[chimerax-users] Opening .xyz file in ChimeraX

[Carina Luo]

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 at 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 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> 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
> _______________________________________________
> ChimeraX-users mailing list
> ChimeraX-users at cgl.ucsf.edu
> Manage subscription:
> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.rbvi.ucsf.edu/pipermail/chimerax-users/attachments/20221123/7a0de58a/attachment.html>