id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
9193	Computing molecular solvent excluded surface is slow for large numbers of atoms	Eric Pettersen	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Computing molecule SES surfaces with large numbers of atoms (>500,000) is much slower than expected.  For a 6 million atom virus capsid (6b1t) it took an hour using large grid spacing 2.5.  These surfaces are computed by the NIAID NIH 3D pipeline.

Log:
Could not find tool ""Tabbed Toolbar""  
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 2bbv format mmcif fromDatabase pdbe_bio maxAssemblies 1

Summary of feedback from opening 2bbv fetched from pdbe_bio  
---  
warning | Missing or incomplete entity_poly_seq table. Inferred polymer
connectivity.  
  
2bbv bioassembly 1 title:  
The refined three-dimensional structure of an insect virus At 2.8 angstroms
resolution [more info...]  
  
Chain information for 2bbv bioassembly 1 #1  
---  
Chain | Description  
A AA AAA AAB AAC AAD AAE AAF AAG AAH AAI AAJ AAK AAL AAM AAN AAO AAP AAQ AAR
AAS AAT AAU AAV AAW AAX AAY AAZ AB ABA ABB ABC ABD ABE ABF ABG AC AD AE AF AG
AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX AY AZ | RNA
(5'-R(*UP*CP*UP*UP*AP*UP*AP*UP*CP*U)-3')  
B BA BAA BAB BAC BAD BAE BAF BAG BAH BAI BAJ BAK BAL BAM BAN BAO BAP BAQ BAR
BAS BAT BAU BAV BAW BAX BAY BAZ BB BBA BBB BBC BBD BBE BBF BBG BC BD BE BF BG
BH BI BJ BK BL BM BN BO BP BQ BR BS BT BU BV BW BX BY BZ D DA DAA DAB DAC DAD
DAE DAF DAG DAH DAI DAJ DAK DAL DAM DAN DAO DAP DAQ DAR DAS DAT DAU DAV DAW
DAX DAY DAZ DB DBA DBB DBC DBD DBE DBF DBG DC DD DE DF DG DH DI DJ DK DL DM DN
DO DP DQ DR DS DT DU DV DW DX DY DZ | PROTEIN (BLACK BEETLE VIRUS CAPSID
PROTEIN)  
C CA CAA CAB CAC CAD CAE CAF CAG CAH CAI CAJ CAK CAL CAM CAN CAO CAP CAQ CAR
CAS CAT CAU CAV CAW CAX CAY CAZ CB CBA CBB CBC CBD CBE CBF CBG CC CD CE CF CG
CH CI CJ CK CL CM CN CO CP CQ CR CS CT CU CV CW CX CY CZ E EA EAA EAB EAC EAD
EAE EAF EAG EAH EAI EAJ EAK EAL EAM EAN EAO EAP EAQ EAR EAS EAT EAU EAV EAW
EAX EAY EAZ EB EBA EBB EBC EBD EBE EBF EBG EC ED EE EF EG EH EI EJ EK EL EM EN
EO EP EQ ER ES ET EU EV EW EX EY EZ G GA GAA GAB GAC GAD GAE GAF GAG GAH GAI
GAJ GAK GAL GAM GAN GAO GAP GAQ GAR GAS GAT GAU GAV GAW GAX GAY GAZ GB GBA GBB
GBC GBD GBE GBF GBG GC GD GE GF GG GH GI GJ GK GL GM GN GO GP GQ GR GS GT GU
GV GW GX GY GZ | PROTEIN (BLACK BEETLE VIRUS CAPSID PROTEIN)  
F FA FAA FAB FAC FAD FAE FAF FAG FAH FAI FAJ FAK FAL FAM FAN FAO FAP FAQ FAR
FAS FAT FAU FAV FAW FAX FAY FAZ FB FBA FBB FBC FBD FBE FBF FBG FC FD FE FF FG
FH FI FJ FK FL FM FN FO FP FQ FR FS FT FU FV FW FX FY FZ | PROTEIN (BLACK
BEETLE VIRUS CAPSID PROTEIN)  
  
Non-standard residues in 2bbv bioassembly 1 #1  
---  
CA — (CA)  
  
2bbv bioassembly 1 mmCIF Assemblies  
---  
1| complete icosahedral assembly  
2| icosahedral asymmetric unit  
3| icosahedral pentamer  
4| icosahedral 23 hexamer  
5| icosahedral asymmetric unit, std point frame  
6| crystal asymmetric unit, crystal frame  
  
Opened 1 biological assemblies for 2bbv  

> time surface enclose #1 sharp false grid 2.0

> surface enclose #1 sharpBoundaries false gridSpacing 2.0

command time 26.56 seconds  
draw time 0.07606 seconds  




OpenGL version: 4.1 ATI-4.12.7
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac18,3
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 4.2 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 8 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      System Firmware Version: 512.0.0.0.0
      OS Loader Version: 577~170
      SMC Version (system): 2.41f2

Software:

    System Software Overview:

      System Version: macOS 13.4 (22F66)
      Kernel Version: Darwin 22.5.0
      Time since boot: 14 days, 23 hours, 10 minutes

Graphics/Displays:

    Radeon Pro 580:

      Chipset Model: Radeon Pro 580
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67df
      Revision ID: 0x00c0
      ROM Revision: 113-D000AA-931
      VBIOS Version: 113-D0001A1X-025
      EFI Driver Version: 01.00.931
      Metal Support: Metal 2
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 5K (5120 x 2880)
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


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}}}
"	enhancement	closed	normal		Surface		fixed		phil.cruz@…				all	ChimeraX