Suppress log scrolling if log link clicked

[goddard@…]

The following bug report has been submitted:
Platform:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-08-02)
Description
Clicking on a a chain in the log chain table makes the log scroll to the bottom, I guess to show the command that shows that chain.  This makes the chain table not very useful for selecting different chains and ligands.  Would be nice to somehow supress the log scrolling when clicking links in the chain table.  In fact maybe clicking any link in the log should supress automatically scrolling the log to the bottom.

Log:
UCSF ChimeraX version: 0.91 (2019-08-02)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6jlu

Summary of feedback from opening 6jlu fetched from pdb  
---  
notes | Fetching compressed mmCIF 6jlu from
http://files.rcsb.org/download/6jlu.cif  
Fetching CCD OEX from http://ligand-expo.rcsb.org/reports/O/OEX/OEX.cif  
Fetching CCD FE2 from http://ligand-expo.rcsb.org/reports/F/FE2/FE2.cif  
Fetching CCD PHO from http://ligand-expo.rcsb.org/reports/P/PHO/PHO.cif  
Fetching CCD SQD from http://ligand-expo.rcsb.org/reports/S/SQD/SQD.cif  
Fetching CCD PL9 from http://ligand-expo.rcsb.org/reports/P/PL9/PL9.cif  
Fetching CCD BCT from http://ligand-expo.rcsb.org/reports/B/BCT/BCT.cif  
Fetching CCD DGD from http://ligand-expo.rcsb.org/reports/D/DGD/DGD.cif  
Fetching CCD KC1 from http://ligand-expo.rcsb.org/reports/K/KC1/KC1.cif  
Fetching CCD A86 from http://ligand-expo.rcsb.org/reports/A/A86/A86.cif  
Fetching CCD DD6 from http://ligand-expo.rcsb.org/reports/D/DD6/DD6.cif  
Fetching CCD KC2 from http://ligand-expo.rcsb.org/reports/K/KC2/KC2.cif  
  
6jlu title:  
Structure of PSII-FCP supercomplex from a centric diatom Chaetoceros gracilis
at 3.02 angstrom resolution [more info...]  
  
Chain information for 6jlu #1  
---  
Chain | Description  
0 10 | FCP-E  
1 11 12 13 14 15 16 17 18 2 3 4 5 6 7 8 | FCP-A  
19 9 | FCP-F  
A a | PsbA  
B b | PsbB  
C c | PsbC  
D d | PsbD  
E e | PsbE  
F f | PsbF  
G g | Psb31  
H h | Photosystem II reaction center protein H  
I i | PsbI  
J j | PsbJ  
K k | PsbK  
L l | PsbL  
M m | PsbM  
N n | Psb34  
O o | Extrinsic protein in photosystem II  
P p | FCP-D  
Q q | Extrinsic protein in photosystem II  
R r | PsbG  
T t | PsbT  
U u | Extrinsic protein in photosystem II  
V v | Cytochrome c-550  
W w | PsbW  
X x | Photosystem II reaction center X protein  
Y y | PsbY  
Z z | PsbZ  
  
Non-standard residues in 6jlu #1  
---  
A86 —
(3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-
beta,beta-caroten-3'-yl acetate (Fucoxanthin)  
BCR — β-carotene  
BCT — bicarbonate ion  
CL — chloride ion  
CLA — chlorophyll A  
DD6 — (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-
carotene-3,3'-diol (Diadinoxanthin)  
DGD — digalactosyl diacyl glycerol (DGDG)  
FE2 — Fe (II) ion  
HEM — protoporphyrin IX containing Fe (HEME)  
KC1 — Chlorophyll c1  
KC2 — Chlorophyll c2  
LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole  
LMG — 1,2-distearoyl-monogalactosyl-diglyceride  
OEX — Ca-MN4-O5 cluster  
PHO — pheophytin A  
PL9 —
2,3-dimethyl-5-(3,7,11,15,19,23,27,31,35-nonamethyl-2,6,10,14,18,22,26,30,34-hexatriacontanonaenyl-2,5-cyclohexadiene-1,4-dione-2,3-dimethyl-5-solanesyl-1,4-benzoquinone
(plastoquinone 9)  
SQD — 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-α-D-glucopyranosyl]-Sn-glycerol
(sulfoquinovosyldiacylglycerol)  
  
  

> open 9839 fromDatabase emdb

Summary of feedback from opening 9839 fetched from emdb  
---  
note | Fetching compressed map 9839 from
ftp://ftp.wwpdb.org/pub/emdb/structures/EMD-9839/map/emd_9839.map.gz  
  
Opened emd_9839.map, grid size 340,340,340, pixel 1.31, shown at level 0.0137,
step 2, values float32  

> hide #!1 models

> hide #!2 models

> show #!1 models

> select /15:34-205

1280 atoms, 1306 bonds, 1 model selected  

> select /18:34-205

1304 atoms, 1330 bonds, 1 model selected  

> select :A86

5952 atoms, 6204 bonds, 1 model selected  

> select :CLA

12491 atoms, 13411 bonds, 920 pseudobonds, 2 models selected  

> select :KC1

990 atoms, 1078 bonds, 88 pseudobonds, 2 models selected  

> select :KC2

1620 atoms, 1764 bonds, 144 pseudobonds, 2 models selected  

> select /1-8

38044 atoms, 39486 bonds, 700 pseudobonds, 2 models selected  




OpenGL version: 4.1 ATI-2.11.20
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

[Greg Couch]

In Command.run, it calls logger.logger.info(msg, is_html=True, add_newline=False). Which ends up calling the log tool's Log.log(), which adds the message and calls self.show_page_source()/_show(). Which in turn calls QWebEnginePage's setHtml() if small or load() if big. Would need an asynchronous method called after the page was loaded to reposition it. Position is via javascript with window.scrollTo().

[Greg Couch]

Fixed. Overrode link_clicked in tool to set flag to suppress scrolling. Then execute the link (which is done via ui.thread_safe()). Then added another thread_safe function to reenable scrolling.

[Elaine Meng]

The problem of scrolling to the bottom of the Log from clicking chain-ID or residue-name links in info tables has re-emerged. Tested in UCSF ChimeraX version: 1.1.dev202008260138 (2020-08-26)

[pett]

The use of a regulating timer to prevent excessive slowdowns when many commands log in a short period of time (e.g. multiple commands on a single line) probably interferes with the scroll-suppression trick.

[pett]

Fixed on develop and release branches.