id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16405 MemoryError saving map in session chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.19045 ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open E:\\\DATA\\\IMAGE\\\KCNQ2_Blocker\\\Fig1\\\1104\\\Fig1-1105.cxs Opened 3_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc as #3, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 2_map_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc as #4, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 2_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 1 as #6.2, grid size 240,240,240, pixel 0.93, shown at level 0.008, step 1, values float32 Opened 2_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 2 as #6.3, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 2_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 3 as #6.4, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 2_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 4 as #6.5, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 1_map_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc as #7, grid size 240,240,240, pixel 0.93, shown at level 0.00768, step 1, values float32 Opened 2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 0 as #5.1, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 1 as #5.2, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 2 as #5.3, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 3 as #5.4, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc 1 as #11.2, grid size 240,240,240, pixel 0.93, shown at level 0.00768, step 1, values float32 Opened 1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc 2 as #11.3, grid size 240,240,240, pixel 0.93, shown at level 0.00768, step 1, values float32 Opened 1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc 3 as #11.4, grid size 240,240,240, pixel 0.93, shown at level 0.00768, step 1, values float32 Log from Tue Nov 5 12:59:07 2024UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open E:\\\DATA\\\IMAGE\\\KCNQ2_Blocker\\\Fig1\\\1104\\\Fig1-1104.cxs Opened 3_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc as #3, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 2_map_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc as #4, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 2_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 1 as #6.2, grid size 240,240,240, pixel 0.93, shown at level 0.008, step 1, values float32 Opened 2_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 2 as #6.3, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 2_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 3 as #6.4, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 2_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 4 as #6.5, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 1_map_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc as #7, grid size 240,240,240, pixel 0.93, shown at level 0.00768, step 1, values float32 Opened 2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 0 as #5.1, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 1 as #5.2, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 2 as #5.3, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 3 as #5.4, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc 1 as #11.2, grid size 240,240,240, pixel 0.93, shown at level 0.00768, step 1, values float32 Opened 1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc 2 as #11.3, grid size 240,240,240, pixel 0.93, shown at level 0.00768, step 1, values float32 Opened 1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc 3 as #11.4, grid size 240,240,240, pixel 0.93, shown at level 0.00768, step 1, values float32 Log from Mon Nov 4 16:06:22 2024UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open E:\\\DATA\\\IMAGE\\\KCNQ2_Blocker\\\Fig1\\\1031\\\Fig1-1103.cxs Opened 2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc as #3, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 1_map_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc as #4, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 1_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 1 as #6.2, grid size 240,240,240, pixel 0.93, shown at level 0.008, step 1, values float32 Opened 1_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 2 as #6.3, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 1_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 3 as #6.4, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 1_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 4 as #6.5, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 3_map_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc as #7, grid size 240,240,240, pixel 0.93, shown at level 0.00768, step 1, values float32 Opened 2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 0 as #5.1, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 1 as #5.2, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 2 as #5.3, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 3 as #5.4, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 3_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc 1 as #11.2, grid size 240,240,240, pixel 0.93, shown at level 0.00768, step 1, values float32 Opened 3_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc 2 as #11.3, grid size 240,240,240, pixel 0.93, shown at level 0.00768, step 1, values float32 Opened 3_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc 3 as #11.4, grid size 240,240,240, pixel 0.93, shown at level 0.00768, step 1, values float32 Log from Sun Nov 3 17:25:07 2024UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open E:\\\DATA\\\IMAGE\\\KCNQ2_Blocker\\\Fig1\\\Fig1-1031.cxs Opened 2_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc as #3, grid size 240,240,240, pixel 0.93, shown at step 1, values float32 Opened 1_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc as #4, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 2_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 1 as #5.2, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 2_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 2 as #5.3, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 2_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 3 as #5.4, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 1_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 1 as #6.2, grid size 240,240,240, pixel 0.93, shown at level 0.008, step 1, values float32 Opened 1_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 2 as #6.3, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 1_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 3 as #6.4, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 1_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 4 as #6.5, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 3_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc as #7, grid size 240,240,240, pixel 0.93, shown at level 0.00768, step 1, values float32 Log from Fri Nov 1 00:35:11 2024UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open E:\\\DATA\\\IMAGE\\\KCNQ2_Blocker\\\Fig1\\\Fig1.cxs Opened 2_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc as #3, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 1_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc as #4, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 2_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 1 as #5.2, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 2_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 2 as #5.3, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 2_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 3 as #5.4, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 1_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 1 as #6.2, grid size 240,240,240, pixel 0.93, shown at level 0.008, step 1, values float32 Opened 1_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 2 as #6.3, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 1_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 3 as #6.4, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 1_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 4 as #6.5, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Log from Tue Sep 10 17:05:02 2024 Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > E:/DataProcess_MODEL/data/KCNQ2_Blocker_structures_QingDao/0910_KCNQ2_CaM_XE991_closed_real_space_refined_006-1_real_space_refined_007.pdb > E:/DataProcess_MODEL/data/KCNQ2_Blocker_structures_QingDao/240910_KCNQ2_CaM_PIP2_XE991_open_real_space_refined_012-1.pdb Chain information for 0910_KCNQ2_CaM_XE991_closed_real_space_refined_006-1_real_space_refined_007.pdb #1 --- Chain | Description B C D E | No description available Chain information for 240910_KCNQ2_CaM_PIP2_XE991_open_real_space_refined_012-1.pdb #2 --- Chain | Description A B C D | No description available > ui tool show ""Color Actions"" > set bgColor white > close #1 > open > E:/DataProcess_MODEL/data/KCNQ2_Blocker_structures_QingDao/0910_KCNQ2_CaM_XE991_closed_real_space_refined_006-1_real_space_refined_007.pdb Summary of feedback from opening E:/DataProcess_MODEL/data/KCNQ2_Blocker_structures_QingDao/0910_KCNQ2_CaM_XE991_closed_real_space_refined_006-1_real_space_refined_007.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 ASN E 71 LEU E 85 1 15 Start residue of secondary structure not found: HELIX 2 2 TRP E 91 THR E 114 5 24 Start residue of secondary structure not found: HELIX 3 3 GLU E 119 GLY E 149 1 31 Start residue of secondary structure not found: HELIX 4 4 CYS E 152 TYR E 154 5 3 Start residue of secondary structure not found: HELIX 5 5 GLY E 156 ALA E 164 1 9 18 messages similar to the above omitted Chain information for 0910_KCNQ2_CaM_XE991_closed_real_space_refined_006-1_real_space_refined_007.pdb #1 --- Chain | Description A B C D | No description available > dssp > cartoon style width 1.15 thickness 0.3 > setattr b radius 0.27 Assigning radius attribute to 43446 items > hide #1.1 models > hide #2.1 models > hide #!2 models > show #!2 models > select #1 /A-D:1042-1148 3396 atoms, 3432 bonds, 428 residues, 1 model selected > select #1 /A-D:1006-1148 4504 atoms, 4552 bonds, 572 residues, 1 model selected > color sel #b48a76 > select #1 /A-D:1006-1148 #2 /A-D:1006-1148 13020 atoms, 13116 bonds, 1144 residues, 2 models selected > select up 13684 atoms, 13776 bonds, 1172 residues, 2 models selected > select up 19512 atoms, 19652 bonds, 1640 residues, 2 models selected > select down 13684 atoms, 13776 bonds, 1172 residues, 2 models selected > select down 13020 atoms, 13116 bonds, 1144 residues, 2 models selected > select #1 /A-D:1006-1148 #2 /A-D:1006-1148 13020 atoms, 13116 bonds, 1144 residues, 2 models selected > color sel #b48a76 > color sel #a86965 > select clear > color sel #b48a76 > color sel #a86965 > color sel #b48a76 > color sel #b88884 > color sel #b48a76 [Repeated 1 time(s)] > color sel #928178 > color sel #a99e93 > select clear > select #1 /A-D:70-600 10732 atoms, 10996 bonds, 8 pseudobonds, 1316 residues, 2 models selected > color sel #00a3af > select clear > hide #!2 models > select #1 /A-D:70-600 10732 atoms, 10996 bonds, 8 pseudobonds, 1316 residues, 2 models selected > color sel #83ccd2 > select clear > lighting soft > graphics silhouettes true > graphics silhouettes false > lighting flat [Repeated 1 time(s)] > lighting full > lighting simple > lighting soft > lighting full > lighting flat [Repeated 1 time(s)] > lighting full > lighting shadows false > lighting soft > lighting simple > graphics silhouettes false > select #1 /A-D:70-600 10732 atoms, 10996 bonds, 8 pseudobonds, 1316 residues, 2 models selected > color sel #7997b4 > select clear > hide #!1 models > show #!2 models > select #2 /A-D:70-600 18576 atoms, 18864 bonds, 8 pseudobonds, 1436 residues, 2 models selected > color sel #97b479 > select clear > show #!1 models > hide #!1 models > select #1 /A-D:1006-1148 #2 /A-D:1006-1148 13020 atoms, 13116 bonds, 1144 residues, 2 models selected > color sel #b49679 > select clear > show #!1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > hide #!1 models > show #!2 models > select clear [Repeated 1 time(s)] > select #2/X:1201@O08 1 atom, 1 residue, 1 model selected > select up 49 atoms, 53 bonds, 1 residue, 1 model selected > select up 27505 atoms, 27845 bonds, 2013 residues, 1 model selected > select down 49 atoms, 53 bonds, 1 residue, 1 model selected > color sel ##b4797a Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color sel #b4797a > color sel orange red > select clear > show #!1 models > hide #!2 models > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 49 atoms, 53 bonds, 1 residue, 1 model selected > color sel yellow > color sel orange > ui tool show ""Color Actions"" > set bgColor gold > set bgColor #ffd70000 > undo > set bgColor white > set bgColor #ffffff00 > color sel gold target acspfl [Repeated 2 time(s)] > select clear > hide #!1 models > show #!2 models > hide #!2 models > show #!1 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > open > E:/DataProcess_MODEL/data/KCNQ2_Blocker_structures_QingDao/2_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc Opened 2_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc as #3, grid size 240,240,240, pixel 0.93, shown at level 0.00801, step 1, values float32 > open > E:/DataProcess_MODEL/data/KCNQ2_Blocker_structures_QingDao/1_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc Opened 1_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc as #4, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!4 models > volume #3 level 0.0078 > hide #!4 models > surface dust #3 size 9.3 > show #!4 models > hide #!3 models > surface dust #4 size 9.3 > hide #!4 models > volume #3 level 0.0075 > surface dust #3 size 9.3 > volume #3 level 0.0078 > ui tool show ""Color Zone"" > color zone #3 near #1 distance 3.5 > surface dust #3 size 9.3 > surface dust #3 size 5 > surface dust #3 size 3 > surface dust #3 size 2.5 > surface dust #3 size 5 > surface dust #4 size 5 > volume splitbyzone #3 Opened 2_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 0 as #5.1, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 2_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 1 as #5.2, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 2_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 2 as #5.3, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 2_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 3 as #5.4, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 > close #5.1 > surface dust #3 size 4.5 > surface dust #5.3 size 5 > surface dust #5.2 size 9.3 > surface dust #5.3 size 9.3 > surface dust #5.4 size 9.3 > surface dust size 5 Missing or invalid ""surfaces"" argument: invalid surfaces specifier > surface dust #5 size 5 > select clear > show #!2 models > hide #!1 models > show #!4 models > hide #!5 models > hide #!2 models > show #!2 models > color zone #4 near #2 distance 3.5 > color #4 #bcbcbcff models > hide #!4 models > select ::name=""PIO"" 364 atoms, 364 bonds, 4 residues, 1 model selected > show sel atoms > hide H [Repeated 1 time(s)] > color sel hot pink > color sel #b47997 > color sel hot pink > ui tool show ""Color Actions"" > color sel cornflower blue target acspfl > color sel dark turquoise target acspfl > color sel medium aquamarine target acspfl > color sel medium turquoise target acspfl > color sel turquoise target acspfl > color sel cyan target acspfl > color sel dark orange target acspfl > color sel orange target acspfl [Repeated 2 time(s)] > show #!1 models > hide #!1 models > color sel #a69425 > color sel #c3d825 > color sel #d0576b > color sel #867ba9 > select clear > select #2/X:1201@C11 1 atom, 1 residue, 1 model selected > select up 49 atoms, 53 bonds, 1 residue, 1 model selected > select up 27505 atoms, 27845 bonds, 2013 residues, 1 model selected > select down 49 atoms, 53 bonds, 1 residue, 1 model selected > color sel orange > color sel orange red > select clear > show #!4 models > color zone #4 near #2 distance 3.5 > volume splitbyzone #4 Opened 1_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 0 as #6.1, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 1_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 1 as #6.2, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 1_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 2 as #6.3, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 1_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 3 as #6.4, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 1_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 4 as #6.5, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 > volume splitbyzone #4 Opened 1_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 0 as #7.1, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 1_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 1 as #7.2, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 1_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 2 as #7.3, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 1_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 3 as #7.4, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 1_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 4 as #7.5, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 > surface dust #6 size 5 > surface dust #7 size 5 > close #7.1 > undo > hide #!7 models > show #!7 models > hide #!6 models > hide #!7 models > show #!6 models > hide #!6 models > show #!5 models > hide #!5 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!7 models > hide #!7 models > show #!7 models > close #7 > hide #!6.2 models > show #!6.2 models > hide #!6.1 models > close #6.1 > save E:/DATA/IMAGE/KCNQ2_Blocker/Fig1/Fig1.cxs > hide #!6 models > show #!6 models > hide #!6 models > hide #!2 atoms > show #!1 models > hide atoms > select ::name=""LIG"" 98 atoms, 106 bonds, 2 residues, 2 models selected > show sel atoms > select ::name=""PIO"" 364 atoms, 364 bonds, 4 residues, 1 model selected > show sel atoms > select clear > hide H > select clear > hide #!2 models > hide #!1 models > show #!5 models > hide #!5 models > show #!6 models > hide #!6 models > show #!1 models > view [Repeated 1 time(s)] > show #!2 models > hide #!1 models > view > show #!1 models > hide #!2 models > view [Repeated 4 time(s)] > show #!2 models > view orient > hide #!2 models > turn x 90 [Repeated 2 time(s)] > turn y 5 [Repeated 10 time(s)] > view orient > turn x 90 [Repeated 2 time(s)] > turn y 5 [Repeated 12 time(s)] > turn y -5 [Repeated 3 time(s)] > turn y 5 > view name side1 > show #!2 models > hide #!1 models > turn y -5 [Repeated 1 time(s)] > turn y 5 [Repeated 2 time(s)] > turn y -5 > view name side1 > show #!1 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!1 models > view side1 [Repeated 1 time(s)] > show #!1 models > hide #!2 models > show #!2 models > hide #!2 models > ui tool show ""Side View"" > view name side1 > view name side2 > viewside2 Unknown command: viewside2 > view side1 > turn y 5 [Repeated 2 time(s)] > turn y -5 [Repeated 1 time(s)] > view name side1 > view name side2 [Repeated 1 time(s)] > show #!2 models > hide #!1 models > show #!1 models > hide #!1 models > hide #!2 models > show #!4 models > hide #!4 models > show #!5 models > hide #!5 models > show #!5 models > show #!6 models > hide #!5 models > lighting soft > show #!5 models > hide #!6 models > show #!6 models > lighting simple > hide #!6 models > hide #!5 models > show #!6 models > show #!5 models > hide #!5 models > show #!5 models > hide #!6 models > lighting soft > color #5.2 yellow models > lighting simple > lighting soft > lighting full > lighting soft > graphics silhouettes true > graphics silhouettes false > lighting simple [Repeated 1 time(s)] > lighting soft > save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\Q2_XE991_C_sideview_map.tif width 3000 > height 3000 transparentBackground true > view > save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\Q2_XE991_C_sideview_map.tif width 3000 > height 3000 transparentBackground true > hide #!5 models > show #!5 models > show #!6 models > hide #!5 models > lighting soft > lighting simple > lighting soft > lighting simple > lighting soft > lighting simple > lighting full > save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\Q2_XE991_O_sideview_map.tif width 3000 > height 3000 transparentBackground true [Repeated 1 time(s)] > show #!5 models > hide #!6 models > lighting full > save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\Q2_XE991_C_sideview_map.tif width 3000 > height 3000 transparentBackground true > hide #!5 models > show #!1 models > lighting simple > view > show #!2 models > show #!5 models > hide #!5 models > view > view name side1 > hide #!2 models > select clear [Repeated 1 time(s)] > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 49 atoms, 53 bonds, 1 residue, 1 model selected > color sel byhetero > select clear > save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\Q2_XE991_C_sideview_pdb.tif width 3000 > height 3000 transparentBackground true > hide #!1 models > show #!2 models > select ::name=""LIG"" 98 atoms, 106 bonds, 2 residues, 2 models selected > color sel & #!2 byhetero > select ::name=""PIO"" 364 atoms, 364 bonds, 4 residues, 1 model selected > color sel byhetero > select clear > save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\Q2_XE991_PIP2_O_sideview_pdb.tif width > 3000 height 3000 transparentBackground true > show #!1 models > view side2 > hide #!2 models > hide #!1 models > show #!2 models > save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\Q2_XE991_PIP2_O_sideview_pdb.tif width > 3000 height 3000 transparentBackground true > hide #!2 models > combine #1 > combine #2 > rename #7 gate-closed > rename #8 gate-open > cartoon style width 1.15 thickness 0. Invalid ""thickness"" argument: Must be greater than 0 > setattr b radius 0.27 Assigning radius attribute to 86892 items > setattr b radius 0.27 Assigning radius attribute to 86892 items > cartoon style width 1.15 thickness 0.3 > hide #7.1 models > hide #8.1 models > select clear > select ::name=""PIO"" 728 atoms, 728 bonds, 8 residues, 2 models selected > hide sel & #!8 atoms > select ::name=""LIG"" 196 atoms, 212 bonds, 4 residues, 4 models selected > hide sel & #!7-8 atoms > select clear > save E:/DATA/IMAGE/KCNQ2_Blocker/Fig1/Fig1.cxs includeMaps true > select #7 /A:305-325 158 atoms, 161 bonds, 21 residues, 1 model selected > select #7 /A:308-325 /C:308-325 #8 /A:308-325 /C:308-325 810 atoms, 818 bonds, 72 residues, 2 models selected > select ~sel 84770 atoms, 86066 bonds, 56 pseudobonds, 7732 residues, 28 models selected > hide sel & #!7-8 cartoons > select ~sel 810 atoms, 818 bonds, 72 residues, 2 models selected > turn y 5 [Repeated 5 time(s)] > turn y -5 > hide #!8 models > select clear > show #!8 models > hide #!7 models > show #!7 models > hide #!7 models > select #8/C:310 7 atoms, 6 bonds, 1 residue, 1 model selected > select #8/A:310 7 atoms, 6 bonds, 1 residue, 1 model selected > select clear > hide #!8 models > show #!8 models > show #!7 models > select #8/C:308 14 atoms, 14 bonds, 1 residue, 1 model selected > hide sel cartoons > select #7/C:308 7 atoms, 7 bonds, 1 residue, 1 model selected > hide sel cartoons > select clear > select #7 /A:308 /C:308 #8 /A:308 /C:308 42 atoms, 42 bonds, 4 residues, 2 models selected > hide sel cartoons > select clear > combine #7 #8 Remapping chain ID 'A' in gate-open #8 to 'E' Remapping chain ID 'B' in gate-open #8 to 'F' Remapping chain ID 'C' in gate-open #8 to 'G' Remapping chain ID 'D' in gate-open #8 to 'H' Remapping chain ID 'X' in gate-open #8 to 'Y' > cartoon style width 1.15 thickness 0.3 > setattr b radius 0.27 Assigning radius attribute to 130338 items > select clear > hide #!9 models > hide #!7 models > hide #!8 models > show #!8 models > show #!7 models > hide #!8 models > select #7/C:314 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 6 atom styles > color sel byhetero > select #7/A:314 6 atoms, 5 bonds, 1 residue, 1 model selected > color sel byhetero > show sel atoms > style sel stick Changed 6 atom styles > select #7/C:318 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select #7/A:318 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel byhetero > style sel stick Changed 8 atom styles > show sel atoms > select clear > view name gate1 > show #!8 models > hide #!7 models > view > show #!7 models > view name gate1 > hide #!7 models > show #!7 models > hide #!7 models > show #!9 models Drag select of 3 residues > select up 346 atoms, 354 bonds, 44 residues, 1 model selected > hide #!9 models > select clear > show #!9 models > hide #!9 models > select #8/C:314 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 11 atom styles > color sel byhetero > select #8/A:314 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 11 atom styles > select #8/C:318 19 atoms, 18 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 19 atom styles > select #8/A:318 19 atoms, 18 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 19 atom styles > color sel byhetero [Repeated 1 time(s)]Drag select of 12 atoms, 10 bonds, 12 residues > color sel byhetero > select clear > hide H > select clear > view gate1 > select clear > select #8/C:310 7 atoms, 6 bonds, 1 residue, 1 model selected > show #!9 models > hide #!8 models Drag select of 3 residues > select up 346 atoms, 354 bonds, 44 residues, 1 model selected > hide sel cartoons > select clear > select #9/G:310 7 atoms, 6 bonds, 1 residue, 1 model selected > select #9/G:310 /E:310 14 atoms, 12 bonds, 2 residues, 1 model selected > select ~sel 128356 atoms, 130322 bonds, 84 pseudobonds, 11704 residues, 30 models selected > hide sel & #!9 cartoons > show sel & #!9 atoms > undo > select clear Drag select of 2 residues > select clear Drag select of 2 residues > show sel atoms > hide sel cartoons > style sel stick Changed 14 atom styles > color sel byhetero > hide H > show #!8 models > select clear > save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\Q2_XE991_PIP2_O_side-gate.tif width > 3000 height 3000 transparentBackground true > show #!7 models > hide #!8 models > hide #!9 models > save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\Q2_XE991_C_side-gate.tif width 3000 > height 3000 transparentBackground true > show #!8 models > show #!9 models > save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\merge_side-gate-1.tif width 3000 > height 3000 transparentBackground true > save E:/DATA/IMAGE/KCNQ2_Blocker/Fig1/Fig1.cxs > hide #!7 models > show #!7 models > hide #!9 models > show #!9 models > combine #7 #8 #9 Remapping chain ID 'A' in gate-open #8 to 'E' Remapping chain ID 'B' in gate-open #8 to 'F' Remapping chain ID 'C' in gate-open #8 to 'G' Remapping chain ID 'D' in gate-open #8 to 'H' Remapping chain ID 'X' in gate-open #8 to 'Y' Remapping chain ID 'A' in combination #9 to 'I' Remapping chain ID 'B' in combination #9 to 'J' Remapping chain ID 'C' in combination #9 to 'K' Remapping chain ID 'D' in combination #9 to 'L' Remapping chain ID 'E' in combination #9 to 'M' Remapping chain ID 'F' in combination #9 to 'N' Remapping chain ID 'G' in combination #9 to 'O' Remapping chain ID 'H' in combination #9 to 'P' Remapping chain ID 'X' in combination #9 to 'Z' Remapping chain ID 'Y' in combination #9 to 'a' > hide #!9 models > hide #!8 models > hide #!7 models > setattr b radius 0.27 Assigning radius attribute to 217230 items > cartoon style width 1.15 thickness 0.3 > hide #!10 atoms > select clear > save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\merge_side-gate-1.tif width 3000 > height 3000 transparentBackground true > hide #!10 models > show #!9 models > show #!8 models > show #!7 models > save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\merge_side-gate-2.tif width 3000 > height 3000 transparentBackground true > save E:/DATA/IMAGE/KCNQ2_Blocker/Fig1/Fig1.cxs includeMaps true > hide #!9 models > hide #!8 models > hide #!7 models > show #!1 models > hide #!1 models > show #!6 models > view side1 > lighting full > surface dust #6.2 size 9.3 > surface dust #6.3 size 9.3 > surface dust #6.4 size 9.3 > surface dust #6.5 size 9.3 > surface dust #6.2 size 9.3 > surface dust #6.3 size 9.3 > surface dust #6.4 size 9.3 > surface dust #6.5 size 9.3 > surface dust #6.2 size 9.3 > surface dust #6.3 size 9.3 > surface dust #6.4 size 9.3 > surface dust #6.5 size 9.3 > surface dust #6 size 9 > surface dust #6.2 size 9 > surface dust #6.2 size 12 > surface dust #6.2 size 16 > surface dust #6.2 size 19 > surface dust #6.2 size 10 > surface dust #6.2 size 12 > volume #6.2 level 0.008 > volume #6.2 level 0.008996 > volume #6.2 level 0.008 > select clear > save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\Q2_XE991_PIP2_O_sideview_map.tif width > 3000 height 3000 transparentBackground true > save E:/DATA/IMAGE/KCNQ2_Blocker/Fig1/Fig1.cxs includeMaps true > show #!2 models > show #!1 models > hide #!6 models > hide #!2 models > show #!7 models > hide #!7 models > rename #9 gate-open-1 > rename #10 combination-gate > combine #1 > combine #2 > hide #11.1 models > hide #12.1 models > rename #11 vsd-closed > rename #12 vsd-open > lighting simple > hide #!11 models > hide #!12 models > show #!5 models > hide #!1 models > lighting flat [Repeated 1 time(s)] > lighting full > graphics silhouettes false > lighting soft > lighting simple > graphics silhouettes true > graphics silhouettes false > lighting soft > lighting simple > lighting soft > lighting full > lighting simple [Repeated 1 time(s)] > lighting soft > lighting full > lighting soft > show #!6 models > hide #!5 models > view side1 > show #!5 models > hide #!6 models > ui mousemode right clip > select #5.3 3 models selected > select clear > select #5.3 3 models selected > select clear > select #5.3 3 models selected > select clear > hide #!5 models > show #!5 models > view side1 > hide #!5.2 models > show #!5.2 models > hide #!5 models > show #!11 models > show #!12 models > cartoon style width 1.15 thickness 0.3 > lighting simple > select clear > hide #!11 models > show #!11 models > show #!11-12 surfaces > hide #!12 models > undo [Repeated 1 time(s)] > hide #!11-12 surfaces > select clear > hide #!12 models > select clear > show #!11 surfaces > hide #!11 surfaces > hide #!11 models > show #!11 models > show #!11 surfaces [Repeated 1 time(s)] > hide #!11 surfaces > show #!11 atoms > hide #!11 atoms > select ::name=""LIG"" 588 atoms, 636 bonds, 12 residues, 8 models selected > show sel & #!11 atoms > select clear > hide H > select clear > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > select #11 /A:119-212 #12 /A:119-212 1386 atoms, 1409 bonds, 2 pseudobonds, 173 residues, 4 models selected > show #!12 models > select #11 /A:119-212 #12 /A:119-212 1386 atoms, 1409 bonds, 2 pseudobonds, 173 residues, 4 models selected > select ~sel 255354 atoms, 259263 bonds, 166 pseudobonds, 23239 residues, 36 models selected > hide sel & #!11-12 cartoons > hide sel & #!11-12 atoms > select clear > matchmaker #11 #12 Missing required ""to"" argument > matchmaker #11 to #12 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker vsd-open, chain B (#12) with vsd-closed, chain D (#11), sequence alignment score = 2358.4 RMSD between 235 pruned atom pairs is 0.622 angstroms; (across all 472 pairs: 23.501) Drag select of 3 residues > undo [Repeated 3 time(s)] > close #11 > hide #!12 models > show #!12 models > close #12 > combine #1 #2 Remapping chain ID 'A' in 240910_KCNQ2_CaM_PIP2_XE991_open_real_space_refined_012-1.pdb #2 to 'E' Remapping chain ID 'B' in 240910_KCNQ2_CaM_PIP2_XE991_open_real_space_refined_012-1.pdb #2 to 'F' Remapping chain ID 'C' in 240910_KCNQ2_CaM_PIP2_XE991_open_real_space_refined_012-1.pdb #2 to 'G' Remapping chain ID 'D' in 240910_KCNQ2_CaM_PIP2_XE991_open_real_space_refined_012-1.pdb #2 to 'H' Remapping chain ID 'X' in 240910_KCNQ2_CaM_PIP2_XE991_open_real_space_refined_012-1.pdb #2 to 'Y' > select #10 /A:119-212 /E:119-212 1386 atoms, 1409 bonds, 2 pseudobonds, 173 residues, 2 models selected > select #11 /A:119-212 /E:119-212 1386 atoms, 1409 bonds, 2 pseudobonds, 173 residues, 2 models selected > select ~sel 255354 atoms, 259263 bonds, 166 pseudobonds, 23239 residues, 34 models selected > hide sel & #!11 cartoons > hide sel & #!11 atoms > cartoon style width 1.15 thickness 0.3 > setattr b radius 0.27 Assigning radius attribute to 260676 items > select clear > hide #11.1 models > rename #11 VSD > select #11/E:192 11 atoms, 11 bonds, 1 residue, 1 model selected > hide sel cartoons > select #11 /A:195-211 145 atoms, 145 bonds, 17 residues, 1 model selected > setattr sel res ss_id 999 Assigning ss_id attribute to 17 items > setattr sel res ss_type 1 Assigning ss_type attribute to 17 items > select clear > select #11 /A:198 201 Expected a keyword > select #11/E:200 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #11/E:204 17 atoms, 15 bonds, 2 residues, 1 model selected > select #11 /A:198 /A:201 /A:204 /A:207 /A:210 #11 /E:198 /A:201 /E:204 > /E:207 /E:210 95 atoms, 86 bonds, 9 residues, 1 model selected > show sel atoms > style sel stick Changed 95 atom styles > color sel byhetero > select clear > select #11 /A:137 /A:140 /A:172 #11 /E:137 /E:140 /E:172 56 atoms, 52 bonds, 6 residues, 1 model selected > show sel atoms > style sel stick Changed 56 atom styles > color sel byhetero > select clear > select #11/E:201 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 11 atom styles > color sel byhetero > select clear > view side1 > view > select clear > select #11/E:193 5 atoms, 4 bonds, 1 residue, 1 model selected > hide sel cartoons > select #11/E:194 7 atoms, 6 bonds, 1 residue, 1 model selected > hide sel cartoons > select clear > view VSD1 Expected an objects specifier or a view name or a keyword > view name VSD1 [Repeated 1 time(s)] > save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\VSD.tif width 3000 height 3000 > transparentBackground true > hide #!11 models > show #!11 models > hide #!11 models > show #!11 models > save E:/DATA/IMAGE/KCNQ2_Blocker/Fig1/Fig1.cxs includeMaps true ——— End of log from Tue Sep 10 17:05:02 2024 ——— opened ChimeraX session > show #!1 models > hide #!1 models > show #!2 models > hide #!2 models > rename #1 KCNQ2_XE991_closed > rename #2 KCNQ2_P_XE991_open > show #!2 models > hide #!2 models > show #!1 models > hide #!1 models > show #!3 models > hide #!3 models > show #!4 models > hide #!4 models > show #!3 models > hide #!3 models > show #!5 models > hide #!5 models > show #!6 models > show #!2 models > hide #!2 models > hide #!6 models > show #!7 models > hide #!7 models > close #7-9 > show #!10 models > hide #!10 models > hide #!11 models > close #10-11 > show #!1 models > hide #!1 models > rename #1 KCNQ2_XE991_PLL_closed > show #!2 models > view side1 > show #!1 models > hide #!2 models > hide #!1 models > show #!4 models > hide #!4 models > show #!3 models > hide #3.1 models > show #3.1 models > hide #3.1 models > rename #1 2_KCNQ2_XE991_PLL_closed > rename #2 1_KCNQ2_P_XE991_open > show #!5 models > hide #!5 models > save E:/DATA/IMAGE/KCNQ2_Blocker/Fig1/Fig1-1031.cxs includeMaps true > open > E:/DataProcess_MODEL/data/KCNQ2_Blocker_structures_QingDao/KCNQ2_Blocker_summary_0928/structures/XE991/3_KCNQ2_XE991_close/3_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc > E:/DataProcess_MODEL/data/KCNQ2_Blocker_structures_QingDao/KCNQ2_Blocker_summary_0928/structures/XE991/3_KCNQ2_XE991_close/KCNQ2_XE991_closed_real_space_refined_001.pdb Opened 3_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc as #7, grid size 240,240,240, pixel 0.93, shown at level 0.00768, step 1, values float32 Chain information for KCNQ2_XE991_closed_real_space_refined_001.pdb #8 --- Chain | Description A C D | No description available B | No description available > hide #!3 models > hide #!7 models > hide #!8 models > show #!8 models > close #1 > open > E:/DataProcess_MODEL/data/KCNQ2_Blocker_structures_QingDao/KCNQ2_Blocker_summary_0928/structures/XE991/2_KCNQ2_PIP2_XE991_PLL_close/2_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc Opened 2_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc as #1, grid size 240,240,240, pixel 0.93, shown at level 0.00801, step 1, values float32 > color #1 #779999ff models > color #1 #7997b4ff models > hide #!1 models > show #!1 models > close #1 > open > E:/DataProcess_MODEL/data/KCNQ2_Blocker_structures_QingDao/KCNQ2_Blocker_summary_0928/structures/XE991/2_KCNQ2_PIP2_XE991_PLL_close/KCNQ2_CaM_XE991_closed_real_space_refined_006-1.pdb Chain information for KCNQ2_CaM_XE991_closed_real_space_refined_006-1.pdb #1 --- Chain | Description B C D E | No description available > rename #1 KCNQ2_P_XE991_PLL_closed > hide #!8 models > hide #!1 models > close #1 > open > E:/DataProcess_MODEL/data/Q2_P_XE991_PLL/RealSpaceRefine_9/1020_KCNQ2_CaM_XE991_closed-1_real_space_refined_009.pdb Chain information for 1020_KCNQ2_CaM_XE991_closed-1_real_space_refined_009.pdb #1 --- Chain | Description A B C D | No description available > color #1 #779999ff > color #1 #7997b4ff > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 49 atoms, 53 bonds, 1 residue, 1 model selected > color sel orange > select clear [Repeated 2 time(s)] > select #1/C:1201@O08 1 atom, 1 residue, 1 model selected > select up 49 atoms, 53 bonds, 1 residue, 1 model selected > color sel orange red > show #!5 models > hide #!5 models > show #!6 models > hide #!6 models > show #!8 models > hide #!8 models > rename #1 2_KCNQ2_p_XE991_PLL_closed > rename #8 3_KCNQ2_XE991_closed > hide #!1 models > show #!1 models > show #!2 models > hide #!2 models > hide #!1 models > color #8 #bb4477ff > color #8 #b4797aff > show #!8 models > select #8 /A-D:1006-1149 1126 atoms, 1138 bonds, 143 residues, 1 model selected > select clear > show #!8 atoms > undo > show #!8 cartoons [Repeated 1 time(s)] > show #!7 models > hide #!7 models > select #8 /A-D:1006-1149 1126 atoms, 1138 bonds, 143 residues, 1 model selected > color sel #b49679 > select clear > close #8 > show #!1 models > show #!2 models > hide #!2 models > hide #1.1 models > select #1 /A-D:1006-1149 4504 atoms, 4552 bonds, 572 residues, 1 model selected > color > color sel #b49679 > select clear > hide #!1 atoms > select ::name=""LIG"" 98 atoms, 106 bonds, 2 residues, 2 models selected > show sel & #!1 atoms > hide H > select clear > select #1/B:564 7 atoms, 6 bonds, 1 residue, 1 model selected > select clear > select #1/C:1201@C16 1 atom, 1 residue, 1 model selected > select up 49 atoms, 53 bonds, 1 residue, 1 model selected > color sel byhetero > select clear > cartoon style width 1.15 thickness 0.3 > sdd Unknown command: sdd > setattr b radius 0.27 Assigning radius attribute to 43446 items > select clear > show #!2 models > hide #!2 models > hide #!1 models > show #!2 models > show #!1 models > hide #!2 models > hide #!1 models > show #!1 models > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 49 atoms, 53 bonds, 1 residue, 1 model selected > color sel yellow > color sel byhetero > select clear > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > view side2 > view side1 > turn x 90 > ui tool show ""Side View"" > hide #!1 models > show #!2 models > hide #!2 models > show #!1 models > hide #!1 models > show #!1 models > combine #1 > hide #!1 models > combine #2 > cartoon style width 1.15 thickness 0.3 > setattr b radius 0.27 Assigning radius attribute to 86892 items > hide #!8 models > hide #!9 models > show #!8 models > select #8/B 3809 atoms, 3887 bonds, 3 pseudobonds, 472 residues, 2 models selected > select ~sel 81771 atoms, 83005 bonds, 53 pseudobonds, 7332 residues, 30 models selected > undo [Repeated 1 time(s)] > select clear [Repeated 1 time(s)] > select #1 /B-D:70-700 8049 atoms, 8247 bonds, 6 pseudobonds, 987 residues, 2 models selected > select #8 /B-D:70-700 8049 atoms, 8247 bonds, 6 pseudobonds, 987 residues, 2 models selected > color (#!8 & sel) dark gray > select clear > select #8 /A 3809 atoms, 3887 bonds, 3 pseudobonds, 472 residues, 2 models selected > select ~sel 81771 atoms, 83005 bonds, 53 pseudobonds, 7332 residues, 30 models selected > color (#!8 & sel) light gray > select clear > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 49 atoms, 53 bonds, 1 residue, 1 model selected > color sel yellow > color sel byhetero > select clear > select #8 /A-D:1006-1149 4504 atoms, 4552 bonds, 572 residues, 1 model selected > hide sel cartoons > select clear [Repeated 1 time(s)] > view name top1 > show #!9 models > hide #!8 models > select #9 /A-D:1006-1149 8516 atoms, 8564 bonds, 572 residues, 1 model selected > hide sel cartoons [Repeated 1 time(s)] > select #9 /A- Expected a keyword > select #9 /A 6864 atoms, 6948 bonds, 4 pseudobonds, 503 residues, 2 models selected > select ~sel 78716 atoms, 79944 bonds, 52 pseudobonds, 7301 residues, 30 models selected > color (#!9 & sel) light gray > select clear > show #!8 models > hide #!8 models > select clear [Repeated 1 time(s)] > hide #!9 atoms > undo > select ::name=""PIO"" 728 atoms, 728 bonds, 8 residues, 2 models selected > hide sel & #!9 atoms > select clear [Repeated 1 time(s)] > select #9/X:1201@C15 1 atom, 1 residue, 1 model selected > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 49 atoms, 53 bonds, 1 residue, 1 model selected > color sel orange red > color sel byhetero > select clear > show #!8 models > hide #!9 models > save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\1031\2_Q2_P_XE991_PLL_top.tif width > 3000 height 3000 transparentBackground true > show #!9 models > hide #!8 models > rename #8 top_2_KCNQ2_p_XE991_PLL_closed > rename #9 top_1_KCNQ2_P_XE991_open > save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\1031\2_Q2_P_XE991_top.tif width 3000 > height 3000 transparentBackground true > save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\1031\1_Q2_P_XE991_top.tif width 3000 > height 3000 transparentBackground true > show #!1 models > hide #!9 models > view side1 > view side2 > save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\1031\2_Q2_P_XE991_PLL_side.tif width > 3000 height 3000 transparentBackground true > save E:/DATA/IMAGE/KCNQ2_Blocker/Fig1/Fig1-1031.cxs includeMaps true ——— End of log from Fri Nov 1 00:35:11 2024 ——— opened ChimeraX session > show #!7 models > hide #!7 models > show #!6 models > hide #!6 models > show #!4 models > hide #!4 models > show #!3 models > hide #!3 models > show #3.1 models > hide #3.1 models > show #3.1 models > hide #!3.1 models > show #!4 models > hide #!4 models > show #!5 models > hide #!5 models > hide #!3 models > show #!3 models > show #3.1 models > hide #!3.1 models > show #3.1 models > color #3.1 #bcbcbcff > color #3.1 #b2b2b2ff > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!5 models > hide #!5 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!5 models > hide #!5 models > hide #!5.3 models > show #!5.3 models > hide #!3.1 models > hide #!5 models > hide #!3 models > rename #3 > 2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc > rename #4 > 1_mapKCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc > rename #4 > 1_map_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc > show #!7 models > hide #!7 models > hide #!1 models > show #!7 models > save E:/DATA/IMAGE/KCNQ2_Blocker/Fig1/Fig1-1103.cxs includeMaps true [Repeated 1 time(s)] > show #!4 models > hide #!4 models > surface dust #7 size 9.3 > show #!2 models > hide #!2 models > show #!3 models > hide #!7 models > show #3.1 models > show #!1 models > ui tool show ""Color Zone"" > color zone #3 near #1 distance 3.5 > show #!5 models > hide #!5 models > hide #!3 models > show #!5 models > close #5 > hide #3.1 models > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 49 atoms, 53 bonds, 1 residue, 1 model selected > color sel yellow > show #!4 models > hide #!4 models > show #!3 models > show #3.1 models > color zone #3 near #1 distance 3.5 > color #3 #bcbcbcff models > color zone #3 near #1 distance 3.5 > volume splitbyzone #3 Opened 2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 0 as #5.1, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 1 as #5.2, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 2 as #5.3, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 3 as #5.4, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 > hide #!5.1 models > surface dust #5.2 size 9.3 > surface dust #5.3 size 9.3 > surface dust #5.4 size 9.3 > hide #!5 models > show #!5 models > select clear > close #5 > hide #!1 models > show #!1 models > show #!3 models > color zone #3 near #1 distance 3.5 > volume splitbyzone #3 Opened 2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 0 as #5.1, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 1 as #5.2, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 2 as #5.3, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 Opened 2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 3 as #5.4, grid size 240,240,240, pixel 0.93, shown at level 0.0078, step 1, values float32 > hide #!5.1 models > hide #!1 models > surface dust #5.2 size 9.3 > surface dust #5.3 size 9.3 > surface dust #5.4 size 9.3 > surface dust #5 size 5 > show #!6 models > hide #!6 models > hide #!5 models > show #!1 models > hide #!1 models > show #!2 models > hide #!2 models > rename #6 > ""1_KCNQ2_PIP2_XE991_map_open_3.14A_job119_B65_postprocess_resampled.mrc > split"" > rename #6 > ""1_map_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc > split"" > open > E:/DataProcess_MODEL/data/Q2_XE991/RealSpaceRefine_6/KCNQ2_XE991_close_real_space_refined_002-ABCD_real_space_refined_006.pdb Chain information for KCNQ2_XE991_close_real_space_refined_002-ABCD_real_space_refined_006.pdb #10 --- Chain | Description A B C D | No description available > cartoon style width 1.15 thickness 0.3 > setattr b radius 0.27 Assigning radius attribute to 102629 items > select clear > hide #10.1 models > hide #!10 atoms > select ::name=""LIG"" 245 atoms, 265 bonds, 5 residues, 5 models selected > show sel & #!10 atoms > select #10/C:151 6 atoms, 5 bonds, 1 residue, 1 model selected > hide H > select #10/C:1145 8 atoms, 7 bonds, 1 residue, 1 model selected > color #10 #B4797a > select clear > select #10 /A-D:1006-1149 4504 atoms, 4552 bonds, 572 residues, 1 model selected > color > color sel #b49679 > select #10 /A-D:1006-1149 4504 atoms, 4552 bonds, 572 residues, 1 model selected > color sel #b49679 > select clear > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > color sel tan > select #10 /A-D:1006-1149 4504 atoms, 4552 bonds, 572 residues, 1 model selected > color sel tan > show #!2 models > hide #!2 models > combine #1 > hide #!10 models > select #11/A:1018 6 atoms, 5 bonds, 1 residue, 1 model selected > select up 119 atoms, 121 bonds, 14 residues, 1 model selected > select up 1126 atoms, 1138 bonds, 143 residues, 1 model selected > select ~sel 115160 atoms, 117092 bonds, 79 pseudobonds, 11459 residues, 36 models selected > delete atoms (#!11 & sel) > delete bonds (#!11 & sel) > select clear > close #11 > show #!10 models > select #10 /A-D:1006-1149 4504 atoms, 4552 bonds, 572 residues, 1 model selected > color sel #b49679 > select clear > select #10/A:1201@O08 1 atom, 1 residue, 1 model selected > select up 49 atoms, 53 bonds, 1 residue, 1 model selected > select up 3892 atoms, 3974 bonds, 478 residues, 1 model selected > select down 49 atoms, 53 bonds, 1 residue, 1 model selected > color sel yellow > select clear > show #!7 models > hide #!7 models > color zone #7 near #10 distance 3.5 > show #!7 models > volume splitbyzone #7 Opened 3_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc 0 as #11.1, grid size 240,240,240, pixel 0.93, shown at level 0.00768, step 1, values float32 Opened 3_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc 1 as #11.2, grid size 240,240,240, pixel 0.93, shown at level 0.00768, step 1, values float32 Opened 3_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc 2 as #11.3, grid size 240,240,240, pixel 0.93, shown at level 0.00768, step 1, values float32 Opened 3_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc 3 as #11.4, grid size 240,240,240, pixel 0.93, shown at level 0.00768, step 1, values float32 > rename #10 > 3_KCNQ2_XE991_close_real_space_refined_002-ABCD_real_space_refined_006.pdb > close #11.1 > select clear > rename #5 > ""2_splitmap_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc > split"" > rename #6 > ""1_splitmap_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc > split"" > rename #11 > ""3_splitmapQ2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc split"" > rename #11 > ""3_splitmap_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc > split"" > rename #7 3_map_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc > hide #!10 models > surface dust #11.2 size 9.3 > surface dust #11.3 size 9.3 > surface dust #11.4 size 9.3 > surface dust #11 size 5 > lighting soft > view side2 > ui tool show ""Side View"" > lighting soft > view side2 [Repeated 1 time(s)] > save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\1031\3_Q2_XE991_sideview_map.tif width > 3000 height 3000 transparentBackground true > view side1 > save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\1031\3_Q2_XE991_sideview_map.tif width > 3000 height 3000 transparentBackground true > show #!10 models > hide #!11 models > lighting simple > select #10/A:1201@C15 1 atom, 1 residue, 1 model selected > select #10/A:1201@C15 1 atom, 1 residue, 1 model selected > select up 49 atoms, 53 bonds, 1 residue, 1 model selected > color sel byhetero > select clear > view side2 > save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\1031\3_Q2_XE991_sideview_pdb.tif width > 3000 height 3000 transparentBackground true > view top1 > select #10 /A-D:1006-1149 4504 atoms, 4552 bonds, 572 residues, 1 model selected > hide sel atoms > hide sel cartoons > select clear > select #10/C:157 14 atoms, 15 bonds, 1 residue, 1 model selected > select up 88 atoms, 90 bonds, 10 residues, 1 model selected > select up 951 atoms, 977 bonds, 115 residues, 1 model selected > select up 957 atoms, 982 bonds, 116 residues, 1 model selected > select up 2225 atoms, 2286 bonds, 273 residues, 1 model selected > select up 2229 atoms, 2289 bonds, 274 residues, 1 model selected > select up 2717 atoms, 2783 bonds, 334 residues, 1 model selected > select up 2724 atoms, 2789 bonds, 335 residues, 1 model selected > select up 3843 atoms, 3921 bonds, 477 residues, 1 model selected > select down 2724 atoms, 2789 bonds, 335 residues, 1 model selected > select down 2717 atoms, 2783 bonds, 334 residues, 1 model selected > select down 2229 atoms, 2289 bonds, 274 residues, 1 model selected > select up 2717 atoms, 2783 bonds, 334 residues, 1 model selected > select ~sel 98284 atoms, 99846 bonds, 65 pseudobonds, 9379 residues, 41 models selected > color (#!10 & sel) light gray > select clear > select #10/A:1201@C15 1 atom, 1 residue, 1 model selected > select up 49 atoms, 