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brisvag committed Sep 30, 2022
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2 changes: 1 addition & 1 deletion _sources/index.ipynb
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Expand Up @@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "markdown",
"id": "9622beb0",
"id": "c0c06842",
"metadata": {},
"source": [
"# teamtomo.org - home\n",
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8 changes: 7 additions & 1 deletion _sources/walkthroughs/EMPIAR-10164/m.md
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Expand Up @@ -32,7 +32,13 @@ Mask one of the halfmaps to include only the central hexamer in `Dynamo` then us
relion_mask_create --i <latest_halfmap>.mrc --angpix 1.6 --extend_inimask 5 --o mask_1.6Apx.mrc --ini_threshold 0.05
```

Provide this mask to `M`, and then select the final particle positions (e.g: `run_it019_data.star`) as the input for particle poses. Click `FINISH` to generate the new species.
If using Relion3.1+, we need to reformat the final particle positions `.star` file using `relion_star_downgrade` to the Relion3.0 specification (Warp does not support Relion 3.1+):

```bash
relion_star_downgrade -s run_it019_data.star
```

M will only look for file names with the pattern `*_data.star`, so we need to rename the output from `relion_star_downgrade` (e.g., from `run_it019_data_rln3.0.star` to `rln3.0_run_it019_data.star`). Now, select this reformatted `.star` file containing the final particle positions from Relion as the input for particle poses in M. Click `FINISH` to generate the new species.

## Refinement Parameters

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4 changes: 2 additions & 2 deletions _sources/walkthroughs/EMPIAR-10164/particle-picking.md
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Expand Up @@ -39,7 +39,7 @@ The provided scripts are just a few lines long, and are given for convenience an

We can now take a look at the resulting particle positions, written in the output file `dynamo/findparticles/results/ite_0001/averages/refined_table_ref_001_ite_0001.tbl`.

We can use [`view_particles.m`](https://github.com/teamtomo/teamtomo.github.io/tree/master/walkthroughs/EMPIAR-10164/scripts/view_particles.m) to open a 3D viewer and examine them. Open matlab in `dynamo/findparticles/results/ite_0001/` and run:
We can use [`view_particles.m`](https://github.com/teamtomo/teamtomo.github.io/tree/master/walkthroughs/EMPIAR-10164/scripts/view_particles.m) to open a 3D viewer and examine them. Open matlab in `dynamo/findparticles/results/ite_0001/averages/` and run:

`````{tab-set}
````{tab-item} Command
Expand Down Expand Up @@ -117,7 +117,7 @@ dwrite(nodup, 'result_10Apx_nodup.tbl');

This will create a new table called `result_10Apx_nodup.tbl`, reducing clusters of multiple particles within 4 pixels (half the distance we measured earlier) to a single particle.

The next step is to remove particles that don't belong to the lattice. To do so, we use [`check_radial_distribution.m`](https://github.com/teamtomo/teamtomo.github.io/tree/master/walkthroughs/EMPIAR-10164/scripts/check_radial_distribution.m).
The next step is to remove particles that don't belong to the lattice. To do so, we use [`check_radial_distribution.m`](https://github.com/teamtomo/teamtomo.github.io/tree/master/walkthroughs/EMPIAR-10164/scripts/check_radial_distribution.m) (which requires [`dtneighbours_in_range.m`](https://github.com/teamtomo/teamtomo.github.io/tree/master/walkthroughs/EMPIAR-10164/scripts/dtneighbours_in_range.m)).

