id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2028 """color modify"" not consistently reversible" olibclarke@… Greg Couch "{{{ The following bug report has been submitted: Platform: Darwin-18.6.0-x86_64-i386-64bit ChimeraX Version: 0.91 (2019-06-07) Description Hi, The ""color modify"" command behaves strangely: https://www.dropbox.com/s/s6wwakr5zs05l7h/color_adjust.mov?dl=0 I would expect that these commands should be reversible, but it doesn't seem to be the case. For example, if I run ""color modify sel whiteness 100"" on a thing that was previously cornflower blue, it turns white - so far so sensible. But if I then run ""color modify sel whiteness 1"", it turns red. This is unexpected. If I run ""color modify sel whiteness 1"" on something that is initially cornflower blue, it does not become red - just a darker blue. I guess this is because of the definition of the HWB scheme but it is a little counterintuitive. Also, repeated commands like ""color modify sel whiteness +5"" do not do anything - the first command modifies whiteness by the requested amount, but subsequent commands don't anything - presumably the reference whiteness value is not being updated, so it is still setting to +5 vs the original value, rather than the updated value? I really like this concept by the way, and it seems like the kind of functionality that would be well served by a future GUI panel with sliders for each kind of modification to apply to the selection. Cheers Oli Log: > camera ortho > cofr centerOfView > volume voxelLimit 100000 showPlane false limitVoxelCount false voxelLimitForOpen 10000 > alias crosshairs_on log text crosshairs_on: diaplays 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 UCSF ChimeraX version: 0.91 (2019-06-07) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/oliverclarke/Dropbox/Downloads/model_moved.pdb_modified.pdb Summary of feedback from opening /Users/oliverclarke/Dropbox/Downloads/model_moved.pdb_modified.pdb --- warnings | Duplicate atom serial number found: 819 Duplicate atom serial number found: 820 Duplicate atom serial number found: 821 Duplicate atom serial number found: 822 Duplicate atom serial number found: 823 103573 messages similar to the above omitted Chain information for model_moved.pdb_modified.pdb #1 --- Chain | Description A B G I | No description available F | No description available H J O | No description available > crosshairs_on crosshairs_on: diaplays crosshairs at center of rotation and places cofr at center of view > lighting simple > lighting full > lighting soft > set subdivision 10 > set subdivision 1 > cofr frontCenter > select /A:4871@CB 1 atom, 1 model selected > select up 9 atoms, 8 bonds, 1 model selected > style stick Changed 141366 atom styles > select up 4 atoms, 2 bonds, 1 model selected > select up 26 atoms, 26 bonds, 1 model selected > select up 347 atoms, 356 bonds, 1 model selected > cofr centerOfView showPivot 10,0.5 > color modify sel whiteness 50 > select clear > select /A:4174@CZ 1 atom, 1 model selected > select up 2 atoms, 1 bond, 1 model selected > select up 8 atoms, 7 bonds, 1 model selected > color modify sel whiteness +5 > color modify sel whiteness -5 > color modify sel whiteness -5 > color modify sel whiteness -5 > color modify sel whiteness -5 > color modify sel whiteness -5 > color modify sel whiteness -5 > color modify sel whiteness -5 > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness 50 > color modify sel whiteness 50 > color modify sel whiteness 50 > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness +1 > color modify sel whiteness +0.5 > color modify sel whiteness -0.5 > select /G:4075@CD 1 atom, 1 model selected > select up 9 atoms, 8 bonds, 1 model selected > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness -5 > color modify sel whiteness 50 > color modify sel whiteness 980 > color modify sel whiteness 1000 > color modify sel whiteness 1000 > color modify sel whiteness 1000 > color modify sel whiteness 100 > color modify sel whiteness 10 > color modify sel whiteness 10 > color modify sel whiteness 1 > color modify sel whiteness 4 > color modify sel whiteness 6 > select /I:4541@CD2 1 atom, 1 model selected > select up 14 atoms, 15 bonds, 1 model selected > color modify sel whiteness 6 > color modify sel whiteness 6 > color modify sel whiteness 6 > color modify sel whiteness 6 > color modify sel whiteness 6 > color modify sel whiteness 6 > color modify sel whiteness 1 > color modify sel whiteness 10 > color modify sel whiteness 10000 > color modify sel whiteness 1000000 > color modify sel whiteness 11 > color modify sel whiteness 1 > close all > open 1bl8 1bl8 title: Potassium channel (KCSA) from streptomyces lividans [more info...] Chain information for 1bl8 #1 --- Chain | Description A B C D | protein (potassium channel protein) > color ""cornflower blue"" > crosshairs_off > select 2824 atoms, 2896 bonds, 26 pseudobonds, 2 models selected > color modify sel whiteness 100 > color modify sel whiteness 1 > color modify sel whiteness 100 > color modify sel whiteness 1 > color modify sel whiteness 0.1 > color modify sel whiteness 0 > color ""cornflower blue"" > color modify sel whiteness 1 > color modify sel whiteness 0 > color modify sel whiteness 100 > color modify sel whiteness 1 > color ""cornflower blue"" > color modify sel whiteness 1 > color modify sel whiteness 100 > color modify sel whiteness 1 > color ""cornflower blue"" > color modify sel whiteness 1 > select clear > select /A:101 7 atoms, 6 bonds, 1 model selected > select up 188 atoms, 190 bonds, 1 model selected > color modify sel whiteness 1 > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness +50 > color modify sel whiteness +50 > color modify sel whiteness -50 > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness +5 > color modify sel whiteness +5 OpenGL version: 4.1 ATI-2.9.26 OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine OpenGL vendor: ATI Technologies Inc. }}} " defect closed normal Depiction not a bug Elaine Meng all ChimeraX