id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1608 Problem reshowing volume series sitins07@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Linux-4.15.0-42-generic-x86_64-with-debian-buster-sid ChimeraX Version: 0.9 (2019-01-12) Description While several (5) volume series opened, also the corresponding bars are created, when you press hide in volume viewer on one of the series and move the bar (occasionaly) you cannot make visible the whole series again (tryed: press show in volume viewer, pressed show in checkbox in model panel on each volume in seriaes and the top one, tryed to move the series bar to animate, commands show #5 and show #5.4 (no error and no result)) Log: > toolshed show ""Density Map Toolbar"" UCSF ChimeraX version: 0.9 (2019-01-12) How to cite UCSF ChimeraX > open /home/vpetryc/cluster/projects/Tu/nch/MultiBody/128_nch_tc_shoulder_try2_less- translation/analyse_component001_bin0??.mrc vseries true Opened map series analyse_component001_bin001.mrc, 10 images, grid size 128,128,128, pixel 2.32, shown at level 0.0848, step 1, values float32 > open /home/vpetryc/cluster/projects/Tu/nch/MultiBody/128_nch_tc_shoulder_try2_less- translation/analyse_component002_bin0??.mrc vseries true Opened map series analyse_component002_bin001.mrc, 10 images, grid size 128,128,128, pixel 2.32, shown at level 0.0846, step 1, values float32 > vseries slider #2 > vseries slider #1 > open /home/vpetryc/cluster/projects/Tu/nch/MultiBody/128_nch_tc_shoulder_try2_less- translation/analyse_component003_bin0??.mrc vseries true Opened map series analyse_component003_bin001.mrc, 10 images, grid size 128,128,128, pixel 2.32, shown at level 0.0846, step 1, values float32 > vseries slider #3 > vseries slider #2 > close #1 #2 #3 > open /home/vpetryc/cluster/projects/Tu/nch/MultiBody/128_nch_tc_shoulder- tc_try1/analyse_component001_bin0??.mrc vseries true File not found: /home/vpetryc/cluster/projects/Tu/nch/MultiBody/128_nch_tc_shoulder- tc_try1/analyse_component001_bin0??.mrc > open /home/vpetryc/cluster/projects/Tu/nch/MultiBody/128_nch_tc_shoulder- tc_try1/analyse_component001_bin0??.mrc vseries true Opened map series analyse_component001_bin001.mrc, 10 images, grid size 128,128,128, pixel 2.32, shown at level 0.0848, step 1, values float32 > open /home/vpetryc/cluster/projects/Tu/nch/MultiBody/128_nch_tc_shoulder- tc_try1/analyse_component002_bin0??.mrc vseries true Opened map series analyse_component002_bin001.mrc, 10 images, grid size 128,128,128, pixel 2.32, shown at level 0.0849, step 1, values float32 > open /home/vpetryc/cluster/projects/Tu/nch/MultiBody/128_nch_tc_shoulder- tc_try1/analyse_component003_bin0??.mrc vseries true Opened map series analyse_component003_bin001.mrc, 10 images, grid size 128,128,128, pixel 2.32, shown at level 0.0848, step 1, values float32 > open /home/vpetryc/cluster/projects/Tu/nch/MultiBody/128_nch_tc_shoulder- tc_try1/analyse_component004_bin0??.mrc vseries true Opened map series analyse_component004_bin001.mrc, 10 images, grid size 128,128,128, pixel 2.32, shown at level 0.0851, step 1, values float32 > open /home/vpetryc/cluster/projects/Tu/nch/MultiBody/128_nch_tc_shoulder- tc_try1/analyse_component005_bin0??.mrc vseries true Opened map series analyse_component005_bin001.mrc, 10 images, grid size 128,128,128, pixel 2.32, shown at level 0.0848, step 1, values float32 > vseries slider #1 > vseries slider #2 > vseries slider #3 > vseries slider #4 > vseries slider #5 > lighting full > lighting soft > lighting shadows true intensity 0.5 > lighting simple > open /home/vpetryc/Projects/nch/MultiBody/nc_272_focustc15A_10_5A_c3.mrc Opened nc_272_focustc15A_10_5A_c3.mrc, grid size 272,272,272, pixel 1.16, shown at level 0.04, step 2, values float32 > open /home/vpetryc/Projects/nch/MultiBody/nc_272_focustc15A_10_5A_c4.mrc Opened nc_272_focustc15A_10_5A_c4.mrc, grid size 272,272,272, pixel 1.16, shown at level 0.0404, step 2, values float32 > open /home/vpetryc/Projects/nch/MultiBody/nc_272_focustc15A_10_5A_c5.mrc Opened nc_272_focustc15A_10_5A_c5.mrc, grid size 272,272,272, pixel 1.16, shown at level 0.0423, step 2, values float32 > open /home/vpetryc/Projects/nch/MultiBody/nc_272_focustc15A_10_5A_c7.mrc Opened nc_272_focustc15A_10_5A_c7.mrc, grid size 272,272,272, pixel 1.16, shown at level 0.0421, step 2, values float32 > open /home/vpetryc/Projects/nch/MultiBody/nc_272_focustc15A_10_5A_c9.mrc Opened nc_272_focustc15A_10_5A_c9.mrc, grid size 272,272,272, pixel 1.16, shown at level 0.0425, step 2, values float32 > hide #!1 models > hide #!2 models > hide #!3 models > hide #!4 models > hide #!5 models > fitmap #7 inMap #1.1 Fit map nc_272_focustc15A_10_5A_c4.mrc in map analyse_component001_bin001.mrc using 218466 points correlation = 0.9515, correlation about mean = 0.6855, overlap = 319 steps = 72, shift = 16.3, angle = 2.01 degrees Position of nc_272_focustc15A_10_5A_c4.mrc (#7) relative to analyse_component001_bin001.mrc (#1.1) coordinates: Matrix rotation and translation 0.99995921 0.00219292 -0.00876129 -7.50359201 -0.00189548 0.99942634 0.03381417 -15.43997082 0.00883042 -0.03379619 0.99938973 -5.27926179 Axis -0.96612415 -0.25137832 -0.05842152 Axis point 0.00000000 -143.10042773 369.14516562 Rotation angle (degrees) 2.00521808 Shift along axis 11.43909791 > fitmap #10 inMap #1.1 Fit map nc_272_focustc15A_10_5A_c9.mrc in map analyse_component001_bin001.mrc using 155718 points correlation = 0.963, correlation about mean = 0.6286, overlap = 300.4 steps = 72, shift = 16.1, angle = 2.58 degrees Position of nc_272_focustc15A_10_5A_c9.mrc (#10) relative to analyse_component001_bin001.mrc (#1.1) coordinates: Matrix rotation and translation 0.99989321 -0.00665499 -0.01301076 -5.10385606 0.00720362 0.99906684 0.04258578 -18.15967105 0.01271521 -0.04267496 0.99900809 -4.42871403 Axis -0.94598307 -0.28543425 0.15376382 Axis point 0.00000000 -145.78086037 360.69240375 Rotation angle (degrees) 2.58288747 Shift along axis 9.33057760 > show #!1 models > vseries slider #1 > close #1 > open /home/vpetryc/cluster/projects/Tu/nch/MultiBody/128_nch_tc_shoulder- tc_try1/analyse_component001_bin0??.mrc vseries true Opened map series analyse_component001_bin001.mrc, 10 images, grid size 128,128,128, pixel 2.32, shown at level 0.0848, step 1, values float32 > vseries slider #1 > fitmap #9 inMap #1.1 Fit map nc_272_focustc15A_10_5A_c7.mrc in map analyse_component001_bin001.mrc using 173821 points correlation = 0.9572, correlation about mean = 0.632, overlap = 307.4 steps = 68, shift = 16.3, angle = 2.1 degrees Position of nc_272_focustc15A_10_5A_c7.mrc (#9) relative to analyse_component001_bin001.mrc (#1.1) coordinates: Matrix rotation and translation 0.99993117 0.00280089 -0.01139386 -7.12762886 -0.00240350 0.99939339 0.03474311 -15.38011241 0.01148426 -0.03471334 0.99933132 -5.59323082 Axis -0.94740521 -0.31206392 -0.07098932 Axis point 0.00000000 -143.10125947 332.85249817 Rotation angle (degrees) 2.10071307 Shift along axis 11.94939048 > close session > select up Nothing selected > open /home/vpetryc/cluster/projects/Tu/nch/MultiBody/128_nch_tc_arm_1/analyse_component001_bin0??.mrc vseries true Opened map series analyse_component001_bin001.mrc, 10 images, grid size 128,128,128, pixel 2.32, shown at level 0.0851, step 1, values float32 > close #1 > open /home/vpetryc/cluster/projects/Tu/nch/Refine3D/128_nch_tc_shoulder- tc_comp1_-11_-6/run_class001.mrc Opened run_class001.mrc, grid size 128,128,128, pixel 2.32, shown at level 0.0653, step 1, values float32 > open /home/vpetryc/cluster/projects/Tu/nch/MultiBody/128_nch_tc_shoulder_try2_less- translation/analyse_component001_bin0??.mrc vseries true Opened map series analyse_component001_bin001.mrc, 10 images, grid size 128,128,128, pixel 2.32, shown at level 0.0848, step 1, values float32 > open /home/vpetryc/cluster/projects/Tu/nch/MultiBody/128_nch_tc_shoulder_try2_less- translation/analyse_component001_bin0??.mrc vseries true Opened map series analyse_component001_bin001.mrc, 10 images, grid size 128,128,128, pixel 2.32, shown at level 0.0848, step 1, values float32 > open /home/vpetryc/cluster/projects/Tu/nch/Refine3D/128_nch_tc_shoulder- tc_comp1_5_10/run_it008_half2_class001.mrc Opened run_it008_half2_class001.mrc, grid