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<p class="MsoNormal">Hi Vincent,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">the depthCue is in relation to your clipping planes, so you have to play with these values as well.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/lighting.html<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><i>“</i><b><i><span style="font-size:13.5pt;font-family:Times;color:black">depthCueStart</span></i></b><i><span style="font-size:13.5pt;font-family:Times;color:black"> start<br>
<b>depthCueEnd</b> end<br>
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 (<b>0.5</b> to <b>1.0</b> in <b>simple</b> lighting). See also: </span></i><b><i><u><span style="font-size:13.5pt;font-family:Times;color:blue">clip</span></u></i></b><i>”<o:p></o:p></i></p>
<p class="MsoNormal"><i><o:p> </o:p></i></p>
<p class="MsoNormal"><i><o:p> </o:p></i></p>
<p class="MsoNormal">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):<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">lighting depthcue true depthCueStart 0.45 depthCueEnd 0.5<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Best,<o:p></o:p></p>
<p class="MsoNormal">Moritz<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black">ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu> on behalf of vincent Chaptal via ChimeraX-users <ChimeraX-users@cgl.ucsf.edu><br>
<b>Reply-To: </b>vincent Chaptal <vincent.chaptal@ibcp.fr><br>
<b>Date: </b>Thursday, February 17, 2022 at 03:43<br>
<b>To: </b>ChimeraX Users Help <ChimeraX-users@cgl.ucsf.edu><br>
<b>Subject: </b>[chimerax-users] fine tuning depthcue<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
</div>
<p><b><span style="color:white;background:red"> External Email - Use Caution </span></b><o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-size:13.5pt;font-family:"Courier New"">Hi,
<br>
<br>
I've been playing around a lot with depthcue-ing but I can't get it to do quite what I would like.
<br>
<br>
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).
<br>
<br>
my script includes:<br>
lighting full #(sometimes I use soft too)<br>
lighting shadows true intensity 0.3<br>
lighting qualityOfShadows finer<br>
lighting depthcue true depthCueStart 0.1 depthCueEnd 1.0<br>
<br>
<br>
First, I have selected one residue and setting the rotation around it by using "cofr sel"<br>
<br>
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.
<br>
<br>
Could you help me please. I missed the meaning of these values, so I'm blind on their use.
<br>
Thank you<br>
Vincent</span><o:p></o:p></p>
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<p class="MsoNormal">-- <br>
<br>
<o:p></o:p></p>
<p class="p1"><span class="s1">Vincent Chaptal, PhD</span><o:p></o:p></p>
<p class="p1"><span class="s1">Director of GdR APPICOM</span><o:p></o:p></p>
<p class="p1"><span class="s1">Drug Resistance and Membrane Proteins Lab</span><o:p></o:p></p>
<p class="p2"><o:p> </o:p></p>
<p class="p1"><span class="s1">MMSB -UMR5086</span><o:p></o:p></p>
<p class="p1"><span class="s1">7 passage du Vercors</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p1"><span class="s1">69007 LYON</span><o:p></o:p></p>
<p class="p1"><span class="s1">FRANCE</span><o:p></o:p></p>
<p class="p1"><span class="s1">+33 4 37 65 29 01</span><o:p></o:p></p>
<p class="p1"><span class="s1"><a href="http://secure-web.cisco.com/1qf1gtPsaDzNiHqRz6WcUF6iazTrdll-QQ3AqpL1rr8LUg7jgg2ZFXLo_1B_Z_jUqXXttNSzQcOj8FCcso0y-TUw4q9tdalX6K89qGVBXJpJpVW7YvYztTWoohHWhZe9iQY8dV09SSM_FsKzoqtDgzYZAk8lXFoVkSE6vvV8-xwB3x4aa9igOrtnHzmRWGkdPROZCGRgyX_NZJZWopELKJRbMr5mWjIsiTGPZzbSq4NfXrWGdcjKbFpekOeieikd5BhVwjglvr6-kGJNeUVtApp5HiyYD0gt98dK2dXJfyTISwT875g50j8StKT4z1wR2Q3lR2pWjmsTO07MqLaGm9w/http%3A%2F%2Fwww.appicom.cnrs.fr">http://www.appicom.cnrs.fr</a></span><o:p></o:p></p>
<p class="p1"><span class="s1"><a href="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">http://mmsb.cnrs.fr/en/</a></span><o:p></o:p></p>
<p class="p1"><o:p> </o:p></p>
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