id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2020 Clipping relative to center of rotation 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 Request: Allow near/far clipping relative to center of rotation. This is useful when viewing models in maps. I would like to be able to use a command like ""clip near -5 far 5 position cofr"" to clip the view to a 10Å slab centered on the center of rotation. Currently the only way to do this is to get the center of rotation and then specify it as xyz, which is not useful if one wants to use this command frequently. Particularly useful when using ""cofr centerofview on"". Also, I'm not sure whether this is a bug or as intended, but currently ""surface cap"" overrides the ""capfaces false"" option for mesh maps. So if I have a mesh map with ""capfaces false"", caps will still be shown where the map is clipped by the near clip plane if ""surface cap"" is on. Cheers Oli Log: > camera ortho > cofr centerOfView > alias crosshairs_on cofr centerofview showpivot 10,0.3 > alias crosshairs_off cofr centerofview showpivot false 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/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 > help repr No help found for 'repr' > style selAtoms stick Changed 141366 atom styles > color gold > color byhetero > 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 step 1, values float32 > hide #!2 models > show #!2 models > select #1 141366 atoms, 143964 bonds, 88 pseudobonds, 1 model selected > ui mousemode rightMode ""translate selected models"" > select #2 3 models selected > select #1 141366 atoms, 143964 bonds, 88 pseudobonds, 1 model selected > select #2 3 models selected > select #1 141366 atoms, 143964 bonds, 88 pseudobonds, 1 model selected Missing required ""in_map"" argument > help fitmap > fitmap #1 inMap #2 Fit molecule model_moved.pdb_modified.pdb (#1) to map 4cmc_apocam_combined_map.mrc (#2) using 141366 atoms average map value = 0.05699, steps = 72 shifted from previous position = 2.36 rotated from previous position = 0.00377 degrees atoms outside contour = 31542, contour level = 0.027623 Position of model_moved.pdb_modified.pdb (#1) relative to 4cmc_apocam_combined_map.mrc (#2) coordinates: Matrix rotation and translation 1.00000000 -0.00004257 -0.00004754 -4.92281485 0.00004257 1.00000000 0.00001579 -4.25131684 0.00004754 -0.00001579 1.00000000 -7.79360639 Axis -0.24017357 -0.72315004 0.64758835 Axis point 153166.35002518 0.00000000 -107547.54238915 Rotation angle (degrees) 0.00376671 Shift along axis -0.79037876 > fitmap #1 inMap #2 Fit molecule model_moved.pdb_modified.pdb (#1) to map 4cmc_apocam_combined_map.mrc (#2) using 141366 atoms average map value = 0.05699, steps = 28 shifted from previous position = 0.00903 rotated from previous position = 0.00113 degrees atoms outside contour = 31528, contour level = 0.027623 Position of model_moved.pdb_modified.pdb (#1) relative to 4cmc_apocam_combined_map.mrc (#2) coordinates: Matrix rotation and translation 1.00000000 -0.00002610 -0.00005001 -4.91848828 0.00002610 1.00000000 0.00000531 -4.24159143 0.00005001 -0.00000532 1.00000000 -7.79394133 Axis -0.09379795 -0.88262286 0.46062873 Axis point 161511.97918513 0.00000000 -97203.11576919 Rotation angle (degrees) 0.00324637 Shift along axis 0.61495636 > ~select Nothing selected > help volume > volume #2 squareMesh false meshLighting false > volume #2 squareMesh false meshLighting false twoSidedLighting false > volume #2 squareMesh false meshLighting false twoSidedLighting false capFaces false > volume #2 squareMesh false meshLighting false twoSidedLighting false capFaces false Unknown command: collor #2 #00000000cccc > color #2 #00000000cccc > help clip > help section No help found for 'section' > help slab No help found for 'slab' > clip near 10 far 10 clip far plane is in front of near plane > view orient cofr false > view cofr false > clip near 10 far -10 clip far plane is in front of near plane > view cofr false > clip near -10 far 10 > crosshairs_on > set subdivision 1 > lighting simple > volume #2 squareMesh false meshLighting false twoSidedLighting false capFaces false Unknown command: collor #2 #00000000cccc > volume #2 squareMesh false meshLighting false twoSidedLighting false capFaces false > surface cap false > set bgColor black > clip near -5 far 5 > help clip > clip near -5 far 5 > clip near -5 far 5 > clip near -5 far 5 > select clear > select clear > select clear > cofr Center of rotation: 272.96 307.4 234.91 center of view > select up Nothing selected Expected a keyword > cofr Center of rotation: 272.96 307.4 234.91 center of view Expected a keyword Invalid ""position"" argument: Expected 3 floats or object specifier > clip near -5 far 5 position 272.0, 307, 235 OpenGL version: 4.1 ATI-2.9.26 OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine OpenGL vendor: ATI Technologies Inc. }}} " enhancement closed normal General Controls fixed Elaine Meng all ChimeraX