Opening .xyz file in ChimeraX

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Carina Luo

23 Nov 2022 23 Nov '22

7:52 a.m.

Hello,

I am trying to open an .xyz file in ChimeraX. I installed SEQCROW (1.5.9) as prompted, but ChimeraX still says "Opener for format 'XYZ file' is not installed; see log for more info."

Here is the output I got when I installed SEQCROW (1.5.9): Downloading bundle SEQCROW-1.5.9-py3-none-any.whl

Errors may have occurred when running pip:

pip standard error: ---

[notice] A new release of pip available: 22.2.2 -> 22.3.1 [notice] To update, run: C:\Program Files\ChimeraX\bin\ChimeraX.exe -m pip install --upgrade pip ---

pip standard output: --- Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing c:\users\user\downloads\seqcrow-1.5.9-py3-none-any.whl Requirement already satisfied: jinja2 in c:\program files\chimerax\bin\lib\site-packages (from SEQCROW==1.5.9) (3.1.2) Collecting Send2Trash Downloading Send2Trash-1.8.0-py3-none-any.whl (18 kB) Requirement already satisfied: ChimeraX-Core<=1.5,>=1.2 in c:\program files\chimerax\bin\lib\site-packages (from SEQCROW==1.5.9) (1.5rc202210312311) Requirement already satisfied: scipy in c:\program files\chimerax\bin\lib\site-packages (from SEQCROW==1.5.9) (1.9.0) Requirement already satisfied: psutil in c:\program files\chimerax\bin\lib\site-packages (from SEQCROW==1.5.9) (5.9.1) Requirement already satisfied: MarkupSafe>=2.0 in c:\program files\chimerax\bin\lib\site-packages (from jinja2->SEQCROW==1.5.9) (2.1.1) Requirement already satisfied: numpy<1.25.0,>=1.18.5 in c:\program files\chimerax\bin\lib\site-packages (from scipy->SEQCROW==1.5.9) (1.23.1) Installing collected packages: Send2Trash, SEQCROW Successfully installed SEQCROW-1.5.9 Send2Trash-1.8.0

Could you please help me figure out what I still need to do in order to successfully open .xyz files in ChimeraX?

Sincerely,

Carina

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Anthony James Schaefer

23 Nov 23 Nov

8:17 a.m.

Carina,

After installing a bundle, ChimeraX needs to be restarted before you can open its file formats. If this issue persists after restarting ChimeraX, submit a bug report through Help -> Report a Bug on the ChimeraX menu.

Tony ________________________________ From: ChimeraX-users chimerax-users-bounces@cgl.ucsf.edu on behalf of Carina Luo via ChimeraX-users chimerax-users@cgl.ucsf.edu Sent: Wednesday, November 23, 2022 8:52 AM To: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Subject: [chimerax-users] Opening .xyz file in ChimeraX

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]

Hello,

I am trying to open an .xyz file in ChimeraX. I installed SEQCROW (1.5.9) as prompted, but ChimeraX still says "Opener for format 'XYZ file' is not installed; see log for more info."

Here is the output I got when I installed SEQCROW (1.5.9): Downloading bundle SEQCROW-1.5.9-py3-none-any.whl

Errors may have occurred when running pip:

pip standard error: ---

[notice] A new release of pip available: 22.2.2 -> 22.3.1 [notice] To update, run: C:\Program Files\ChimeraX\bin\ChimeraX.exe -m pip install --upgrade pip ---

Could you please help me figure out what I still need to do in order to successfully open .xyz files in ChimeraX?

Sincerely,

Carina

Eric Pettersen

9:06 a.m.

Hi Carina Also, the fact that a restart is required is a bug. I will open a ticket in the ChimeraX bug-tracking database with you and Tony on the recipient list so that you will be notified when it gets fixed.

--Eric

Eric Pettersen UCSF Computer Graphics Lab

...

On Nov 23, 2022, at 8:17 AM, Anthony James Schaefer via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:

Carina,

After installing a bundle, ChimeraX needs to be restarted before you can open its file formats. If this issue persists after restarting ChimeraX, submit a bug report through Help -> Report a Bug on the ChimeraX menu.

Tony From: ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu mailto:chimerax-users-bounces@cgl.ucsf.edu> on behalf of Carina Luo via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> Sent: Wednesday, November 23, 2022 8:52 AM To: chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] Opening .xyz file in ChimeraX

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]

Hello,

I am trying to open an .xyz file in ChimeraX. I installed SEQCROW (1.5.9) as prompted, but ChimeraX still says "Opener for format 'XYZ file' is not installed; see log for more info."

