[chimerax-users] Opening .xyz file in ChimeraX

[Eric Pettersen]

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