANCE

+33 4 37 65 29 01

http://www.appicom.cnrs.fr

http://mmsb.cnrs.fr/en/

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