Feedback & Issue with ChimeraX1.9

[shantanukhatri007@…]

Dear ChimeraX Development Team,

First and foremost, I want to express my sincere appreciation for the
incredible tool you have created. ChimeraX has been an invaluable resource,
and I truly admire the effort and dedication that goes into its development.
Recently, I’ve encountered an issue with the interface. In previous
versions, I used to see the log, models panel, and toolbar automatically
upon startup. However, after installing the newer stable build of ChimeraX,
now I need to open them manually each time. Additionally, when I do so, the
toolbar section occupies excessive space, and the alignment of the logs and
models makes them almost unreadable and difficult to use.Additionally, it
is no longer possible to drag and align the toolbar, log, and models panels
as in previous versions, making it difficult to customize the interface to
my preference

I wanted to check if this is a known issue with windows users or if there
might be something I am missing. I have tried reinstalling multiple times,
and I am using a high-end laptop with an Intel Ultra 9 processor, ample
RAM, and a powerful GPU. Despite this, the problem persists.
I would greatly appreciate any guidance on resolving this. Thank you once
again for such a fantastic tool—I truly enjoy using it!

I have also attached few screenshots for your kind perusal.

Best regards,
*Shantanu Khatri*,
*PhD Scholar (CSIR-Senior Research Fellow)*

Screenshot 2025-05-14 235544.png​

Screenshot 2025-05-14 235716.png​

Screenshot 2025-05-14 235654.png​

Screenshot 2025-05-14 235809.png​

[shantanukhatri007@…]

P.S. I have also attempted troubleshooting the issue by checking options
like 'Start at ChimeraX startup' for all panels, but unfortunately, this
did not work as well.

On Thu, May 15, 2025 at 12:05 AM Shantanu Khatri <
shantanukhatri007@gmail.com> wrote:

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[pett]

Screenshots from the mail didn't make it into the ticket, so attaching by hand

[Tom Goddard]

It would probably be most helpful if you sent a screenshot of the entire ChimeraX window as it appears when you start ChimeraX.

[shantanukhatri007@…]

Also there is no previous config file that was generated. And I also tried
tweaking dpi scaling but unfortunately nothing seems to be working.
Thank you .
*Shantanu Khatri*,
*PhD Scholar (CSIR-SRF)*


On Thu, 15 May, 2025, 12:48 am Shantanu Khatri, <shantanukhatri007@gmail.com>
wrote:

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>> #17679: Feedback & Issue with ChimeraX1.9
>> ------------------------------------------+----------------------
>>           Reporter:  shantanukhatri007@…  |      Owner:  pett
>>               Type:  defect               |     Status:  accepted
>>           Priority:  normal               |  Milestone:
>>          Component:  UI                   |    Version:
>>         Resolution:                       |   Keywords:
>>         Blocked By:                       |   Blocking:
>> Notify when closed:                       |   Platform:  all
>>            Project:  ChimeraX             |
>> ------------------------------------------+----------------------
>> Comment (by Tom Goddard):
>>
>>  It would probably be most helpful if you sent a screenshot of the entire
>>  ChimeraX window as it appears when you start ChimeraX.
>> --
>> Ticket URL: <
>> https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/17679#comment:3>
>> ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
>> ChimeraX Issue Tracker
>>
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[Tom Goddard]

Your screenshot of the ChimeraX window looks normal except for the missing Model Panel and Log and Command Line. All those panels can be hidden and saved in preferences. So I would suggest reseting all your ChimeraX preferences. Those are saved in

C:\Users\<user-name>\AppData\Local\UCSF\ChimeraX\

as described in the ChimeraX manual here

​https://www.cgl.ucsf.edu/chimerax/docs/user/preferences.html

I would suggest deleting or renaming that directory. Then start ChimeraX and it will recreate the directory with the default initial settings.

[Tom Goddard]

If reseting to default preferences does not fix it. I suggest starting ChimeraX and using menu entry Help / Report a Bug.... That will send us information about your operating system and computer that may give us a clue what is going wrong.

[pett]

This one didn't make it either. Hoping to have the problem fixed soon.

[shantanukhatri007@…]

Dear Team,
I have attempted to reset ChimeraX to its default preferences and even
deleted the directory stored inside the Local folder, but unfortunately,
the issue persists. The log remains unreadable/unusbale, and I am unable to
drag or adjust it.
I have attached a screenshot showing the problem for reference. I will also
submit a bug report to provide further details.
Looking forward to your guidance on resolving this issue.

Best regards,
Shantanu

On Thu, May 15, 2025 at 1:53 AM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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Screenshot 2025-05-15 172936.png​

[shantanukhatri007@…]

Added by email2trac

[shantanukhatri007@…]

PS- I have also sent the bug report  (From chimeraX) .

On Thu, May 15, 2025 at 5:34 PM Shantanu Khatri <shantanukhatri007@gmail.com>
wrote:

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>> #17679: Feedback & Issue with ChimeraX1.9
>> ------------------------------------------+----------------------
>>           Reporter:  shantanukhatri007@…  |      Owner:  pett
>>               Type:  defect               |     Status:  accepted
>>           Priority:  normal               |  Milestone:
>>          Component:  UI                   |    Version:
>>         Resolution:                       |   Keywords:
>>         Blocked By:                       |   Blocking:
>> Notify when closed:                       |   Platform:  all
>>            Project:  ChimeraX             |
>> ------------------------------------------+----------------------
>> Changes (by pett):
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>>  * Attachment "Screenshot 2025-05-15 004711.png" added.
>>
>>  This one didn't make it either.  Hoping to have the problem fixed soon.
>> --
>> Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/17679>
>> ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
>> ChimeraX Issue Tracker
>>
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[shantanukhatri007@…]

I wanted to share some mpre observations regarding ChimeraX version 1.9 and
the beta release of version 1.10. I am pleased to inform you that the issue
I previously encountered has been resolved in version 1.10 ( beta).
Additionally, I noticed two things in version 1.9:
- There is no startup message.
- Windows C++ graphics compilation does not occur, unlike what I have
observed when installing ChimeraX 1.10.


On Thu, May 15, 2025 at 5:38 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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Screenshot 2025-05-15 172936-1.png​

[shantanukhatri007@…]

Added by email2trac

[pett]

Glad 1.10 works!