Bug with the user-defined selector

[Suli-Anne.Laurin@…]

Greeting,

I want to report a bug that happened to me twice working on two different sessions with different original .cif files.

I selected multiple residues and saved them as a user-defined selector. It works for a while. And then the selector fetching would fail at some point and will select the whole chain instead. From when that bug arise, it will not be possible to save any user-defined selector on that chain.

This is the example of the log showing that I saved only one residue in the selection, and when I fetch it, it selects the whole chain which is 259 residues.

select #2/R:179
7 atoms, 6 bonds, 1 residue, 1 model selected
name frozen Active_mutated sel
select Active_mutated
1957 atoms, 6 bonds, 259 residues, 1 model selected

Best,
Thank you,
Suli-Anne Laurin
Ph.D. candidate | Michel Bouvier's laboratory (3343)
Institut de recherche en immunologie et en cancérologie (IRIC)
Université de Montréal | Pavillon Marcelle-Coutu | Office 3346
2950, chemin de Polytechnique | Montréal (Québec) | H3C 3J7
suli-anne.laurin@umontreal.ca  | (514) 343-6111 ext. 0306

[pett]

Hi Suli-Anne,

Thanks for reporting this problem. Since "name frozen" works 99.9% of the time, we would need a bit more info in order to reproduce and fix this issue. The next time this happens to you, please use the Help→Report a Bug menu item to report the error. Using that method will include a lot more crucial information in the report, including what version of ChimeraX you were using, as well as the entire contents of the log -- which will allow us to see what operations occurred between the "name frozen" definition and the problematic "select" command, which will give us a much better chance of tracking down the cause of the problem. Sorry I can't be more immediately helpful.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[Suli-Anne.Laurin@…]

Hi,

Thank you for the feedback,
I did want to use the Report a bug option but it was saying the server was not available.

In term of log, there were no other action between the "selection" (define selector/name frozen) and the "fetching" (user-defined selector/select). If i open the file, and run the name frozen on a random amino acid and then fetch that select, it will select the whole protein. But I do think there is something that happened in the previous manipulation that then prevents to select specific items in the whole chain (ie what triggered the first occurrence of the problem).

I will try to report next time it happens (but unfortunately it happens often randomly and then I have saved/changed session and the log where the problem would have arisen is lost)

Thank you
Suli-Anne Laurin
Ph.D. candidate | Michel Bouvier's laboratory (3343)
Institut de recherche en immunologie et en cancérologie (IRIC)
Université de Montréal | Pavillon Marcelle-Coutu | Office 3346
2950, chemin de Polytechnique | Montréal (Québec) | H3C 3J7
suli-anne.laurin@umontreal.ca  | (514) 343-6111 ext. 0306
________________________________
De : ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Envoyé : 21 novembre 2024 18:44
À : pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>; Suli-Anne.Laurin@hotmail.com <Suli-Anne.Laurin@hotmail.com>
Objet : Re: [ChimeraX] #16346: Bug with the user-defined selector

#16346: Bug with the user-defined selector
-----------------------------------------+--------------------
          Reporter:  Suli-Anne.Laurin@…  |      Owner:  pett
              Type:  defect              |     Status:  closed
          Priority:  normal              |  Milestone:
         Component:  Command Line        |    Version:
        Resolution:  can't reproduce     |   Keywords:
        Blocked By:                      |   Blocking:
Notify when closed:                      |   Platform:  all
           Project:  ChimeraX            |
-----------------------------------------+--------------------
Changes (by pett):

 * resolution:   => can't reproduce
 * status:  accepted => closed

Comment:

 Hi Suli-Anne,
         Thanks for reporting this problem.  Since "name frozen" works
 99.9% of the time, we would need a bit more info in order to reproduce and
 fix this issue.  The next time this happens to you, please use the
 Help→Report a Bug menu item to report the error.  Using that method will
 include a lot more crucial information in the report, including what
 version of ChimeraX you were using, as well as the entire contents of the
 log -- which will allow us to see what operations occurred between the
 "name frozen" definition and the problematic "select" command, which will
 give us a much better chance of tracking down the cause of the problem.
 Sorry I can't be more immediately helpful.

 --Eric

         Eric Pettersen
         UCSF Computer Graphics Lab
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/16346#comment:2>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[pett]

Hi Suli-Anne,

I wrote a script that names a selection of a residue in 1f66 and then uses that selector 100 times, and it worked right each time, so it is definitely something with your structure or the operations you are doing earlier that is triggering this behavior. If you can ever consistently reproduce this, please let me know how. Even if you can't consistently reproduce it, if it happens again try reporting it with Help→Report a Bug (which _should_ work) and you still can't report it that way, right click on the log to bring up a menu where you can save the contents of the log, and include that file with your report. That will help tremendously in trying to debug the issue.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab