id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3348 Filled rings unusably slow on large structures goddard@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Darwin-19.4.0-x86_64-i386-64bit ChimeraX Version: 1.1.dev202006011833 (2020-06-01 18:33:55 UTC) Description Filled rings take 128 seconds to display on a large structure 4v88. This takes so long the user will probably kill the program assuming it is hung (I did the first time). A main strength of ChimeraX is speed with large structures. Log: UCSF ChimeraX version: 1.1.dev202006011833 (2020-06-01) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 4v88 format mmcif fromDatabase pdb Summary of feedback from opening 4v88 fetched from pdb --- warnings | Atom OP1 has no neighbors to form bonds with according to residue template for G /A5:420 Atom OP2 has no neighbors to form bonds with according to residue template for G /A5:420 Ignoring microheterogeneity for label_seq_id 3 in chain BO Ignoring microheterogeneity for label_seq_id 4 in chain BO Ignoring microheterogeneity for label_seq_id 11 in chain BO Ignoring microheterogeneity for label_seq_id 13 in chain BO Ignoring microheterogeneity for label_seq_id 16 in chain BO 35 messages similar to the above omitted 4v88 title: The structure of the eukaryotic ribosome at 3.0 A resolution. [more info...] Chain information for 4v88 #1 --- Chain | Description A1 A5 | 25S rRNA A2 | 18S ribosomal RNA A3 A7 | 5S rRNA A4 A8 | 5.8S rRNA A6 | 18S rRNA AA CA | 40S ribosomal protein S0-A AB CB | 40S ribosomal protein S1-A AC CC | 40S ribosomal protein S2 AD CD | 40S ribosomal protein S3 AE CE | 40S ribosomal protein S4-A AF CF | 40S ribosomal protein S5 AG CG | 40S ribosomal protein S6-A AH CH | 40S ribosomal protein S7-A AI CI | 40S ribosomal protein S8-A AJ CJ | 40S ribosomal protein S9-A AK CK | 40S ribosomal protein S10-A AL CL | 40S ribosomal protein S11-A AM CM | 40S ribosomal protein S12 AN CN | 40S ribosomal protein S13 AO CO | 40S ribosomal protein S14-A AP CP | 40S ribosomal protein S15 AQ CQ | 40S ribosomal protein S16-A AR CR | 40S ribosomal protein S17-A AS CS | 40S ribosomal protein S18-A AT CT | 40S ribosomal protein S19-A AU CU | 40S ribosomal protein S20 AV CV | 40S ribosomal protein S21-A AW CW | 40S ribosomal protein S22-A AX CX | 40S ribosomal protein S23-A AY CY | 40S ribosomal protein S24-A AZ CZ | 40S ribosomal protein S25-A Aa Ca | 40S ribosomal protein S26-A Ab Cb | 40S ribosomal protein S27-A Ac Cc | 40S ribosomal protein S28-A Ad Cd | 40S ribosomal protein S29-A Ae Ce | 40S ribosomal protein S30-A Af Cf | 40S ribosomal protein S31 Ag Cg | Guanine nucleotide-binding protein subunit beta-like protein (ASC1, RACK1) Ah | Suppressor protein STM1 BA DA | 60S ribosomal protein L2-A BB DB | 60S ribosomal protein L3 BC DC | 60S ribosomal protein L4-A BD DD | 60S ribosomal protein L5 BE DE | 60S ribosomal protein L6-A BF DF | 60S ribosomal protein L7-A BG DG | 60S ribosomal protein L8-A BH DH | 60S ribosomal protein L9-A BI DI | 60S ribosomal protein L10 BJ DJ | 60S ribosomal protein L11-A BL DL | 60S ribosomal protein L13-A BM DM | 60S ribosomal protein L14-A BN DN | 60S ribosomal protein L15-A BO DO | 60S ribosomal protein L16-A, 60S ribosomal protein L16-B BP DP | 60S ribosomal protein L17-A BQ DQ | 60S ribosomal protein L18-A BR DR | 60S ribosomal protein L19-A BS DS | 60S ribosomal protein L20-A BT DT | 60S ribosomal protein L21-A BU DU | 60S ribosomal protein L22-A BV DV | 60S ribosomal protein L23-A BW DW | 60S ribosomal protein L24-A BX DX | 60S ribosomal protein L25 BY DY | 60S ribosomal protein L26-A BZ DZ | 60S ribosomal protein L27-A Ba Da | 60S ribosomal protein L28 Bb Db | 60S ribosomal protein L29 Bc Dc | 60S ribosomal protein L30 Bd Dd | 60S ribosomal protein L31-A Be De | 60S ribosomal protein L32 Bf Df | 60S ribosomal protein L33-A Bg Dg | 60S ribosomal protein L34-A Bh Dh | 60S ribosomal protein L35-A Bi Di | 60S ribosomal protein L36-A Bj Dj | 60S ribosomal protein L37-A Bk Dk | 60S ribosomal protein L38 Bl Dl | 60S ribosomal protein L39 Bm Dm | 60S ribosomal protein L40 Bn Dn | 60S ribosomal protein L41-A Bo Do | 60S ribosomal protein L42-A Bp Dp | 60S ribosomal protein L43-A Ch | Suppressor protein STM1 DK | Ribosomal protein L12 Dq | 60S acidic ribosomal protein P0 Dr | Ribosomal protein P1 α Ds | Ribosomal protein P2 β Non-standard residues in 4v88 #1 --- MG — magnesium ion OHX — osmium (III) hexammine (osmium(6+) hexaazanide) ZN — zinc ion 4v88 mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly > time style stick > style stick Changed 413613 atom styles command time 0.3252 seconds draw time 0.391 seconds > time style ring thick > style ringFill thick Changed 36905 residue ring styles command time 0.0361 seconds draw time 128.8 seconds > zoom 4 > lighting simple > lighting soft OpenGL version: 4.1 ATI-3.8.24 OpenGL renderer: AMD Radeon Pro Vega 20 OpenGL Engine OpenGL vendor: ATI Technologies Inc.Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro15,3 Processor Name: 8-Core Intel Core i9 Processor Speed: 2.4 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache (per Core): 256 KB L3 Cache: 16 MB Hyper-Threading Technology: Enabled Memory: 32 GB Boot ROM Version: 1037.100.362.0.0 (iBridge: 17.16.14281.0.0,0) Software: System Software Overview: System Version: macOS 10.15.4 (19E287) Kernel Version: Darwin 19.4.0 Time since boot: 24 days 20:05 Graphics/Displays: Intel UHD Graphics 630: Chipset Model: Intel UHD Graphics 630 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3e9b Revision ID: 0x0002 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal: Supported, feature set macOS GPUFamily2 v1 Radeon Pro Vega 20: Chipset Model: Radeon Pro Vega 20 Type: GPU Bus: PCIe PCIe Lane Width: x8 VRAM (Total): 4 GB Vendor: AMD (0x1002) Device ID: 0x69af Revision ID: 0x00c0 ROM Revision: 113-D2060I-087 VBIOS Version: 113-D20601MA0T-016 Option ROM Version: 113-D20601MA0T-016 EFI Driver Version: 01.01.087 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal: Supported, feature set macOS GPUFamily2 v1 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2880 x 1800 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.8 }}} " enhancement closed normal Performance fixed Greg Couch all ChimeraX