Nucleotides slow

[goddard@…]

The following bug report has been submitted:
Platform:        Darwin-19.3.0-x86_64-i386-64bit
ChimeraX Version: 0.92 (2020-02-27)
Description
Nucleotide slabs takes minutes to display with 4u25.  Not too usable with that slow speed.

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 4hus

4hus title:  
Crystal structure of streptogramin group A antibiotic acetyltransferase VatA
from Staphylococcus aureus in complex with virginiamycin M1 [more info...]  
  
Chain information for 4hus #1  
---  
Chain | Description  
A B C | Virginiamycin A acetyltransferase  
  
Non-standard residues in 4hus #1  
---  
CL — chloride ion  
EDO — 1,2-ethanediol (ethylene glycol)  
NA — sodium ion  
PEG — di(hydroxyethyl)ether  
PGE — triethylene glycol  
SO4 — sulfate ion  
VIR — virginiamycin M1  
  
  

> select ::name="VIR"

38 atoms, 40 bonds, 1 model selected  

> open 4hus format mmCIF fromDatabase pdb

4hus title:  
Crystal structure of streptogramin group A antibiotic acetyltransferase VatA
from Staphylococcus aureus in complex with virginiamycin M1 [more info...]  
  
Chain information for 4hus #2  
---  
Chain | Description  
A B C | Virginiamycin A acetyltransferase  
  
Non-standard residues in 4hus #2  
---  
CL — chloride ion  
EDO — 1,2-ethanediol (ethylene glycol)  
NA — sodium ion  
PEG — di(hydroxyethyl)ether  
PGE — triethylene glycol  
SO4 — sulfate ion  
VIR — virginiamycin M1  
  
  

> move x 50 models #2

> select ::name="VIR"

76 atoms, 80 bonds, 2 models selected  

> delete #2 & ~sel

> select clear

> addh #2

Summary of feedback from adding hydrogens to 4hus #2  
---  
notes | Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
34 hydrogens added  
  

> color #2 & C cyan

> color #2 & C lightblue

> color #1 & C & :VIR lightblue

> color #1 & C & :VIR cornflowerblue

> color #1 & C & :VIR lightblue

> select #1 & :VIR

38 atoms, 40 bonds, 1 model selected  

> style sel sphere

Changed 38 atom styles  

> style sel ball

Changed 38 atom styles  

> style sel sphere

Changed 38 atom styles  

> select clear

> rename #2 streptograminA

> rename #2 "streptogramin A"

> rename #1 VatA

> save /Users/goddard/ucsf/presentations/byers-mar2020/data/streptogramin1.cxs

> save /Users/goddard/ucsf/presentations/byers-
> mar2020/data/virginiamycynM1.pdb models #2

> open 4u25

4u25 title:  
Crystal structure of the E. coli ribosome bound to virginiamycin M1. [more
info...]  
  
Chain information for 4u25 #3  
---  
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 #3  
---  
MG — magnesium ion  
VIR — virginiamycin M1  
ZN — zinc ion  
  
4u25 mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  
  

> select /B*

94871 atoms, 101987 bonds, 3845 pseudobonds, 5 models selected  

> select /B* /D*

186575 atoms, 200979 bonds, 7418 pseudobonds, 5 models selected  

> select /C* /D*

145381 atoms, 156520 bonds, 5256 pseudobonds, 5 models selected  

> select ::name="VIR"

186 atoms, 194 bonds, 3 models selected  

> lighting soft

> delete /C* /D*

> select clear

> select :VIR

148 atoms, 154 bonds, 3 models selected  

> select #3/BD:28@CD

1 atom, 1 model selected  

> ui mousemode rightMode "translate selected models"

> select clear

> graphics quality

Subdivision 1, atom triangles 28, bond triangles 28, ribbon divisions 20  

Expected a keyword  

> graphics quality atomTriangles 50

> color :VIR & C lightblue

> save /Users/goddard/ucsf/presentations/byers-mar2020/data/streptogramin2.cxs

> rename #3 "E coli ribosome"

> ui mousemode rightMode zoom

> ui mousemode rightMode translate

> save /Users/goddard/ucsf/presentations/byers-mar2020/data/streptogramin2.cxs

> select nucleic

97739 atoms, 109453 bonds, 4465 pseudobonds, 3 models selected  

> hide nucleic

> show nucleic ribbons

> select clear

> lighting simple

> show nucleic atoms

> style nucleic stick

Changed 97739 atom styles  

> select clear

> nucleotides tube/slab shape box




OpenGL version: 4.1 ATI-3.5.5
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.