id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3126 Nucleotide stub takes 10 minutes to display for ribosome goddard@… Greg Couch "{{{ The following bug report has been submitted: Platform: Darwin-19.4.0-x86_64-i386-64bit ChimeraX Version: 0.94 (2020-04-16) Description Took approximately 20 minutes to show nucleotide stubs for 4v9d. This is nearly as bad as a crash since no one will wait 20 minutes. Since a primary strength of ChimeraX is fast handling of large structures and ribosome structures are very common this is a serious problem. If the code cannot be optimized it might be best to have nucleotides show a warning if requested on more than 1000 residues and not change the style unless a ""noWarn true"" option is given. Log: UCSF ChimeraX version: 0.94.dev202004160103 (2020-04-16) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 4v9d Summary of feedback from opening 4v9d fetched from pdb --- note | Fetching compressed mmCIF 4v9d from http://files.rcsb.org/download/4v9d.cif 4v9d title: Structures of the bacterial ribosome in classical and hybrid states of tRNA binding [more info...] Chain information for 4v9d #1 --- Chain | Description AA BA | 16S rRNA AB BB | 30S ribosomal protein S2 AC BC | 30S ribosomal protein S3 AD BD | 30S ribosomal protein S4 AE BE | 30S ribosomal protein S5 AF BF | 30S ribosomal protein S6 AG BG | 30S ribosomal protein S7 AH BH | 30S ribosomal protein S8 AI BI | 30S ribosomal protein S9 AJ BJ | 30S ribosomal protein S10 AK BK | 30S ribosomal protein S11 AL BL | 30S ribosomal protein S12 AM BM | 30S ribosomal protein S13 AN BN | 30S ribosomal protein S14 AO BO | 30S ribosomal protein S15 AP BP | 30S ribosomal protein S16 AQ BQ | 30S ribosomal protein S17 AR BR | 30S ribosomal protein S18 AS BS | 30S ribosomal protein S19 AT BT | 30S ribosomal protein S20 AU BU | 30S ribosomal protein S21 AV BV | phenylalanine specific transfer RNA AX BX | messenger RNA AY | ribosome recycling factor C0 D0 | 50S ribosomal protein L32 C1 D1 | 50S ribosomal protein L33 C2 D2 | 50S ribosomal protein L34 C3 D3 | 50S ribosomal protein L35 C4 D4 | 50S ribosomal protein L36 CA DA | 23S rRNA CB | 5S rRNA CC DC | 50S ribosomal protein L2 CD DD | 50S ribosomal protein L3 CE DE | 50S ribosomal protein L4 CF DF | 50S ribosomal protein L5 CG DG | 50S ribosomal protein L6 CH DH | 50S ribosomal protein L9 CI DI | 50S ribosomal protein L11 CJ DJ | 50S ribosomal protein L13 CK DK | 50S ribosomal protein L14 CL DL | 50S ribosomal protein L15 CM DM | 50S ribosomal protein L16 CN DN | 50S ribosomal protein L17 CO DO | 50S ribosomal protein L18 CP DP | 50S ribosomal protein L19 CQ DQ | 50S ribosomal protein L20 CR DR | 50S ribosomal protein L21 CS DS | 50S ribosomal protein L22 CT DT | 50S ribosomal protein L23 CU DU | 50S ribosomal protein L24 CV DV | 50S ribosomal protein L25 CW | 50S ribosomal protein L27 CX DX | 50S ribosomal protein L28 CY DY | 50S ribosomal protein L29 CZ DZ | 50S ribosomal protein L30 DB | 5S rRNA DW | 50S ribosomal protein L27 Non-standard residues in 4v9d #1 --- MG — magnesium ion ZN — zinc ion 4v9d mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly > hide atoms > show cartoons > nucleotides slab > style nucleic stick Changed 199371 atom styles > nucleotides stubs > show atoms OpenGL version: 4.1 ATI-3.8.24 OpenGL renderer: AMD Radeon Pro Vega 20 OpenGL Engine OpenGL vendor: ATI Technologies Inc. }}} " defect assigned normal Performance Eric Pettersen all ChimeraX