id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2021 """cofr centerofview"" not honoring clip changes" olibclarke@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Darwin-18.6.0-x86_64-i386-64bit ChimeraX Version: 0.9 (2019-06-05) Description Bug: Center of rotation does not remain locked to the center of view when ""cofr centerofview"" is used. See screen recording: https://www.dropbox.com/s/dnoig3j3hoa2ivq/cofr_centerofview_bug.mov?dl=0 Basically, if I have cofr centerofview on, and then adjust the near/far clip planes, the cofr remains in its old position - even if I execute ""cofr centerofview on"" a second time. It should I think remain locked to the xy screen center, equidistant between the near/far clip planeswhen used in this mode. Cheers Oli Log: > camera ortho > cofr centerOfView > volume voxelLimit 100000 showPlane false limitVoxelCount false voxelLimitForOpen 10000 > alias crosshairs_on cofr centerofview showpivot 5,0.2 > alias crosshairs_off cofr centerofview showpivot false > alias cootmode volume style mesh 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 UCSF ChimeraX version: 0.9 (2019-06-05) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/oliverclarke/Dropbox/Downloads/4cmc_apocam_combined_map.mrc Opened 4cmc_apocam_combined_map.mrc, grid size 785,781,790, pixel 0.707,0.707,0.707, shown at level 0.0177, step 4, values float32 > 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 #2 --- Chain | Description A B G I | No description available F | No description available H J O | No description available > cootmode Changed 143964 bond radii Changed 141366 atom styles > select #2 141366 atoms, 143964 bonds, 88 pseudobonds, 1 model selected > ui mousemode rightMode ""translate selected models"" > fitmap #2 inMap #1 Fit molecule model_moved.pdb_modified.pdb (#2) to map 4cmc_apocam_combined_map.mrc (#1) using 141366 atoms average map value = 0.05699, steps = 52 shifted from previous position = 0.412 rotated from previous position = 0.00375 degrees atoms outside contour = 39682, contour level = 0.032805 Position of model_moved.pdb_modified.pdb (#2) relative to 4cmc_apocam_combined_map.mrc (#1) coordinates: Matrix rotation and translation 1.00000000 -0.00003598 -0.00005438 -4.92470927 0.00003598 1.00000000 0.00000632 -4.25555325 0.00005437 -0.00000632 1.00000000 -7.78825804 Axis -0.09646757 -0.83003535 0.54930440 Axis point 140494.43927345 0.00000000 -91055.00597494 Rotation angle (degrees) 0.00375341 Shift along axis -0.27079003 > select clear > toolshed show ""Side View"" > cofr centerOfView > crosshairs_on > cofr centerOfView showPivot 10,0.4 > cofr centerOfView showPivot 10,0.4 > view cofr false > cofr centerOfView showPivot 10,0.5 > cofr centerOfView showPivot 10,0.5 > cofr centerOfView showPivot 10,0.5 > help cofr > cofr centerOfView showPivot 10,0.5 > cofr centerOfView showPivot 10,0.5 OpenGL version: 4.1 ATI-2.9.26 OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine OpenGL vendor: ATI Technologies Inc. }}} " defect closed normal General Controls fixed Elaine Meng all ChimeraX