id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3270 Bfactor sharpening on resampled map olibclarke@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Darwin-19.4.0-x86_64-i386-64bit ChimeraX Version: 0.93 (2020-04-03) Description Hi, Not sure if this is a bug but it is unexpected behavior: The bfactor sharpening command (volume gaussian #map bfactor) when applied to any map that has been resampled on a finer grid than the original (e.g. volume resample #2 spacing 0.5), generates a cloud of fine points (see screenshot), whereas the same bfactor applied in the same way to the original map behaves as expected (generating a slightly sharper map). Cheers Oli Log: > camera ortho > cofr centerOfView > alias focus view cofr false > alias crosshair_on cofr centerofview showpivot true > alias crosshair_off cofr centerofview showpivot false > alias symclip clip near -$1 far $1 position cofr > alias cootmode_wire ~rib; disp; color gold; color byhet; size #* stickradius > 0.08; volume #* capfaces false style mesh meshlighting false squaremesh > false color #307fff step 1; surface cap false; lighting flat depthcue true > depthcuestart 0.2 depthcueend 1.0; graphics silhouettes false; set bgcolor > black; symclip 15 > alias cootmode_surf ~rib; disp; color gold; color byhet; size #* stickradius > 0.08; volume #* capfaces false style surface color #307fff3c step 1; surface > cap false; lighting flat depthcue true depthcuestart 0.2 depthcueend 1.0; > graphics silhouettes false; set bgcolor black; symclip 15 > alias cootmode_surf_white ~rib; disp; color orange red; color byhet; size #* > stickradius 0.08; volume #* capfaces false style surface color #002fff3d > step 1; surface cap false; lighting flat depthcue true depthcuestart 0.2 > depthcueend 1.0; graphics silhouettes false; set bgcolor white; symclip 15 UCSF ChimeraX version: 0.93 (2020-04-03) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/olibclarke1/Dropbox/chimera > models/oli_initial.updated_modified_real_space_refined.pdb"" format PDB Chain information for oli_initial.updated_modified_real_space_refined.pdb #1 --- Chain | Description B | No description available D | No description available > open ""/Users/olibclarke1/Dropbox/chimera > models/resolve_cryoem_2_b_blur_100.mrc"" format mrc Opened resolve_cryoem_2_b_blur_100.mrc, grid size 320,320,320, pixel 0.83, shown at level 0.0236, step 2, values float32 > cootmode_wire Changed 6192 bond radii > volume #2 level 0.1842 > symclip 3 > close all > open ""/Users/olibclarke1/Library/Application Support/ChimeraX/0.93/site- > packages/chimerax/isolde/demo_data/6out/6out.pdb"" 6out.pdb title: Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP asymmetric unit In T=3 symmetry [more info...] Chain information for 6out.pdb #1 --- Chain | Description A B C | capsid protein VP1 > open 20205 fromDatabase emdb Opened emd_20205.map, grid size 98,112,104, pixel 1.07,1.07,1.07, shown at level 0.287, step 1, values float32 > volume #2 level 0.174 > cootmode_wire Changed 11622 bond radii > symclip 3 > volume #2 level 0.1113 > volume resample #2 spacing 0.5 > cootmode_wire Changed 11622 bond radii > symclip 3 > symclip 5 > symclip 3 > lighting depthCueEnd 0.5 > lighting depthCueEnd 1 > lighting depthCueStart 0 > symclip 3 > volume #3 level 0.1306 Drag select of > ui mousemode rightMode clip > volume #3 level 0.1043 > volume #2 level 0.07989 > volume gaussian #2 bfactor -50 > volume #4 level 0.4006 > volume gaussian #3 bfactor -50 > focus OpenGL version: 4.1 ATI-3.8.24 OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine OpenGL vendor: ATI Technologies Inc. File attachment: Screenshot 2020-05-20 20.56.53.png }}} [attachment:""Screenshot 2020-05-20 20.56.53.png""] " defect closed normal Volume Data not a bug all ChimeraX