size 128,128,128, pixel 2.32, shown at level 0.0521, step 1, values float32 > close #1 > close #2 > close #3 > close #4 > open /home/vpetryc/cluster/projects/Tu/nch/MultiBody/128_nch_tc_shoulder- tc_try2-fixed_body/analyse_component001_bin0??.mrc vseries true Opened map series analyse_component001_bin001.mrc, 10 images, grid size 128,128,128, pixel 2.32, shown at level 0.0841, step 1, values float32 > open /home/vpetryc/cluster/projects/Tu/nch/MultiBody/128_nch_tc_shoulder- tc_try2-fixed_body/analyse_component002_bin0??.mrc vseries true Opened map series analyse_component002_bin001.mrc, 10 images, grid size 128,128,128, pixel 2.32, shown at level 0.0844, step 1, values float32 > show #!2.9 models > hide #!2 models > show #!2.1 models > hide #!2.10 models > show #!2.10 models > vseries slider #1 > vseries slider #2 > show #!2.10 models > hide #!2.8 models > hide #!2 models > show #!2 models > close #2 > hide #!1.10 models > close #1 > open /home/vpetryc/cluster/projects/Tu/nch/MultiBody/128_nch_tc_shoulder- tc_try2-fixed_body/analyse_component001_bin0??.mrc vseries true Opened map series analyse_component001_bin001.mrc, 10 images, grid size 128,128,128, pixel 2.32, shown at level 0.0841, step 1, values float32 > open /home/vpetryc/cluster/projects/Tu/nch/MultiBody/128_nch_tc_shoulder- tc_try2-fixed_body/analyse_component002_bin0??.mrc vseries true Opened map series analyse_component002_bin001.mrc, 10 images, grid size 128,128,128, pixel 2.32, shown at level 0.0844, step 1, values float32 > vseries slider #1 > vseries slider #2 > open /home/vpetryc/cluster/projects/Tu/nch/MultiBody/128_nch_tc_shoulder- tc_try2-fixed_body/analyse_component003_bin0??.mrc vseries true Opened map series analyse_component003_bin001.mrc, 10 images, grid size 128,128,128, pixel 2.32, shown at level 0.0841, step 1, values float32 > vseries slider #3 > close #1 > close #2 > close #3 > select up Nothing selected > select up Nothing selected > open /home/vpetryc/cluster/projects/Tu/nch/MultiBody/128_nch_tc_arm_2-fixed/analyse_component001_bin0??.mrc vseries true File not found: /home/vpetryc/cluster/projects/Tu/nch/MultiBody/128_nch_tc_arm_2-fixed/analyse_component001_bin0??.mrc > open /home/vpetryc/cluster/projects/Tu/nch/MultiBody/128_nch_tc_arm_2-fixed/analyse_component001_bin0??.mrc vseries true Opened map series analyse_component001_bin001.mrc, 10 images, grid size 128,128,128, pixel 2.32, shown at level 0.0846, step 1, values float32 > open /home/vpetryc/cluster/projects/Tu/nch/MultiBody/128_nch_tc_arm_2-fixed/analyse_component002_bin0??.mrc vseries true Opened map series analyse_component002_bin001.mrc, 10 images, grid size 128,128,128, pixel 2.32, shown at level 0.0851, step 1, values float32 > open /home/vpetryc/cluster/projects/Tu/nch/MultiBody/128_nch_tc_arm_2-fixed/analyse_component003_bin0??.mrc vseries true Opened map series analyse_component003_bin001.mrc, 10 images, grid size 128,128,128, pixel 2.32, shown at level 0.0849, step 1, values float32 > open /home/vpetryc/cluster/projects/Tu/nch/MultiBody/128_nch_tc_arm_2-fixed/analyse_component004_bin0??.mrc vseries true Opened map series analyse_component004_bin001.mrc, 10 images, grid size 128,128,128, pixel 2.32, shown at level 0.0853, step 1, values float32 > open /home/vpetryc/cluster/projects/Tu/nch/MultiBody/128_nch_tc_arm_2-fixed/analyse_component005_bin0??.mrc vseries true Opened map series analyse_component005_bin001.mrc, 10 images, grid size 128,128,128, pixel 2.32, shown at level 0.0868, step 1, values float32 > vseries slider #1 > vseries slider #2 > vseries slider #3 > vseries slider #4 > vseries slider #5 > show #!5.1 models > hide #!5.2 models > show #!5.2 models > hide #!5 models > show #!5 models > show #!5.3 models > show #!5.4 models > show #!5.10 models > show #!5.9 models > show #!5.8 models > show #!5.7 models > show #!5.6 models > hide #!5 models > show #!5 models > show #5 > show #5 > show #5.4 OpenGL version: 3.3.0 NVIDIA 390.87 OpenGL renderer: Quadro 2000/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation }}} " defect closed normal Volume Data can't reproduce all ChimeraX