Once again, in the same directory, simply run:
`````{tab-set}
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8 changes: 4 additions & 4 deletions mini-tutorials/dynamo/dipoles-to-vesicles.html
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Expand Up @@ -1098,15 +1098,15 @@ <h3>Convert dipoleSet models into oversampled Vesicle models<a class="headerlink
</div>
</aside>
<div class="sd-tab-set docutils">
<input checked="checked" id="ffea1920-952a-4788-ab2b-6d7271cc918e" name="6a538a5d-5f86-48c8-b462-fc0943f53e9c" type="radio">
</input><label class="sd-tab-label" for="ffea1920-952a-4788-ab2b-6d7271cc918e">
<input checked="checked" id="aa76a86e-66ea-4dff-8125-e87fe767d138" name="95b41a8a-e621-47e3-b14b-32779b792ca0" type="radio">
</input><label class="sd-tab-label" for="aa76a86e-66ea-4dff-8125-e87fe767d138">
Command</label><div class="sd-tab-content docutils">
<div class="highlight-matlab notranslate"><div class="highlight"><pre><span></span><span class="n">dipoles2vesicles</span><span class="p">(</span><span class="s">&#39;warp_catalogue&#39;</span><span class="p">,</span><span class="w"> </span><span class="mf">7.5</span><span class="p">)</span><span class="w"></span>
</pre></div>
</div>
</div>
<input id="3ff86214-4b69-48a8-8ac2-366696ad35a3" name="6a538a5d-5f86-48c8-b462-fc0943f53e9c" type="radio">
</input><label class="sd-tab-label" for="3ff86214-4b69-48a8-8ac2-366696ad35a3">
<input id="eacba07a-3014-4fd2-ab33-5f35c5f44742" name="95b41a8a-e621-47e3-b14b-32779b792ca0" type="radio">
</input><label class="sd-tab-label" for="eacba07a-3014-4fd2-ab33-5f35c5f44742">
Source code</label><div class="sd-tab-content docutils">
<div class="highlight-matlab notranslate"><div class="highlight"><pre><span></span><span class="k">function</span><span class="w"> </span><span class="nf">dipoles2vesicles</span><span class="p">(</span>catalogue_name, distance_between_particles<span class="p">)</span><span class="w"></span>
<span class="c">%%% to be run in the folder which holds your catalogue</span><span class="w"></span>
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24 changes: 12 additions & 12 deletions mini-tutorials/dynamo/dtmslice-controls.html
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Expand Up @@ -963,41 +963,41 @@ <h2>Overview<a class="headerlink" href="#overview" title="Permalink to this head
<section id="viewing-controls">
<h2>Viewing controls<a class="headerlink" href="#viewing-controls" title="Permalink to this headline">#</a></h2>
<div class="sd-tab-set docutils">
<input checked="checked" id="616a2188-29b0-48d7-bf2b-e672d4793e2b" name="c8f2a3cd-61d9-44e2-8e9c-a0e24cf19861" type="radio">
</input><label class="sd-tab-label" for="616a2188-29b0-48d7-bf2b-e672d4793e2b">
<input checked="checked" id="ad8d51f5-8694-447b-b2e9-458475fe49e4" name="d9c53158-e033-4f0b-8a4b-5c2aebfafd56" type="radio">
</input><label class="sd-tab-label" for="ad8d51f5-8694-447b-b2e9-458475fe49e4">
general</label><div class="sd-tab-content docutils">
<p>Some parameters can be controlled from the <code class="docutils literal notranslate"><span class="pre">Shown</span> <span class="pre">slice</span></code> controls on the left hand side of <code class="docutils literal notranslate"><span class="pre">dtmslice</span></code></p>
<p><img alt="shown slice controls" src="../../_images/shown-slice.png" /></p>
</div>
<input id="02e8d7a5-1857-4b4d-9a4b-64531dd30e8e" name="c8f2a3cd-61d9-44e2-8e9c-a0e24cf19861" type="radio">
</input><label class="sd-tab-label" for="02e8d7a5-1857-4b4d-9a4b-64531dd30e8e">
<input id="c9a5d9e4-0462-46ea-b7b5-142521e3e222" name="d9c53158-e033-4f0b-8a4b-5c2aebfafd56" type="radio">
</input><label class="sd-tab-label" for="c9a5d9e4-0462-46ea-b7b5-142521e3e222">
moving a slice</label><div class="sd-tab-content docutils">
<p>A slice can be moved along it’s projection direction by <code class="docutils literal notranslate"><span class="pre">left-click</span></code> + dragging the mouse
or using the mouse wheel.</p>
<p><img alt="moving a slice" src="../../_images/move-slice.gif" /></p>
</div>
<input id="ff3c26bd-38a4-4802-8614-673eec9ce916" name="c8f2a3cd-61d9-44e2-8e9c-a0e24cf19861" type="radio">
</input><label class="sd-tab-label" for="ff3c26bd-38a4-4802-8614-673eec9ce916">
<input id="e99364be-1111-4c7b-9fbf-e0503cf5e865" name="d9c53158-e033-4f0b-8a4b-5c2aebfafd56" type="radio">
</input><label class="sd-tab-label" for="e99364be-1111-4c7b-9fbf-e0503cf5e865">
projection direction</label><div class="sd-tab-content docutils">
<p>The projection direction can easily be changed between
‘x’, ‘y’ or ‘z’ by hitting the <code class="docutils literal notranslate"><span class="pre">x</span></code>, <code class="docutils literal notranslate"><span class="pre">y</span></code> or <code class="docutils literal notranslate"><span class="pre">z</span></code> keys with your mouse on the slice.
