id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2103 Solo blobs olibclarke@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Darwin-18.6.0-x86_64-i386-64bit ChimeraX Version: 0.91 (2019-06-18) Description Hi, I love the new Measure and Color blobs tool! One suggestion - would it be possible to add an option to unshow the rest of the map, and just show that blob? Or to create a new surface model from that blob? This would be useful when showing for example ligand density in the context of a structure. Cheers Oli Log: > camera ortho > cofr centerOfView > 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; disp; 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; disp; 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 > alias symclip clip near -$1 far $1 position cofr > alias section clip near $1 far $1 UCSF ChimeraX version: 0.91 (2019-06-18) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/oliverclarke/Desktop/test4.cxs opened ChimeraX session > crosshairs_on crosshairs_on: displays crosshairs at center of rotation and places cofr at center of view > section 1 > section 1 > section 1 > section 1 > section -1 > section -1 > section -1 > section -1 > section -1 > select up 2 atoms, 1 bond, 1 model selected > select up 6 atoms, 5 bonds, 1 model selected > select up 38 atoms, 37 bonds, 1 model selected > select up 1161 atoms, 1169 bonds, 1 model selected > select up 148348 atoms, 151612 bonds, 1 model selected > select up 148348 atoms, 151612 bonds, 3 models selected > select up 148348 atoms, 151612 bonds, 3 models selected > select up 148348 atoms, 151612 bonds, 3 models selected > select down 148348 atoms, 151612 bonds, 1 model selected > select down 1161 atoms, 1169 bonds, 1 model selected > select down 38 atoms, 37 bonds, 1 model selected > select down 6 atoms, 5 bonds, 1 model selected > select down 2 atoms, 1 bond, 1 model selected > select down 1 bond, 1 model selected > select up 2 atoms, 1 bond, 1 model selected > select /I:805@N 1 atom, 1 model selected > crosshairs_on crosshairs_on: displays crosshairs at center of rotation and places cofr at center of view > section -10 > section -10 > section -10 > focus > symclip 10 > focus > rainbow chains > hide #!2 models > symclip 20 > show #!2 models > symclip 4 > focus > symclip 10 > symclip 100 > ui mousemode rightMode ""pick blobs"" > measure blob #!2.1 triangleNumber 659486 color #0000ccff outline true Surface best_new_4cmc_combined_pixcorr.mrc #2.1 blob: volume = 560.19 area = 979.72 size = 44.819 14.785 12.425 > measure blob #!2.1 triangleNumber 660376 color #2e5de9ff outline true Surface best_new_4cmc_combined_pixcorr.mrc #2.1 blob: volume = 560.19 area = 979.72 size = 44.819 14.785 12.425 > measure blob #!2.1 triangleNumber 660376 color #8f86a3ff outline true Surface best_new_4cmc_combined_pixcorr.mrc #2.1 blob: volume = 560.19 area = 979.72 size = 44.819 14.785 12.425 > measure blob #!2.1 triangleNumber 660376 color #972ec8ff outline true Surface best_new_4cmc_combined_pixcorr.mrc #2.1 blob: volume = 560.19 area = 979.72 size = 44.819 14.785 12.425 > measure blob #!2.1 triangleNumber 660376 color #236fe3ff outline true Surface best_new_4cmc_combined_pixcorr.mrc #2.1 blob: volume = 560.19 area = 979.72 size = 44.819 14.785 12.425 > measure blob #!2.1 triangleNumber 660376 color #08e968ff outline true Surface best_new_4cmc_combined_pixcorr.mrc #2.1 blob: volume = 560.19 area = 979.72 size = 44.819 14.785 12.425 > hide #!2.2 models > hide #!2.3 models > hide #!2.4 models > hide #!2.5 models > hide #!2.6 models > hide #!2.7 models > hide #!2.1 models > show #!2.1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > measure blob #!2.1 triangleNumber 138095 color #d8841bff outline true Surface best_new_4cmc_combined_pixcorr.mrc #2.1 blob: volume = 752.03 area = 1173.2 size = 40.009 14.134 12.121 > measure blob #!2.1 triangleNumber 195267 color #8cd31cff outline true Surface best_new_4cmc_combined_pixcorr.mrc #2.1 blob: volume = 60.835 area = 100.5 size = 8.8515 7.133 2.5093 > measure blob #!2.1 triangleNumber 130370 color #831dd9ff outline true Surface best_new_4cmc_combined_pixcorr.mrc #2.1 blob: volume = 3184.4 area = 5100.3 size = 83.011 31.912 26.701 > select #2 3 models selected > select clear OpenGL version: 4.1 ATI-2.9.26 OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine OpenGL vendor: ATI Technologies Inc. }}} " enhancement assigned normal Volume Data a.rohou@… all ChimeraX