id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1646 Clip broken + depth cueing question olibclarke@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Darwin-18.2.0-x86_64-i386-64bit ChimeraX Version: 0.9 (2019-01-26) Description Hi, Clip doesn't seem to be working properly, with either surface or mesh models. When I run a command like `clip near 10 far -10`, the position of the clipping planes shown in the side view window is correct, but nothing is visible in the main window, unless I reset the view. Also, I'm not sure if this is a bug, but it is different behavior to Chimera so I wanted to clarify - depth cueing no longer has any effect on mesh maps when meshlighting is set to false. Is this the intended behavior? Cheers Oli Log: > camera ortho > cofr centerOfView > lighting soft > lighting depthCueColor white UCSF ChimeraX version: 0.9 (2019-01-26) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/olibclarke/Dropbox/Clarke_Lab_Shared/Tg/initial_map_phenix_autosharp.mrc File not found: /Users/olibclarke/Dropbox/Clarke_Lab_Shared/Tg/initial_map_phenix_autosharp.mrc File not found: /Users/olibclarke/Dropbox/Clarke_Lab_Shared/Tg/initial_map_phenix_autosharp.mrc > open /Users/olibclarke/Dropbox/Downloads/cryosparc_P27_J97_006_volume_map_sharp_local.mrc File not found: /Users/olibclarke/Dropbox/Downloads/cryosparc_P27_J97_006_volume_map_sharp_local.mrc File not found: /Users/olibclarke/Dropbox/Downloads/cryosparc_P27_J97_006_volume_map_sharp_local.mrc > open /Users/olibclarke/Dropbox/GPU_sync/cryosparc_P27_J106_006_autosharp.mrc File not found: /Users/olibclarke/Dropbox/GPU_sync/cryosparc_P27_J106_006_autosharp.mrc File not found: /Users/olibclarke/Dropbox/GPU_sync/cryosparc_P27_J106_006_autosharp.mrc > help help:quickstart > open /Users/olibclarke/Dropbox/Downloads/cryosparc_P27_J329_005_volume_map_sharp.mrc Opened cryosparc_P27_J329_005_volume_map_sharp.mrc, grid size 360,360,360, pixel 1.06, shown at level 0.338, step 2, values float32 > help volume > help alia > help alias > help volume Expected a density maps specifieror a keyword Expected a density maps specifieror a keyword > volume #1 style mesh > volume #1 style mesh smoothLines true > volume #1 style mesh smoothLines true squareMesh false > volume #1 style mesh smoothLines true squareMesh false meshLighting false > volume #1 style mesh smoothLines true squareMesh false meshLighting false Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'pseudobonds', 'ribbons', 'rings', or 'surfaces'or a keyword > volume #1 style mesh smoothLines true squareMesh false meshLighting false > color #1 blue Unknown command: background solid black > volume #1 style mesh smoothLines true squareMesh false meshLighting false > color #1 blue Unknown command: background black > help background No help found for 'background' > set bgColor black > volume #1 style mesh smoothLines true squareMesh false meshLighting false > color #1 medium blue > help depthcue No help found for 'depthcue' > help lighting > lighting soft > lighting soft > lighting full > lighting flat > lighting full > lighting flat > set silhouettes false > lighting soft > volume #1 style mesh smoothLines true squareMesh false meshLighting false > color #1 medium blue > lighting depthCue true > volume #1 style mesh smoothLines true squareMesh false meshLighting false > color #1 medium blue > lighting depthCue true Unknown command: depthcue start 0; depthcue end 0.5 > volume #1 style mesh smoothLines true squareMesh false meshLighting false > color #1 medium blue > lighting depthCue true Unknown command: depthcuestart 0; depthcueend 0.5 > volume #1 style mesh smoothLines true squareMesh false meshLighting false > color #1 medium blue > lighting depthCue true Unknown command: depthCueStart 0; depthCueEnd 0.5 > volume #1 style mesh smoothLines true squareMesh false meshLighting false > color #1 medium blue > lighting depthCue true depthCueStart 0 depthCueEnd 0.5 > volume #1 style mesh smoothLines true squareMesh false meshLighting false > color #1 medium blue > lighting depthCue true depthCueStart 0 depthCueEnd 0.1 > volume #1 style mesh smoothLines true squareMesh false meshLighting true > color #1 medium blue > lighting depthCue true depthCueStart 0 depthCueEnd 0.1 > volume #1 style mesh smoothLines true squareMesh false meshLighting true > color #1 medium blue > lighting depthCue true depthCueStart 0 depthCueEnd 1 > volume #1 style mesh smoothLines true squareMesh false meshLighting true > color #1 blue > lighting depthCue true depthCueStart 0 depthCueEnd 1 > lighting soft > lighting simple > lighting soft > help clip > clip near 10 far 10 Unknown command: reset > view cofr false > clip near 10 far 10 > toolshed show ""Side View"" > clip near 10 far -10 > view cofr false > clip near 10 far -10 > clip near 100 far -100 OpenGL version: 4.1 INTEL-12.4.7 OpenGL renderer: Intel(R) Iris(TM) Graphics 6100 OpenGL vendor: Intel Inc. File attachment: Screenshot 2017-05-26 10.23.18.png }}} [attachment:""Screenshot 2017-05-26 10.23.18.png""] " defect closed normal Graphics fixed Tom Goddard all ChimeraX