Thank you, Elaine, that helped. I had not been typing the "lighting" command before the "depthCue". Cheers, Paul Paul Miller (he/him), PhD University Lecturer in Pharmacology Department of Pharmacology University of Cambridge Tennis Court Road Cambridge CB2 1PD +44 1223 761267 https://www.phar.cam.ac.uk/research/miller ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: 05 January 2024 17:23 To: Paul Miller <pm676@cam.ac.uk> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Depth cueing Hi Paul, It's basically the same in ChimeraX as in Chimera -- there is a Side View tool for interactive clipping-plane position adjustment, as well as various command options to set the detailed depth-cueing parameters. <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Ftools%2Fsideview.html&data=05%7C02%7Cpm676%40universityofcambridgecloud.onmicrosoft.com%7C36bbad3dd74340cf77f408dc0e132000%7C49a50445bdfa4b79ade3547b4f3986e9%7C1%7C0%7C638400722533453481%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=CO%2BlDL9EDXXLcptb8Kmm3coujOVBv2moDk9PPsYV%2Ft4%3D&reserved=0<https://rbvi.ucsf.edu/chimerax/docs/user/tools/sideview.html>> In ChimeraX, these options are within the "lighting" command: depthCue, depthCueColor, depthCueStart, depthCueEnd: <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Flighting.html&data=05%7C02%7Cpm676%40universityofcambridgecloud.onmicrosoft.com%7C36bbad3dd74340cf77f408dc0e132000%7C49a50445bdfa4b79ade3547b4f3986e9%7C1%7C0%7C638400722533453481%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=ZYOlOxUe%2FRS8j1eEebuShkeEMGKe%2FxY2WmE%2BfQhJuhY%3D&reserved=0<https://rbvi.ucsf.edu/chimerax/docs/user/commands/lighting.html>> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 5, 2024, at 5:40 AM, Paul Miller via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi
How do I depth cue in ChimeraX? In Chimera I used to be able to precisely control this from the side view window but I cannot find any way of controlling depth cueing in ChimeraX.
Thank you.
Cheers, Paul