[chimerax-users] Opening .xyz file in ChimeraX

[Anthony James Schaefer]

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 at cgl.ucsf.edu> on behalf of Carina Luo via ChimeraX-users <chimerax-users at cgl.ucsf.edu>
Sent: Wednesday, November 23, 2022 8:52 AM
To: chimerax-users at cgl.ucsf.edu <chimerax-users at 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
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