53 bonds, 1 residue, 1 model selected > color sel yellow > color sel byhetero > select clear > view top1 > save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\1031\3_Q2_XE991_top.tif width 3000 > height 3000 transparentBackground true > show #!11 models > hide #!10 models > view side1 > lighting soft > save E:/DATA/IMAGE/KCNQ2_Blocker/Fig1/Fig1-1103.cxs includeMaps true > save E:/DATA/IMAGE/KCNQ2_Blocker/Fig1/1031/Fig1-1103.cxs includeMaps true ——— End of log from Sun Nov 3 17:25:07 2024 ——— opened ChimeraX session > rename #1 3_KCNQ2_p_XE991_PLL_closed > rename #2 2_KCNQ2_P_XE991_open > rename #3 > 3_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc > rename #5 > ""3_splitmap_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc > split"" > rename #4 > 2_map_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc > rename #6 > ""2_splitmap_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc > split"" > rename #7 1_map_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc > rename #8 top_3_KCNQ2_p_XE991_PLL_closed > rename #9 top_2_KCNQ2_P_XE991_open > rename #10 > 1_KCNQ2_XE991_close_real_space_refined_002-ABCD_real_space_refined_006.pdb > rename #11 > ""1_splitmap_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc > split"" > rename #11.2 ""1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc > 1"" > rename #11.3 ""1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc > 2"" > rename #11.4 ""1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc > 3"" > rename #6.2 > ""2_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 1"" > rename #6.3 > ""2_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 2"" > rename #6.4 > ""2_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 3"" > rename #6.5 > ""2_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc 4"" > save E:/DATA/IMAGE/KCNQ2_Blocker/Fig1/1104/Fig1-1104.cxs includeMaps true > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!2 models > hide #!11 models > hide #!2 models > show #!2 models > hide #!2 models > show #!10 models > color #10 #7997b4ff > show #!10 atoms > hide #!10 atoms > show #!10 cartoons > select clear Drag select of 6 residues > select clear > select #10 /A-D 1006-1149 Expected a keyword > select #10 /A-D 1006-1149 Expected a keyword > select #10 /A-D：1006-1149 Expected a keyword > select #10 /A-D:1006-1149 4504 atoms, 4552 bonds, 572 residues, 1 model selected > color sel #b49679 > select clear > select ::name=""LIG"" 245 atoms, 265 bonds, 5 residues, 5 models selected > show sel & #!10 atoms > color (#!10 & sel) yellow > hide H > select clear > show #!11 models > color #11.2 #7997b4ff models > select clear > view side1 [Repeated 1 time(s)] > color #1 #55557fff > color #5.2 #55557fff models > hide #!11 models > show #!11 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > view side1 > lighting full > lighting soft > lighting simple > lighting soft > lighting simple > lighting soft > save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\1104\1_Q2_XE991_map.tif width 3000 > height 3000 transparentBackground true > show #!10 models > hide #!11 models > lighting simple > select #10/A:1201@C17 1 atom, 1 residue, 1 model selected > select up 49 atoms, 53 bonds, 1 residue, 1 model selected > select up 3892 atoms, 3974 bonds, 478 residues, 1 model selected > select down 49 atoms, 53 bonds, 1 residue, 1 model selected > color sel byhetero > save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\1104\1_Q2_XE991_side.tif width 3000 > height 3000 transparentBackground true > select clear > save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\1104\1_Q2_XE991_side.tif width 3000 > height 3000 transparentBackground true > view top1 > combine #10 > hide #!10 models > rename #12 > top_1_KCNQ2_XE991_close_real_space_refined_002-ABCD_real_space_refined_006.pdb > cartoon style width 1.15 thickness 0.3 > setattr b radius 0.27 Assigning radius attribute to 118366 items > select clear > select #12 /A-D:1006-1149 4504 atoms, 4552 bonds, 572 residues, 1 model selected > hide sel cartoons > select clear > hide #12.1 models > select #12/C:157 14 atoms, 15 bonds, 1 residue, 1 model selected > select up 88 atoms, 90 bonds, 10 residues, 1 model selected > select up 951 atoms, 977 bonds, 115 residues, 1 model selected > select up 957 atoms, 982 bonds, 116 residues, 1 model selected > select up 2225 atoms, 2286 bonds, 273 residues, 1 model selected > select up 2229 atoms, 2289 bonds, 274 residues, 1 model selected > select up 2717 atoms, 2783 bonds, 334 residues, 1 model selected > select ~sel 113705 atoms, 115583 bonds, 77 pseudobonds, 11288 residues, 43 models selected > color (#!12 & sel) light gray > select clear > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 49 atoms, 53 bonds, 1 residue, 1 model selected > color sel yellow > color sel byhetero > select clear > save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\1104\1_Q2_XE991_top.tif width 3000 > height 3000 transparentBackground true > color #1 #bb4477ff > color #1 #b4797aff > hide #!12 models > show #!1 models > show #!8 models > hide #!1 models > hide #8.1 models > select clear > select #8/A:156 4 atoms, 3 bonds, 1 residue, 1 model selected > select up 88 atoms, 90 bonds, 10 residues, 1 model selected > select up 951 atoms, 977 bonds, 115 residues, 1 model selected > select up 957 atoms, 982 bonds, 116 residues, 1 model selected > select up 2219 atoms, 2280 bonds, 272 residues, 1 model selected > select up 2225 atoms, 2285 bonds, 273 residues, 1 model selected > select up 2683 atoms, 2749 bonds, 329 residues, 1 model selected > color sel #b4797a > select clear > save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\1104\3_Q2_XE991_top.tif width 3000 > height 3000 transparentBackground true > hide #!8 models > show #!3 models > show #!5 models > color #5.2 #bb4477ff models > color #5.2 #b4797aff models > hide #!3 models > view side1 > lighting soft > hide #!5.4 models > show #!5.4 models > select clear > save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\1104\3_Q2_XE991_map.tif width 3000 > height 3000 transparentBackground true > show #!1 models > hide #!5.2 models > show #!5.2 models > hide #!5 models > select #1 /A-D:1006-1149 4504 atoms, 4552 bonds, 572 residues, 1 model selected > color sel #b49679 > select clear > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 49 atoms, 53 bonds, 1 residue, 1 model selected > color sel yellow > color sel byhetero > select clear > lighting simple > select clear > view side2 > save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\1104\3_Q2_XE991_side.tif width 3000 > height 3000 transparentBackground true > hide #!1 models > show #!12 models > show #!11 models > hide #!11 models > hide #!12 models > show #!10 models > save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\1104\1_Q2_XE991_side.tif width 3000 > height 3000 transparentBackground true > save E:/DATA/IMAGE/KCNQ2_Blocker/Fig1/1104/Fig1-1104.cxs includeMaps true ——— End of log from Mon Nov 4 16:06:22 2024 ——— opened ChimeraX session > show #!5 models > show #!6 models > hide #!6 models > hide #!10 models > hide #!5 models > show #!11 models > lighting soft > lighting simple > lighting soft > lighting full > save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\1104\1.tif width 3000 height 3000 > transparentBackground true > hide #!11 models > show #!5 models > view side1 > ui tool show ""Side View"" > save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\1104\3.tif width 3000 height 3000 > transparentBackground true > show #!11 models > hide #!5 models > save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\1104\1.tif width 3000 height 3000 > transparentBackground true > save E:/DATA/IMAGE/KCNQ2_Blocker/Fig1/1104/Fig1-1105.cxs includeMaps true ——— End of log from Tue Nov 5 12:59:07 2024 ——— opened ChimeraX session > color #11.4 #55ffffff models > color #11.4 lime models > color #11.4 #55ffffff models > color #11.4 #fdb604ff models > color #11.4 #e17f00ff models > color #11.4 #00b7b7ff models > color #11.4 #55ffffff models > color #11.4 #ffaaffff models > save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\Fig1-maps-1204\fig1-Q2X-.tif width > 3000 height 3000 transparentBackground true > save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\Fig1-maps-1204\fig1-Q2X-1.tif width > 3000 height 3000 transparentBackground true > show #!6 models > hide #!6 models > show #!10 models > hide #!10 models > hide #!11 models > show #!12 models > hide #!12 models > show #!4 models > hide #!4 models > show #!5 models > color #5.4 magenta models > color #5.4 #ffaaffff models > color #5.4 magenta models > color #5.4 #ffaaffff models > color #5.4 magenta models > color #5.4 #ff007fff models > color #5.4 magenta models > color #5.4 #38b48bff models > color #11.4 #38b48bff models > save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\Fig1-maps-1204\fig1-Q2X-3.tif width > 3000 height 3000 transparentBackground true > hide #!5 models > show #!7 models > hide #!7 models > show #!11 models > color #11.4 #83ccd2ff models > color #11.4 #a22041ff models > color #5.4 #a22041ff models > show #!5 models > hide #!11 models > color #5.4 #f08300ff models > color #11.4 #f08300ff models > hide #!5 models > show #!11 models > color #11.4 red models > color #11.4 #fdb604ff models > color #5.4 #fdb604ff models > save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\Fig1-maps-1204\fig1-1-Q2X-1.tif width > 3000 height 3000 transparentBackground true > show #!5 models > hide #!11 models > color #5.4 #00a497ff models > color #5.4 #00b9aaff models > color #5.4 #00c3b3ff models > color #5.4 #00c1b1ff models > color #11.4 #00c1b1ff models > show #!10 models > hide #!10 models > show #!11 models > hide #!5 models > save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\Fig1-maps-1204\fig1-1-Q2X-1.tif width > 3000 height 3000 transparentBackground true > ui tool show ""Side View"" > lighting simple > lighting soft > lighting simple > lighting full > lighting soft > lighting simple > save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\Fig1-maps-1204\fig1-1-Q2X-2.tif width > 3000 height 3000 transparentBackground true > hide #!11 models > show #!5 models > save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\Fig1-maps-1204\fig1-3-Q2X-1.tif width > 3000 height 3000 transparentBackground true > color #11.4 #00a497ff models > color #5.4 #00a497ff models > save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\Fig1-maps-1204\fig1-3-Q2X-1.tif width > 3000 height 3000 transparentBackground true > hide #!5 models > show #!11 models > save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\Fig1-maps-1204\fig1-1-Q2X-1.tif width > 3000 height 3000 transparentBackground true > hide #!11 models > show #!6 models > save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\Fig1-maps-1204\fig1-2-Q2X-1.tif width > 3000 height 3000 transparentBackground true > save E:/DATA/IMAGE/KCNQ2_Blocker/Fig1/Fig1-maps-1204/Fig1-1204.cxs Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 285, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py"", line 200, in take_snapshot data = state_from_grid_data(self.grid_data, session_path = session.session_file_path, File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py"", line 310, in state_from_grid_data bytes = dt.matrix().tobytes() MemoryError The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 262, in discovery self.processed[key] = self.process(obj, parents) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 290, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> '2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 2' -> During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 899, in save session.save(output, version=version, include_maps=include_maps) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 625, in save mgr.discovery(self._state_containers) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: '_surface_updaters' -> -> -> 'surface' -> '2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 2' -> : Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> '2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 2' -> ValueError: error processing: '_surface_updaters' -> -> -> 'surface' -> '2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 2' -> : Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> '2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 2' -> File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 285, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py"", line 200, in take_snapshot data = state_from_grid_data(self.grid_data, session_path = session.session_file_path, File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py"", line 310, in state_from_grid_data bytes = dt.matrix().tobytes() MemoryError The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 262, in discovery self.processed[key] = self.process(obj, parents) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 290, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> '2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 2' -> During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 116, in lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output file"", File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 127, in show_save_file_dialog _dlg.display(session, **kw) File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 51, in display run(session, cmd) File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\core\commands\run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\save_command\cmd.py"", line 75, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\save_command\cmd.py"", line 90, in provider_save saver_info.save(session, path, **provider_kw) File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\core_formats\\__init__.py"", line 84, in save return cxs_save(session, path, **kw) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 899, in save session.save(output, version=version, include_maps=include_maps) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 625, in save mgr.discovery(self._state_containers) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: '_surface_updaters' -> -> -> 'surface' -> '2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 2' -> : Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> '2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 2' -> ValueError: error processing: '_surface_updaters' -> -> -> 'surface' -> '2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 2' -> : Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> '2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 2' -> File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. > save E:/DATA/IMAGE/KCNQ2_Blocker/Fig1/Fig1-maps-1204/fig1-1204.cxs > includeMaps true Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 285, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py"", line 200, in take_snapshot data = state_from_grid_data(self.grid_data, session_path = session.session_file_path, File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py"", line 310, in state_from_grid_data bytes = dt.matrix().tobytes() MemoryError The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 262, in discovery self.processed[key] = self.process(obj, parents) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 290, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> '2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 3' -> During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 899, in save session.save(output, version=version, include_maps=include_maps) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 625, in save mgr.discovery(self._state_containers) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: '_surface_updaters' -> -> -> 'surface' -> '2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 3' -> : Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> '2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 3' -> ValueError: error processing: '_surface_updaters' -> -> -> 'surface' -> '2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 3' -> : Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> '2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 3' -> File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 285, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py"", line 200, in take_snapshot data = state_from_grid_data(self.grid_data, session_path = session.session_file_path, File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py"", line 310, in state_from_grid_data bytes = dt.matrix().tobytes() MemoryError The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 262, in discovery self.processed[key] = self.process(obj, parents) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 290, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> '2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 3' -> During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 116, in lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output file"", File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 127, in show_save_file_dialog _dlg.display(session, **kw) File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 51, in display run(session, cmd) File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\core\commands\run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\save_command\cmd.py"", line 75, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\save_command\cmd.py"", line 90, in provider_save saver_info.save(session, path, **provider_kw) File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\core_formats\\__init__.py"", line 84, in save return cxs_save(session, path, **kw) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 899, in save session.save(output, version=version, include_maps=include_maps) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 625, in save mgr.discovery(self._state_containers) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: '_surface_updaters' -> -> -> 'surface' -> '2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 3' -> : Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> '2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 3' -> ValueError: error processing: '_surface_updaters' -> -> -> 'surface' -> '2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 3' -> : Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> '2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 3' -> File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. > save E:/DATA/IMAGE/KCNQ2_Blocker/Fig1/fig1-1204/fig1204-A.cxs includeMaps > true Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 285, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py"", line 200, in take_snapshot data = state_from_grid_data(self.grid_data, session_path = session.session_file_path, File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py"", line 310, in state_from_grid_data bytes = dt.matrix().tobytes() MemoryError The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 262, in discovery self.processed[key] = self.process(obj, parents) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 290, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> '1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc 1' -> During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 899, in save session.save(output, version=version, include_maps=include_maps) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 625, in save mgr.discovery(self._state_containers) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: '_surface_updaters' -> -> -> 'surface' -> '1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc 1' -> : Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> '1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc 1' -> ValueError: error processing: '_surface_updaters' -> -> -> 'surface' -> '1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc 1' -> : Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> '1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc 1' -> File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 285, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py"", line 200, in take_snapshot data = state_from_grid_data(self.grid_data, session_path = session.session_file_path, File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py"", line 310, in state_from_grid_data bytes = dt.matrix().tobytes() MemoryError The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 262, in discovery self.processed[key] = self.process(obj, parents) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 290, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> '1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc 1' -> During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 116, in lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output file"", File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 127, in show_save_file_dialog _dlg.display(session, **kw) File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 51, in display run(session, cmd) File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\core\commands\run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\save_command\cmd.py"", line 75, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\save_command\cmd.py"", line 90, in provider_save saver_info.save(session, path, **provider_kw) File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\core_formats\\__init__.py"", line 84, in save return cxs_save(session, path, **kw) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 899, in save session.save(output, version=version, include_maps=include_maps) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 625, in save mgr.discovery(self._state_containers) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: '_surface_updaters' -> -> -> 'surface' -> '1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc 1' -> : Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> '1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc 1' -> ValueError: error processing: '_surface_updaters' -> -> -> 'surface' -> '1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc 1' -> : Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> '1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc 1' -> File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. > rename #11.2 1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc > rename #11.3 1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc > rename #11.4 1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc > save E:/DATA/IMAGE/KCNQ2_Blocker/Fig1/fig1-1204/1204.cxs includeMaps true Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 285, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py"", line 200, in take_snapshot data = state_from_grid_data(self.grid_data, session_path = session.session_file_path, File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py"", line 310, in state_from_grid_data bytes = dt.matrix().tobytes() MemoryError The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 262, in discovery self.processed[key] = self.process(obj, parents) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 290, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> '2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 2' -> During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 899, in save session.save(output, version=version, include_maps=include_maps) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 625, in save mgr.discovery(self._state_containers) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: '_surface_updaters' -> -> -> 'surface' -> '2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 2' -> : Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> '2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 2' -> ValueError: error processing: '_surface_updaters' -> -> -> 'surface' -> '2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 2' -> : Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> '2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 2' -> File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 285, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py"", line 200, in take_snapshot data = state_from_grid_data(self.grid_data, session_path = session.session_file_path, File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py"", line 310, in state_from_grid_data bytes = dt.matrix().tobytes() MemoryError The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 262, in discovery self.processed[key] = self.process(obj, parents) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 290, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> '2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 2' -> During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 116, in lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output file"", File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 127, in show_save_file_dialog _dlg.display(session, **kw) File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 51, in display run(session, cmd) File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\core\commands\run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\save_command\cmd.py"", line 75, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\save_command\cmd.py"", line 90, in provider_save saver_info.save(session, path, **provider_kw) File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\core_formats\\__init__.py"", line 84, in save return cxs_save(session, path, **kw) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 