id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3239 Graphics window banks to gray viktoriia.huryn@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.18362 ChimeraX Version: 1.0rc202005180441 (2020-05-18 04:41:25 UTC) Description background and my electron dencity in .mrc file till I interact with it (by cliciking on the feild, rotating etc). During the interaction structure is visible, but if stop, after several secs in disappers again and I see gray background. Same for structures from PDB. Log: UCSF ChimeraX version: 1.0rc202005180441 (2020-05-18) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open C:/cryo-EM/288_full_10c_5t_7c_3Dclass/run_it025_class001.mrc C:/cryo- > EM/288_full_10c_5t_7c_3Dclass/run_it025_class002.mrc C:/cryo- > EM/288_full_10c_5t_7c_3Dclass/run_it025_class003.mrc C:/cryo- > EM/288_full_10c_5t_7c_3Dclass/run_it025_class004.mrc C:/cryo- > EM/288_full_10c_5t_7c_3Dclass/run_it025_class005.mrc C:/cryo- > EM/288_full_10c_5t_7c_3Dclass/run_it025_class006.mrc C:/cryo- > EM/288_full_10c_5t_7c_3Dclass/run_it025_class007.mrc C:/cryo- > EM/288_full_10c_5t_7c_3Dclass/run_it025_class008.mrc C:/cryo- > EM/288_full_10c_5t_7c_3Dclass/run_it025_class009.mrc C:/cryo- > EM/288_full_10c_5t_7c_3Dclass/run_it025_class010.mrc Opened run_it025_class001.mrc, grid size 288,288,288, pixel 1.16, shown at level 0.0413, step 2, values float32 Opened run_it025_class002.mrc, grid size 288,288,288, pixel 1.16, shown at level 0.04, step 2, values float32 Opened run_it025_class003.mrc, grid size 288,288,288, pixel 1.16, shown at level 0.0297, step 2, values float32 Opened run_it025_class004.mrc, grid size 288,288,288, pixel 1.16, shown at level 0.0299, step 2, values float32 Opened run_it025_class005.mrc, grid size 288,288,288, pixel 1.16, shown at level 0.0229, step 2, values float32 Opened run_it025_class006.mrc, grid size 288,288,288, pixel 1.16, shown at level 0.0334, step 2, values float32 Opened run_it025_class007.mrc, grid size 288,288,288, pixel 1.16, shown at level 0.0281, step 2, values float32 Opened run_it025_class008.mrc, grid size 288,288,288, pixel 1.16, shown at level 0.0374, step 2, values float32 Opened run_it025_class009.mrc, grid size 288,288,288, pixel 1.16, shown at level 0.0356, step 2, values float32 Opened run_it025_class010.mrc, grid size 288,288,288, pixel 1.16, shown at level 0.036, step 2, values float32 > hide #!1 models > hide #!3 models > hide #!4 models > hide #!2 models > hide #!5 models > hide #!6 models > hide #!7 models > hide #!8 models > hide #!9 models > hide #!10 models > show #!1 models > show #!2 models > select 20 models selected > close #4 > show #!3 models > show #!5 models > show #!6 models > show #!7 models > show #!8 models > show #!9 models > show #!10 models > close #10 > close > close # Expected a models specifier or a keyword > close # Expected a models specifier or a keyword > open C:\cryo-EM\288_full_10c_5t_7c_3Dclass\run_it025_class010.mrc format mrc Opened run_it025_class010.mrc, grid size 288,288,288, pixel 1.16, shown at level 0.036, step 2, values float32 > open 4V7C Summary of feedback from opening 4V7C fetched from pdb --- warnings | Atom OP1 has no neighbors to form bonds with according to residue template for U /BB:1 Atom OP2 has no neighbors to