[chimerax-users] Attribute files in ChimeraX

[David Leeming]

Hi Elaine,

Thank you very much for the advice, I have updated to the daily build and that was causing the issue I was reporting.
However, I'm still a little unsure about how to correctly use the save command
[cid:3e12bc90-9dde-4fcc-9e68-7d330862fffb]
I'm getting this error message when I attempt to run the code on the latest version, however, I'm not sure what's causing this error
[cid:fe76fe7b-f46b-4a2d-b8c4-92d56438e97d]
I'm basing my code on the guide featured below: (https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html)

[cid:8aefe194-26d9-4473-b53d-eaca0f281545]
using the attribute-name from the help online again featured below (https://rbvi.ucsf.edu/chimerax/docs/user/attributes.html#attrnames)

[cid:564d48af-094a-4fd1-aa6b-9a1aa0d9a8d2]

Would it be possible to provide an example of a working command as I'm unsure what exactly is giving me this error?
Apologies if I'm missing something obvious, thank you very much for continued your time and support.

Kind regards,
David
________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: 03 March 2021 16:47
To: David Leeming <david.leeming at student.manchester.ac.uk>
Cc: chimerax-users at cgl.ucsf.edu <chimerax-users at cgl.ucsf.edu>
Subject: Re: [chimerax-users] Attribute files in ChimeraX

Hi David,
I don't know python, but assuming you are using the "save" command correctly, you probably just need to get a newer version of ChimeraX.  If you report problems, it's helpful to include version and platform.

 From looking at the ChimeraX change log, you need to get ChimeraX version 1.2 daily build from Oct 19, 2020 or newer, since that's when the ability to write this file type was added:
<https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog>

Attribute files:
<https://rbvi.ucsf.edu/chimerax/docs/user/formats/defattr.html>

Saving an attribute file:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#attributes>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Mar 3, 2021, at 7:32 AM, David Leeming <david.leeming at student.manchester.ac.uk> wrote:
>
> Dear ChimeraX users,
>
> I'm trying to write a script that will export an attribute file in ChimeraX, (specifically the attribute sasa) I'm looking for a similar output to that of the attribute calculator function in Chimera (see image below)
> <image.png>
> I'm currently trying to run the command below to export the attribute file:
> <image.png>
> However, when I run this script, it produces the error: "No known data format for file suffix '.defattr'"
>
> Any advice on how I can better go about producing this file or how I can modify my script to prevent this error would be greatly appreciated.
> Thank you for your time.
>
> Kind regards,
> David

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