899, in save session.save(output, version=version, include_maps=include_maps) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 625, in save mgr.discovery(self._state_containers) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: '_surface_updaters' -> -> -> 'surface' -> '2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 2' -> : Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> '2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 2' -> ValueError: error processing: '_surface_updaters' -> -> -> 'surface' -> '2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 2' -> : Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> '2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc 2' -> File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. > rename #6.2 > 2_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc > rename #6.3 > 2_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc > rename #6.4 > 2_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc > rename #6.5 > 2_KCNQ2_PIP2_XE991_open_3.14A_job119_B65_postprocess_resampled.mrc > rename #5.1 > 2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc > rename #5.2 > 2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc > rename #5.3 > 2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc > rename #5.4 > 2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc > save E:/DATA/IMAGE/KCNQ2_Blocker/Fig1/fig1-1204/1.cxs includeMaps true Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 285, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py"", line 200, in take_snapshot data = state_from_grid_data(self.grid_data, session_path = session.session_file_path, File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py"", line 310, in state_from_grid_data bytes = dt.matrix().tobytes() MemoryError The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 262, in discovery self.processed[key] = self.process(obj, parents) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 290, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> '2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc' -> During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 899, in save session.save(output, version=version, include_maps=include_maps) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 625, in save mgr.discovery(self._state_containers) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: '_surface_updaters' -> -> -> 'surface' -> '2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc' -> : Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> '2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc' -> ValueError: error processing: '_surface_updaters' -> -> -> 'surface' -> '2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc' -> : Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> '2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc' -> File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 285, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py"", line 200, in take_snapshot data = state_from_grid_data(self.grid_data, session_path = session.session_file_path, File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py"", line 310, in state_from_grid_data bytes = dt.matrix().tobytes() MemoryError The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 262, in discovery self.processed[key] = self.process(obj, parents) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 290, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> '2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc' -> During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 116, in lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output file"", File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 127, in show_save_file_dialog _dlg.display(session, **kw) File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 51, in display run(session, cmd) File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\core\commands\run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\save_command\cmd.py"", line 75, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\save_command\cmd.py"", line 90, in provider_save saver_info.save(session, path, **provider_kw) File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\core_formats\\__init__.py"", line 84, in save return cxs_save(session, path, **kw) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 899, in save session.save(output, version=version, include_maps=include_maps) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 625, in save mgr.discovery(self._state_containers) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: '_surface_updaters' -> -> -> 'surface' -> '2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc' -> : Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> '2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc' -> ValueError: error processing: '_surface_updaters' -> -> -> 'surface' -> '2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc' -> : Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> '2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc' -> File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. > save E:/DATA/IMAGE/KCNQ2_Blocker/Fig1/fig1-1204/1204.cxs Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 285, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py"", line 200, in take_snapshot data = state_from_grid_data(self.grid_data, session_path = session.session_file_path, File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py"", line 310, in state_from_grid_data bytes = dt.matrix().tobytes() MemoryError The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 262, in discovery self.processed[key] = self.process(obj, parents) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 290, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> '2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc' -> During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 899, in save session.save(output, version=version, include_maps=include_maps) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 625, in save mgr.discovery(self._state_containers) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: '_surface_updaters' -> -> -> 'surface' -> '2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc' -> : Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> '2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc' -> ValueError: error processing: '_surface_updaters' -> -> -> 'surface' -> '2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc' -> : Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> '2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc' -> File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 285, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py"", line 200, in take_snapshot data = state_from_grid_data(self.grid_data, session_path = session.session_file_path, File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py"", line 310, in state_from_grid_data bytes = dt.matrix().tobytes() MemoryError The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 262, in discovery self.processed[key] = self.process(obj, parents) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 290, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> '2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc' -> During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 116, in lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output file"", File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 127, in show_save_file_dialog _dlg.display(session, **kw) File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 51, in display run(session, cmd) File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\core\commands\run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\save_command\cmd.py"", line 75, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\save_command\cmd.py"", line 90, in provider_save saver_info.save(session, path, **provider_kw) File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\core_formats\\__init__.py"", line 84, in save return cxs_save(session, path, **kw) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 899, in save session.save(output, version=version, include_maps=include_maps) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 625, in save mgr.discovery(self._state_containers) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: '_surface_updaters' -> -> -> 'surface' -> '2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc' -> : Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> '2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc' -> ValueError: error processing: '_surface_updaters' -> -> -> 'surface' -> '2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc' -> : Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> '2_map_KCNQ2_PIP2_XE991_PLL_close_3.14A_job090_B65_postprocess_resampled.mrc' -> File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. > show #!5 models > hide #!6 models > rename #5.1 1.mrc > rename #5.2 Q2.mrc > rename #5.3 CAM.mrc > rename #5.4 XE991.mrc > save E:/DATA/IMAGE/KCNQ2_Blocker/Fig1/fig1-1204/fig1-1204.cxs includeMaps > true Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 285, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py"", line 200, in take_snapshot data = state_from_grid_data(self.grid_data, session_path = session.session_file_path, File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py"", line 310, in state_from_grid_data bytes = dt.matrix().tobytes() MemoryError The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 262, in discovery self.processed[key] = self.process(obj, parents) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 290, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> 'Q2.mrc' -> During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 899, in save session.save(output, version=version, include_maps=include_maps) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 625, in save mgr.discovery(self._state_containers) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: '_surface_updaters' -> -> -> 'surface' -> 'Q2.mrc' -> : Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> 'Q2.mrc' -> ValueError: error processing: '_surface_updaters' -> -> -> 'surface' -> 'Q2.mrc' -> : Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> 'Q2.mrc' -> File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 285, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py"", line 200, in take_snapshot data = state_from_grid_data(self.grid_data, session_path = session.session_file_path, File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py"", line 310, in state_from_grid_data bytes = dt.matrix().tobytes() MemoryError The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 262, in discovery self.processed[key] = self.process(obj, parents) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 290, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> 'Q2.mrc' -> During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 116, in lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output file"", File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 127, in show_save_file_dialog _dlg.display(session, **kw) File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 51, in display run(session, cmd) File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\core\commands\run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\save_command\cmd.py"", line 75, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\save_command\cmd.py"", line 90, in provider_save saver_info.save(session, path, **provider_kw) File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\core_formats\\__init__.py"", line 84, in save return cxs_save(session, path, **kw) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 899, in save session.save(output, version=version, include_maps=include_maps) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 625, in save mgr.discovery(self._state_containers) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: '_surface_updaters' -> -> -> 'surface' -> 'Q2.mrc' -> : Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> 'Q2.mrc' -> ValueError: error processing: '_surface_updaters' -> -> -> 'surface' -> 'Q2.mrc' -> : Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> 'Q2.mrc' -> File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. > rename #5.2 Q2-1.mrc > save E:/DATA/IMAGE/KCNQ2_Blocker/Fig1/fig1-1204/fig1-1204.cxs includeMaps > true Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 285, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py"", line 200, in take_snapshot data = state_from_grid_data(self.grid_data, session_path = session.session_file_path, File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py"", line 