Confusion with 'OK'

[lp212@…]

The following bug report has been submitted:
Platform:        Darwin-19.6.0-x86_64-i386-64bit
ChimeraX Version: 1.1.1 (2020-10-07 08:32:49 UTC)
Description
There seems to be a bug in 'select zone'. When one first clicks 'apply' and then 'OK', 'apply' correctly selects the zone, but 'OK' seems to apply another instance of 'select zone' to the currently selected area. There's no problem if one clicks 'OK' without using 'apply'.

Log:
UCSF ChimeraX version: 1.1.1 (2020-10-07)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/luca/projects/Primosome-Nsp1/coot/fitted to maps from whole
> particles/24.02.2021_whole_final.pdb" format pdb

Summary of feedback from opening /Users/luca/projects/Primosome-
Nsp1/coot/fitted to maps from whole particles/24.02.2021_whole_final.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 GLU A 8
LEU A 20 1 13  
Start residue of secondary structure not found: HELIX 2 2 PRO A 22 VAL A 35 1
14  
Start residue of secondary structure not found: HELIX 3 3 LYS A 50 ASP A 52 1
3  
Start residue of secondary structure not found: HELIX 4 4 ASN A 62 LYS A 72 1
11  
Start residue of secondary structure not found: HELIX 5 5 ARG A 87 HIS A 91 1
5  
21 messages similar to the above omitted  
End residue of secondary structure not found: HELIX 27 27 PRO B 285 ASN B 298
1 14  
Start residue of secondary structure not found: HELIX 28 28 ARG B 302 ILE B
316 1 15  
Start residue of secondary structure not found: HELIX 29 29 THR B 319 ILE B
332 1 14  
Start residue of secondary structure not found: HELIX 30 30 ASP B 337 GLY B
354 1 18  
Start residue of secondary structure not found: HELIX 31 31 SER B 366 SER B
373 1 8  
Start residue of secondary structure not found: HELIX 32 32 CYS B 384 TYR B
401 1 18  
1 messages similar to the above omitted  
End residue of secondary structure not found: HELIX 34 34 HIS B 419 ASN B 433
1 15  
Start residue of secondary structure not found: HELIX 35 35 HIS B 443 ILE B
454 1 12  
Start residue of secondary structure not found: HELIX 36 36 GLU C 368 GLU C
371 1 4  
Start residue of secondary structure not found: HELIX 37 37 SER C 409 LYS C
426 1 18  
Start residue of secondary structure not found: HELIX 38 38 SER C 482 ARG C
491 1 10  
Start residue of secondary structure not found: HELIX 39 39 LYS C 522 VAL C
526 1 5  
31 messages similar to the above omitted  
End residue of secondary structure not found: HELIX 71 71 LYS D 212 TYR D 235
1 24  
Start residue of secondary structure not found: HELIX 72 72 ASP D 275 SER D
280 1 6  
Start residue of secondary structure not found: HELIX 73 73 GLU D 332 ASP D
336 1 5  
Start residue of secondary structure not found: HELIX 74 74 TYR D 357 ARG D
371 1 15  
Start residue of secondary structure not found: HELIX 75 75 HIS D 386 ASN D
391 1 6  
Start residue of secondary structure not found: HELIX 76 76 PRO D 397 GLY D
412 1 16  
56 messages similar to the above omitted  
End residue of secondary structure not found: SHEET 53 5353 ILE D 271 GLY D
274 0  
Start residue of secondary structure not found: SHEET 54 5454 GLN D 283 ASP D
287 0  
Start residue of secondary structure not found: SHEET 55 5555 SER D 295 LEU D
296 0  
Start residue of secondary structure not found: SHEET 56 5656 VAL D 301 ILE D
307 0  
Start residue of secondary structure not found: SHEET 57 5757 LEU D 314 LEU D
319 0  
Start residue of secondary structure not found: SHEET 58 5858 SER D 340 CYS D
346 0  
1 messages similar to the above omitted  
End residue of secondary structure not found: SHEET 60 6060 HIS D 419 VAL D
423 0  
Start residue of secondary structure not found: SHEET 61 6161 VAL D 453 PHE D
455 0  
Start residue of secondary structure not found: SHEET 62 6262 CYS D 460 ILE D
464 0  
Start residue of secondary structure not found: SHEET 63 6363 ILE D 468 LEU D
471 0  
Start residue of secondary structure not found: SHEET 64 6464 ILE D 485 SER D
486 0  
Start residue of secondary structure not found: SHEET 65 6565 VAL D 537 ILE D
539 0  
6 messages similar to the above omitted  
  
Chain information for 24.02.2021_whole_final.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> show cartoons

> hide atoms

> select /A:625

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select up

125 atoms, 127 bonds, 15 residues, 1 model selected  

> view sel

> select clear

> select /A:615

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show sel target ab

> style sel stick

Changed 9 atom styles  

> color sel byhetero

> cofr sel

> select clear

> select /A:615@CG

1 atom, 1 residue, 1 model selected  

> select up

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select sel @< 5

64 atoms, 56 bonds, 15 residues, 1 model selected  

> select sel @< 5

213 atoms, 194 bonds, 46 residues, 1 model selected  

> select clear

> select /A:615@CG

1 atom, 1 residue, 1 model selected  

> select up

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select sel @< 5

64 atoms, 56 bonds, 15 residues, 1 model selected  

> select clear




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[pett]

Hi Luca,

That's basically how 'OK' works: it's Apply + close window. So if you click 'Apply' and then 'OK' you have applied the zone twice. If you need to close the window without applying again, use the close button in the window's title bar.
Not too many windows actually have an explicit 'Apply' button -- it's for operations that you might want to repeat before closing the window.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[Elaine Meng]

It's explained in what you get by clicking the Help button on the dialog:
<https://rbvi.ucsf.edu/chimerax/docs/user/menu.html#selectzone>

"OK performs the selection and closes the dialog, whereas Apply performs the selection without closing the dialog."

[lp212@…]

Thanks for the explanation, it makes sense now. 

Apologies for sending a bug report, next time I’ll post to the list. 

Best wishes,
Luca

Luca Pellegrini, PhD
Department of Biochemistry
University of Cambridge
Cambridge CB2 1GA
UK