id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2069 Two-way depth cueing olibclarke@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Darwin-18.6.0-x86_64-i386-64bit ChimeraX Version: 0.91 (2019-06-13) Description Feature request: Two depth cue ramps to acheive center-focused lighting. Rationale: Currently, when using depth cueing, depth cue shading increases linearly from start to end. Everything in front of depthcuestart is at maximum brightness. This is undesirable (IMO) when making figures with mesh maps and models, where more pleasing results can be obtained by having maximum brightness at the focus position, with items in both the foreground and background falling off in brightness. This helps reduce the appearance of small bits of clipped map/model in the foreground distracting from the overall composition. This depth cueing model is used in Coot (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2852313/ ; section 3.3). In ChimeraX, this might be acheived by adding a second depth cueing ramp, which ramps up in brightness (rather than down) from start to end, and which would be off by default. Cheers Oli Log: > camera ortho > cofr centerOfView > volume voxelLimit 100000 showPlane false limitVoxelCount false voxelLimitForOpen 10000 > alias crosshairs_on log text crosshairs_on: displays crosshairs at center of rotation and places cofr at center of view; cofr centerofview showpivot 5,0.2 > alias crosshairs_off cofr centerofview showpivot false > alias cootmode volume style mesh step 1 squaremesh false meshlighting true twosidedlighting false capfaces false; surface cap false; size stickradius 0.05; ~rib; color gold target a; color byhet; lighting flat; lighting depthcuestart 0.2 depthcueend 0.7; set silhouettes false; set subdivision 1; crosshairs_on; color #3333851effff target s; style stick; set bgcolor black > alias cootmode_white volume style mesh step 1 squaremesh false meshlighting true twosidedlighting false capfaces false; surface cap false; size stickradius 0.05; ~rib; color orange target a; color byhet; lighting flat; lighting depthcuestart 0.2 depthcueend 0.7; set silhouettes false; set subdivision 1; crosshairs_on; color #00000000cccc target s; style stick; set bgcolor white > alias carve surface zone #* nearatoms sel distance $1 maxcomponents 1 > alias uncarve surface unzone #* > alias focus view cofr false > alias saturation_down color modify $1 saturation - 10 > alias saturation_up color modify $1 saturation + 10 > alias lightness_up color modify $1 lightness + 5 > alias lightness_down color modify $1 lightness - 5 > alias hue_up color modify $1 hue + 5 > alias hue_down color modify $1 hue - 5 UCSF ChimeraX version: 0.91 (2019-06-13) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/oliverclarke/Dropbox/last_frame_rsr_ligands_real_space_refined_ss_annotated.pdb Chain information for last_frame_rsr_ligands_real_space_refined_ss_annotated.pdb #1 --- Chain | Description A B G I | No description available C D E K | No description available F H J O | No description available Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color name invisible 0,0,0,0 Color 'invisible' is 100% transparent, 0% red, 0% green, and 0% blue Expected one of 'default', 'flat', 'full', 'gentle', 'simple', or 'soft' or a keyword > help lighting > lighting depthCueColor invisible > select up Nothing selected > color name part_invisible 0,0,0,50 Color 'part_invisible' is 50% transparent, 0% red, 0% green, and 0% blue Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color #1 part_invisible > color ""cornflower blue"" > color name part_invisible 0,0,0,90 Color 'part_invisible' is 10% transparent, 0% red, 0% green, and 0% blue > color #1 part_invisible > color name part_invisible 0,0,0,10 Color 'part_invisible' is 90% transparent, 0% red, 0% green, and 0% blue > color #1 part_invisible > color ""cornflower blue"" > close all > open /Users/oliverclarke/Dropbox/best_new_4cmc_combined_pixcorr.mrc Opened best_new_4cmc_combined_pixcorr.mrc, grid size 512,512,512, pixel 1.06, shown at level 0.0133, step 2, values float32 > open /Users/oliverclarke/Dropbox/last_frame_rsr_ligands_real_space_refined_ss_annotated.pdb Chain information for last_frame_rsr_ligands_real_space_refined_ss_annotated.pdb #2 --- Chain | Description A B G I | No description available C D E K | No description available F H J O | No description available > cootmode Changed 151612 bond radii crosshairs_on: displays crosshairs at center of rotation and places cofr at center of view Changed 148348 atom styles > toolshed show ""Side View"" > help lighting > lighting depthCueStart 0.5 > lighting depthCueEnd 0 > lighting depthCueStart 0.5 > lighting depthCueEnd 0.7 OpenGL version: 4.1 ATI-2.9.26 OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine OpenGL vendor: ATI Technologies Inc. }}} " enhancement assigned normal Graphics all ChimeraX