310, in state_from_grid_data bytes = dt.matrix().tobytes() MemoryError The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 262, in discovery self.processed[key] = self.process(obj, parents) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 290, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> 'Q2-1.mrc' -> During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 899, in save session.save(output, version=version, include_maps=include_maps) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 625, in save mgr.discovery(self._state_containers) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: '_surface_updaters' -> -> -> 'surface' -> 'Q2-1.mrc' -> : Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> 'Q2-1.mrc' -> ValueError: error processing: '_surface_updaters' -> -> -> 'surface' -> 'Q2-1.mrc' -> : Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> 'Q2-1.mrc' -> File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 285, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py"", line 200, in take_snapshot data = state_from_grid_data(self.grid_data, session_path = session.session_file_path, File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py"", line 310, in state_from_grid_data bytes = dt.matrix().tobytes() MemoryError The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 262, in discovery self.processed[key] = self.process(obj, parents) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 290, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> 'Q2-1.mrc' -> During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 116, in lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output file"", File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 127, in show_save_file_dialog _dlg.display(session, **kw) File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 51, in display run(session, cmd) File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\core\commands\run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\save_command\cmd.py"", line 75, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\save_command\cmd.py"", line 90, in provider_save saver_info.save(session, path, **provider_kw) File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\core_formats\\__init__.py"", line 84, in save return cxs_save(session, path, **kw) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 899, in save session.save(output, version=version, include_maps=include_maps) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 625, in save mgr.discovery(self._state_containers) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: '_surface_updaters' -> -> -> 'surface' -> 'Q2-1.mrc' -> : Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> 'Q2-1.mrc' -> ValueError: error processing: '_surface_updaters' -> -> -> 'surface' -> 'Q2-1.mrc' -> : Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> 'Q2-1.mrc' -> File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. > hide #!5.2 models > show #!5.2 models > save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\Fig1-maps-1204\fig1-3-Q2PXL-1.tif > width 3000 height 3000 transparentBackground true > hide #!5 models > show #!6 models > save E:\DATA\IMAGE\KCNQ2_Blocker\Fig1\Fig1-maps-1204\fig1-2-Q2PX-1.tif width > 3000 height 3000 transparentBackground true > save E:/DATA/IMAGE/KCNQ2_Blocker/Fig1/fig1-1204/1204.cxs includeMaps true Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 285, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py"", line 200, in take_snapshot data = state_from_grid_data(self.grid_data, session_path = session.session_file_path, File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py"", line 310, in state_from_grid_data bytes = dt.matrix().tobytes() MemoryError The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 262, in discovery self.processed[key] = self.process(obj, parents) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 290, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> '1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc' -> During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 899, in save session.save(output, version=version, include_maps=include_maps) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 625, in save mgr.discovery(self._state_containers) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: '_surface_updaters' -> -> -> 'surface' -> '1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc' -> : Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> '1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc' -> ValueError: error processing: '_surface_updaters' -> -> -> 'surface' -> '1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc' -> : Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> '1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc' -> File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 285, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py"", line 200, in take_snapshot data = state_from_grid_data(self.grid_data, session_path = session.session_file_path, File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py"", line 310, in state_from_grid_data bytes = dt.matrix().tobytes() MemoryError The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 262, in discovery self.processed[key] = self.process(obj, parents) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 290, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> '1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc' -> During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 116, in lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output file"", File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 127, in show_save_file_dialog _dlg.display(session, **kw) File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 51, in display run(session, cmd) File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\core\commands\run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\save_command\cmd.py"", line 75, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\save_command\cmd.py"", line 90, in provider_save saver_info.save(session, path, **provider_kw) File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\core_formats\\__init__.py"", line 84, in save return cxs_save(session, path, **kw) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 899, in save session.save(output, version=version, include_maps=include_maps) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 625, in save mgr.discovery(self._state_containers) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: '_surface_updaters' -> -> -> 'surface' -> '1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc' -> : Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> '1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc' -> ValueError: error processing: '_surface_updaters' -> -> -> 'surface' -> '1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc' -> : Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> '1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc' -> File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. > lighting simple > save E:/DATA/IMAGE/KCNQ2_Blocker/Fig1/fig1-1204/111.cxs Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 285, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py"", line 200, in take_snapshot data = state_from_grid_data(self.grid_data, session_path = session.session_file_path, File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py"", line 310, in state_from_grid_data bytes = dt.matrix().tobytes() MemoryError The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 262, in discovery self.processed[key] = self.process(obj, parents) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 290, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> '1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc' -> During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 899, in save session.save(output, version=version, include_maps=include_maps) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 625, in save mgr.discovery(self._state_containers) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: '_surface_updaters' -> -> -> 'surface' -> '1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc' -> : Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> '1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc' -> ValueError: error processing: '_surface_updaters' -> -> -> 'surface' -> '1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc' -> : Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> '1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc' -> File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 285, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py"", line 200, in take_snapshot data = state_from_grid_data(self.grid_data, session_path = session.session_file_path, File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\map\session.py"", line 310, in state_from_grid_data bytes = dt.matrix().tobytes() MemoryError The above exception was the direct cause of the following exception: Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 262, in discovery self.processed[key] = self.process(obj, parents) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 290, in process raise RuntimeError(msg) from e RuntimeError: Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> '1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc' -> During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 116, in lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output file"", File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 127, in show_save_file_dialog _dlg.display(session, **kw) File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\save_command\dialog.py"", line 51, in display run(session, cmd) File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\core\commands\run.py"", line 38, in run results = command.run(text, log=log, return_json=return_json) File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\save_command\cmd.py"", line 75, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\save_command\cmd.py"", line 90, in provider_save saver_info.save(session, path, **provider_kw) File ""D:\Chimera\ChimeraX\bin\lib\site- packages\chimerax\core_formats\\__init__.py"", line 84, in save return cxs_save(session, path, **kw) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 899, in save session.save(output, version=version, include_maps=include_maps) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 625, in save mgr.discovery(self._state_containers) File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) ValueError: error processing: '_surface_updaters' -> -> -> 'surface' -> '1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc' -> : Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> '1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc' -> ValueError: error processing: '_surface_updaters' -> -> -> 'surface' -> '1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc' -> : Error while saving session data for '_surface_updaters' -> -> -> 'surface' -> '1_Q2_XE991_closed_3.43A_job104_B65_postprocess_resampled.mrc' -> File ""D:\Chimera\ChimeraX\bin\lib\site-packages\chimerax\core\session.py"", line 266, in discovery raise ValueError(""error processing: %s: %s"" % (_obj_stack(parents, obj), e)) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 425.45 OpenGL renderer: Quadro K1100M/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.9.11 Locale: zh_CN.cp936 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: windows Manufacturer: Dell Inc. Model: Dell Precision M3800 OS: Microsoft Windows 10 专业版 (Build 19045) Memory: 17,078,124,544 MaxProcessMemory: 137,438,953,344 CPU: 8 Intel(R) Core(TM) i7-4712HQ CPU @ 2.30GHz OSLanguage: zh-CN Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2023.5.7 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9.1 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.1 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.1 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 comtypes: 1.1.14 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.9.26 imagesize: 1.4.1 importlib-metadata: 6.6.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 23.1 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.5.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pywin32: 305 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 setuptools: 67.4.0 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.4.1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.1 traitlets: 5.9.0 typing-extensions: 4.5.0 tzdata: 2023.3 urllib3: 1.26.15 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 WMI: 1.5.1 zipp: 3.15.0 }}} " defect closed normal Sessions limitation Greg Couch all ChimeraX