Here is the output I got when I installed SEQCROW (1.5.9): Downloading bundle SEQCROW-1.5.9-py3-none-any.whl Errors may have occurred when running pip: pip standard error:

[notice] A new release of pip available: 22.2.2 -> 22.3.1 [notice] To update, run: C:\Program Files\ChimeraX\bin\ChimeraX.exe -m pip install --upgrade pip

pip standard output:

Looking in indexes: https://pypi.org/simple https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing c:\users\user\downloads\seqcrow-1.5.9-py3-none-any.whl Requirement already satisfied: jinja2 in c:\program files\chimerax\bin\lib\site-packages (from SEQCROW==1.5.9) (3.1.2) Collecting Send2Trash Downloading Send2Trash-1.8.0-py3-none-any.whl (18 kB) Requirement already satisfied: ChimeraX-Core<=1.5,>=1.2 in c:\program files\chimerax\bin\lib\site-packages (from SEQCROW==1.5.9) (1.5rc202210312311) Requirement already satisfied: scipy in c:\program files\chimerax\bin\lib\site-packages (from SEQCROW==1.5.9) (1.9.0) Requirement already satisfied: psutil in c:\program files\chimerax\bin\lib\site-packages (from SEQCROW==1.5.9) (5.9.1) Requirement already satisfied: MarkupSafe>=2.0 in c:\program files\chimerax\bin\lib\site-packages (from jinja2->SEQCROW==1.5.9) (2.1.1) Requirement already satisfied: numpy<1.25.0,>=1.18.5 in c:\program files\chimerax\bin\lib\site-packages (from scipy->SEQCROW==1.5.9) (1.23.1) Installing collected packages: Send2Trash, SEQCROW Successfully installed SEQCROW-1.5.9 Send2Trash-1.8.0

Could you please help me figure out what I still need to do in order to successfully open .xyz files in ChimeraX? Sincerely, Carina _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

Carina Luo

3:56 p.m.

Thank you for this assistance and for identifying this bug. I am able to open .xyz files after restarting.

On Wed, Nov 23, 2022 at 12:08 PM Eric Pettersen pett@cgl.ucsf.edu wrote:

...

Hi Carina Also, the fact that a restart is required is a bug. I will open a ticket in the ChimeraX bug-tracking database with you and Tony on the recipient list so that you will be notified when it gets fixed.

--Eric

Eric Pettersen UCSF Computer Graphics Lab

On Nov 23, 2022, at 8:17 AM, Anthony James Schaefer via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:

Carina,

After installing a bundle, ChimeraX needs to be restarted before you can open its file formats. If this issue persists after restarting ChimeraX, submit a bug report through Help -> Report a Bug on the ChimeraX menu.

Tony

*From:* ChimeraX-users chimerax-users-bounces@cgl.ucsf.edu on behalf of Carina Luo via ChimeraX-users chimerax-users@cgl.ucsf.edu *Sent:* Wednesday, November 23, 2022 8:52 AM *To:* chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu *Subject:* [chimerax-users] Opening .xyz file in ChimeraX

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]

Hello,

I am trying to open an .xyz file in ChimeraX. I installed SEQCROW (1.5.9) as prompted, but ChimeraX still says "Opener for format 'XYZ file' is not installed; see log for more info."

Here is the output I got when I installed SEQCROW (1.5.9): Downloading bundle SEQCROW-1.5.9-py3-none-any.whl Errors may have occurred when running pip: pip standard error:

[notice] A new release of pip available: 22.2.2 -> 22.3.1 [notice] To update, run: C:\Program Files\ChimeraX\bin\ChimeraX.exe -m pip install --upgrade pip

pip standard output:

Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing c:\users\user\downloads\seqcrow-1.5.9-py3-none-any.whl Requirement already satisfied: jinja2 in c:\program files\chimerax\bin\lib\site-packages (from SEQCROW==1.5.9) (3.1.2) Collecting Send2Trash Downloading Send2Trash-1.8.0-py3-none-any.whl (18 kB) Requirement already satisfied: ChimeraX-Core<=1.5,>=1.2 in c:\program files\chimerax\bin\lib\site-packages (from SEQCROW==1.5.9) (1.5rc202210312311) Requirement already satisfied: scipy in c:\program files\chimerax\bin\lib\site-packages (from SEQCROW==1.5.9) (1.9.0) Requirement already satisfied: psutil in c:\program files\chimerax\bin\lib\site-packages (from SEQCROW==1.5.9) (5.9.1) Requirement already satisfied: MarkupSafe>=2.0 in c:\program files\chimerax\bin\lib\site-packages (from jinja2->SEQCROW==1.5.9) (2.1.1) Requirement already satisfied: numpy<1.25.0,>=1.18.5 in c:\program files\chimerax\bin\lib\site-packages (from scipy->SEQCROW==1.5.9) (1.23.1) Installing collected packages: Send2Trash, SEQCROW Successfully installed SEQCROW-1.5.9 Send2Trash-1.8.0

Could you please help me figure out what I still need to do in order to successfully open .xyz files in ChimeraX? Sincerely, Carina _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users

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Anthony James Schaefer
Carina Luo
Eric Pettersen