form bonds with according to residue template for U /BB:1 Atom O has no neighbors to form bonds with according to residue template for VAL /BP:60 notes | Fetching compressed mmCIF 4v7c from http://files.rcsb.org/download/4v7c.cif Fetching CCD ZN from http://ligand-expo.rcsb.org/reports/Z/ZN/ZN.cif Fetching CCD KBE from http://ligand-expo.rcsb.org/reports/K/KBE/KBE.cif Fetching CCD DPP from http://ligand-expo.rcsb.org/reports/D/DPP/DPP.cif Fetching CCD UAL from http://ligand-expo.rcsb.org/reports/U/UAL/UAL.cif Fetching CCD 5OH from http://ligand-expo.rcsb.org/reports/5/5OH/5OH.cif 4v7c title: Structure of the Ribosome with Elongation Factor G Trapped in the Pre- Translocation State (pre-translocation 70S*tRNA structure) [more info...] Chain information for 4v7c #2 --- Chain | Description AA | 16S ribosomal RNA AB | 30S ribosomal protein S2 AC | 30S ribosomal protein S3 AD | 30S ribosomal protein S4 AE | 30S ribosomal protein S5 AF | 30S ribosomal protein S6 AG | 30S ribosomal protein S7 AH | 30S ribosomal protein S8 AI | 30S ribosomal protein S9 AJ | 30S ribosomal protein S10 AK | 30S ribosomal protein S11 AL | 30S ribosomal protein S12 AM | 30S ribosomal protein S13 AN | 30S ribosomal protein S14 AO | 30S ribosomal protein S15 AP | 30S ribosomal protein S16 AQ | 30S ribosomal protein S17 AR | 30S ribosomal protein S18 AS | 30S ribosomal protein S19 AT | 30S ribosomal protein S20 AU | 30S ribosomal protein S21 AV AW | tRNA AX | mRNA AY | viomycin B1 | 50S ribosomal protein L29 B2 | 50S ribosomal protein L30 B3 | 50S ribosomal protein L32 B4 | 50S ribosomal protein L33 B5 | 50S ribosomal protein L34 B6 | 50S ribosomal protein L35 B7 | 50S ribosomal protein L36 BA | 23S ribosomal RNA BB | 5S ribosomal RNA BC | 50S ribosomal protein L1 BD | 50S ribosomal protein L2 BE | 50S ribosomal protein L3 BF | 50S ribosomal protein L4 BG | 50S ribosomal protein L5 BH | 50S ribosomal protein L6 BI | 50S ribosomal protein L9 BJ | 50S ribosomal protein L10 BK | 50S ribosomal protein L11 BL | 50S ribosomal protein L13 BM | 50S ribosomal protein L14 BN | 50S ribosomal protein L15 BO | 50S ribosomal protein L16 BP | 50S ribosomal protein L17 BQ | 50S ribosomal protein L18 BR | 50S ribosomal protein L19 BS | 50S ribosomal protein L20 BT | 50S ribosomal protein L21 BU | 50S ribosomal protein L22 BV | 50S ribosomal protein L23 BW | 50S ribosomal protein L24 BX | 50S ribosomal protein L25 BY | 50S ribosomal protein L27 BZ | 50S ribosomal protein L28 Non-standard residues in 4v7c #2 --- 5OH — (2S)-amino[(4R,6S)-2-amino-6-hydroxy-3,4,5,6-tetrahydropyrimidin-4-yl]ethanoic acid KBE — beta-lysine ((3S)-3,6-diaminohexanoic acid) UAL — (2Z)-2-amino-3-(carbamoylamino)prop-2-enoic acid ZN — zinc ion > hide #!1 models > show #!1 models OpenGL version: 3.3.0 NVIDIA 445.87 OpenGL renderer: GeForce GTX 1050/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: ASUSTeK COMPUTER INC. Model: VivoBook_ASUSLaptop X570DD_M570DD OS: Microsoft Windows 10 Home (Build 18362) Memory: 6,387,343,360 MaxProcessMemory: 137,438,953,344 CPU: 8 AMD Ryzen 5 3500U with Radeon Vega Mobile Gfx "" PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.8 File attachment: chimera.png }}} [attachment:""chimera.png""] " defect closed normal Graphics can't reproduce all ChimeraX