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