Opened 6 years ago
Last modified 6 years ago
#2896 accepted defect
generic attribute selection slow
Reported by: | Owned by: | Eric Pettersen | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Command Line | Version: | |
Keywords: | Cc: | ||
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Darwin-19.3.0-x86_64-i386-64bit ChimeraX Version: 0.92 (2020-02-27) Description Selecting a ligand from the non-standard residues table for a large structure (select ::name="VIR") is unusably slow, 20 seconds for 300,000 atom ribosome structure. Selecting all takes 1.3 seconds. Command "sel :VIR" takes 0.5 seconds. So apparently it is the ::name="VIR" syntax for the atom spec used by the non-standard residue table link. Log: Startup Messages --- warning | 'clip' is a prefix of an existing command 'clipper' UCSF ChimeraX version: 0.92 (2020-02-27) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 4u25 4u25 title: Crystal structure of the E. coli ribosome bound to virginiamycin M1. [more info...] Chain information for 4u25 #1 --- Chain | Description AA CA | 16S rRNA AB CB | 30S ribosomal protein S2 AC CC | 30S ribosomal protein S3 AD CD | 30S ribosomal protein S4 AE CE | 30S ribosomal protein S5 AF CF | 30S ribosomal protein S6 AG CG | 30S ribosomal protein S7 AH CH | 30S ribosomal protein S8 AI CI | 30S ribosomal protein S9 AJ CJ | 30S ribosomal protein S10 AK CK | 30S ribosomal protein S11 AL CL | 30S ribosomal protein S12 AM CM | 30S ribosomal protein S13 AN CN | 30S ribosomal protein S14 AO CO | 30S ribosomal protein S15 AP CP | 30S ribosomal protein S16 AQ CQ | 30S ribosomal protein S17 AR CR | 30S ribosomal protein S18 AS CS | 30S ribosomal protein S19 AT CT | 30S ribosomal protein S20 AU CU | 30S ribosomal protein S21 B0 D0 | 50S ribosomal protein L32 B1 D1 | 50S ribosomal protein L33 B2 D2 | 50S ribosomal protein L34 B3 D3 | 50S ribosomal protein L35 B4 D4 | 50S ribosomal protein L36 B5 | 50S ribosomal protein L1 BA DA | 23S rRNA BB DB | 5S rRNA BC DC | 50S ribosomal protein L2 BD DD | 50S ribosomal protein L3 BE DE | 50S ribosomal protein L4 BF DF | 50S ribosomal protein L5 BG DG | 50S ribosomal protein L6 BH DH | 50S ribosomal protein L9 BI DI | 50S ribosomal protein L11 BJ DJ | 50S ribosomal protein L13 BK DK | 50S ribosomal protein L14 BL DL | 50S ribosomal protein L15 BM DM | 50S ribosomal protein L16 BN DN | 50S ribosomal protein L17 BO DO | 50S ribosomal protein L18 BP DP | 50S ribosomal protein L19 BQ DQ | 50S ribosomal protein L20 BR DR | 50S ribosomal protein L21 BS DS | 50S ribosomal protein L22 BT DT | 50S ribosomal protein L23 BU DU | 50S ribosomal protein L24 BV DV | 50S ribosomal protein L25 BW DW | 50S ribosomal protein L27 BX DX | 50S ribosomal protein L28 BY DY | 50S ribosomal protein L29 BZ DZ | 50S ribosomal protein L30 Non-standard residues in 4u25 #1 --- MG — magnesium ion VIR — virginiamycin M1 ZN — zinc ion 4u25 mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly > select ::name="VIR" 76 atoms, 80 bonds, 1 model selected > time select ::name="VIR" > select ::name="VIR" 76 atoms, 80 bonds, 1 model selected command time 19.26 seconds draw time 0.03526 seconds > select all 288258 atoms, 310714 bonds, 10871 pseudobonds, 4 models selected > time select all > select all 288258 atoms, 310714 bonds, 10871 pseudobonds, 4 models selected command time 1.318 seconds draw time 0.06209 seconds > time sel :VIR > select :VIR 76 atoms, 80 bonds, 1 model selected command time 0.5361 seconds draw time 0.03183 seconds OpenGL version: 4.1 ATI-3.5.5 OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine OpenGL vendor: ATI Technologies Inc.
Change History (1)
comment:1 by , 6 years ago
Component: | Unassigned → Command Line |
---|---|
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → accepted |
Summary: | ChimeraX bug report submission → generic attribute selection slow |
Note:
See TracTickets
for help on using tickets.
Though this particular usage scenario is large moot (because the chain table no longer uses '::name=val' except when absolutely necessary), the fact that generic attribute selection is so slow is still a problem.
I can't seem to get line profiling to work on methods of Structure; waiting until Greg is around to get some insight there.