id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2068 Transparency retained when coloring 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 Hi, Not sure if this is a bug but it seems unexpected to me. If I define a color that has some degree of transparency (e.g. color name part_invisible 0,0,0,10), and use that to color a model, when I subsequently apply a color that doesn't have tranparency (e.g. a built in color like cornflower blue), the model retains the transparency from the first color. This is not how it worked in Chimera, and is not how I would expect it to work - is this the intended behavior? 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"" OpenGL version: 4.1 ATI-2.9.26 OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine OpenGL vendor: ATI Technologies Inc. }}} " defect closed normal Graphics not a bug all ChimeraX