[3dem] 3dem Digest, Vol 209, Issue 22

[Alister Burt]

Hi Kyle,

I'm sorry you didn't find the tutorial beginner friendly enough - it looks
like reading the helptexts for the commands you have been using might be
useful, these are also available on our API docs pages
<https://urldefense.com/v3/__https://warpem.github.io/warp/reference/warptools/api/general/__;!!Mih3wA!C_KTRyqKiRfryJZvM5Osr9n0UeGNkfhWi63hsMO0JEUFfw19FQv5dibeQBB9HwbAYjvR88WpesnJKi42Isv3weM$ >

re: AreTomo, we provide an AreTomo wrapper similar to the IMOD wrappers
called ts_aretomo (docs
<https://urldefense.com/v3/__https://warpem.github.io/warp/reference/warptools/api/tilt_series/*ts_aretomo__;Iw!!Mih3wA!C_KTRyqKiRfryJZvM5Osr9n0UeGNkfhWi63hsMO0JEUFfw19FQv5dibeQBB9HwbAYjvR88WpesnJKi421ZgGrYE$ >)
which is compatible with AreTomo 1.3.4
If you want to run any external tilt series alignment program you can
follow this guide
<https://urldefense.com/v3/__https://warpem.github.io/warp/reference/warptools/custom_tilt_series_alignments/__;!!Mih3wA!C_KTRyqKiRfryJZvM5Osr9n0UeGNkfhWi63hsMO0JEUFfw19FQv5dibeQBB9HwbAYjvR88WpesnJKi42jiRRIJI$ >,
we require IMOD format results for import into Warp

re: EER file processing you can add `--eer_ngroups` or
`--eer_groupexposure` to your create_settings command, I've added a note
about this to the tutorial

Any problems that come up don't hesitate to reach out, I'm more likely to
see questions asked on the Warp google group
<https://urldefense.com/v3/__https://groups.google.com/u/1/g/warp-em__;!!Mih3wA!C_KTRyqKiRfryJZvM5Osr9n0UeGNkfhWi63hsMO0JEUFfw19FQv5dibeQBB9HwbAYjvR88WpesnJKi42Xx_IpOw$ > or our GitHub issues
<https://urldefense.com/v3/__https://github.com/warpem/warp/issues__;!!Mih3wA!C_KTRyqKiRfryJZvM5Osr9n0UeGNkfhWi63hsMO0JEUFfw19FQv5dibeQBB9HwbAYjvR88WpesnJKi42jdZqteo$ >.

Cheers,

Alister

On Wed, 22 Jan 2025 at 12:00, <3dem-request at ncmir.ucsd.edu> wrote:

> Send 3dem mailing list submissions to
>         3dem at ncmir.ucsd.edu
>
> To subscribe or unsubscribe via the World Wide Web, visit
>         https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
> or, via email, send a message with subject or body 'help' to
>         3dem-request at ncmir.ucsd.edu
>
> You can reach the person managing the list at
>         3dem-owner at ncmir.ucsd.edu
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of 3dem digest..."
>
>
> Today's Topics:
>
>    1. Anyone have a detailed tutorial for Warptools? (Kyle Messina)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 22 Jan 2025 11:37:47 -0600
> From: Kyle Messina <messi144 at umn.edu>
> To: 3dem at ncmir.ucsd.edu
> Subject: [3dem] Anyone have a detailed tutorial for Warptools?
> Message-ID:
>         <
> CA+1M+bBXSVQBqRB5p3A+wgCSsGk573MxfYJiNOV9Jz5U2BC3kA at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hello All,
>
> I've been trying to learn both Warp and Warptools for subtomo averaging but
> I've had issues learning Warptools.  The Quick Start: Tilt Series tutorial
> on the website only focuses on the example dataset but does not go into
> details for other potential options such as processing data with AreTomo2
> instead of IMOD or working with EER files.  I have been running into issues
> due to user error and (probably) lack of general knowledge about Warp
> inputs, outputs and how/why different settings affect your results or are
> needed.
>
> Does anyone have a written tutorial that is beginner friendly? The more
> detailed it is for the various steps and commands the better!
>
> Thank you,
> Kyle Messina
> messi144 at umn.edu
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <
> http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20250122/4c2b1603/attachment-0001.html
> >
>
> ------------------------------
>
> Subject: Digest Footer
>
> _______________________________________________
> 3dem mailing list
> 3dem at ncmir.ucsd.edu
> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
>
>
> ------------------------------
>
> End of 3dem Digest, Vol 209, Issue 22
> *************************************
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20250122/bf1cdfca/attachment.html>