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
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@cgl.ucsf.edu on behalf of vincent Chaptal via ChimeraX-users ChimeraX-users@cgl.ucsf.edu Reply-To: vincent Chaptal vincent.chaptal@ibcp.fr Date: Thursday, February 17, 2022 at 03:43 To: ChimeraX Users Help ChimeraX-users@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.frhttp://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
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@cgl.ucsf.edu on behalf of vincent Chaptal via ChimeraX-users ChimeraX-users@cgl.ucsf.edu *Reply-To: *vincent Chaptal vincent.chaptal@ibcp.fr *Date: *Thursday, February 17, 2022 at 03:43 *To: *ChimeraX Users Help ChimeraX-users@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
participants (2)
-
Hunkeler, Moritz
-
vincent Chaptal