Mouse position controls the new position of the slice.</p>
<p><img alt="xyz-projection" src="../../_images/xyzproj.gif" /></p>
</div>
<input id="359899a7-3576-4177-aba2-85241983ff77" name="c8f2a3cd-61d9-44e2-8e9c-a0e24cf19861" type="radio">
</input><label class="sd-tab-label" for="359899a7-3576-4177-aba2-85241983ff77">
<input id="64715c07-ec80-43d4-b56f-99052ef07e83" name="d9c53158-e033-4f0b-8a4b-5c2aebfafd56" type="radio">
</input><label class="sd-tab-label" for="64715c07-ec80-43d4-b56f-99052ef07e83">
scene perspective</label><div class="sd-tab-content docutils">
<p>You can move the camera around the scene by <code class="docutils literal notranslate"><span class="pre">ctrl</span></code> + <code class="docutils literal notranslate"><span class="pre">left-click</span></code> + dragging the mouse.</p>
<p><img alt="move camera" src="../../_images/move-camera.gif" /></p>
</div>
<input id="f3d8a117-9d05-4aaa-bc26-5037c0bcdb17" name="c8f2a3cd-61d9-44e2-8e9c-a0e24cf19861" type="radio">
</input><label class="sd-tab-label" for="f3d8a117-9d05-4aaa-bc26-5037c0bcdb17">
<input id="a91d756f-9c8d-4e81-bf87-0ce03b34c7ff" name="d9c53158-e033-4f0b-8a4b-5c2aebfafd56" type="radio">
</input><label class="sd-tab-label" for="a91d756f-9c8d-4e81-bf87-0ce03b34c7ff">
saving slices</label><div class="sd-tab-content docutils">
<p>You can save a copy of the active slice in <code class="docutils literal notranslate"><span class="pre">dtmslice</span></code> by hitting the <code class="docutils literal notranslate"><span class="pre">s</span></code> key.</p>
<p><img alt="save slice" src="../../_images/save-slice.gif" /></p>
</div>
<input id="074642b2-0469-45bb-9215-3c0a1f163378" name="c8f2a3cd-61d9-44e2-8e9c-a0e24cf19861" type="radio">
</input><label class="sd-tab-label" for="074642b2-0469-45bb-9215-3c0a1f163378">
<input id="b5d89ce5-47b2-4675-af9d-61720d692c0d" name="d9c53158-e033-4f0b-8a4b-5c2aebfafd56" type="radio">
</input><label class="sd-tab-label" for="b5d89ce5-47b2-4675-af9d-61720d692c0d">
slice thickness</label><div class="sd-tab-content docutils">
<p>A <code class="docutils literal notranslate"><span class="pre">thickness</span></code> of 10 means that the displayed slice will be an average over 10 slices
along the projection direction.</p>
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12 changes: 6 additions & 6 deletions mini-tutorials/dynamo/extract-from-catalogue.html
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Expand Up @@ -958,14 +958,14 @@ <h2>Prerequisites<a class="headerlink" href="#prerequisites" title="Permalink to
<h2>The procedure<a class="headerlink" href="#the-procedure" title="Permalink to this headline">#</a></h2>
<p>Open your catalogue in <code class="docutils literal notranslate"><span class="pre">dcm</span></code> and click through the tabs below to see the whole procedure</p>
<div class="sd-tab-set docutils">
<input checked="checked" id="d9ae7d43-8354-47c8-b768-369a88bd7b12" name="f208cac7-28f0-4db9-ab48-2ad6101405c5" type="radio">
</input><label class="sd-tab-label" for="d9ae7d43-8354-47c8-b768-369a88bd7b12">
<input checked="checked" id="9af5e912-2d11-4e6f-977d-c0b0bc65e87c" name="18875686-0668-45b6-a8f8-93b432e9289a" type="radio">
</input><label class="sd-tab-label" for="9af5e912-2d11-4e6f-977d-c0b0bc65e87c">
select tomograms</label><div class="sd-tab-content docutils">
<p>Select the tomograms you would like to crop from (or use the select all button)
<img alt="select volumes" src="../../_images/select-all-volumes.gif" /></p>
</div>
<input id="69f24f53-e299-4553-8601-9f430062fbaf" name="f208cac7-28f0-4db9-ab48-2ad6101405c5" type="radio">
</input><label class="sd-tab-label" for="69f24f53-e299-4553-8601-9f430062fbaf">
<input id="ca2c2fd1-4834-414a-9330-37015514fe09" name="18875686-0668-45b6-a8f8-93b432e9289a" type="radio">
</input><label class="sd-tab-label" for="ca2c2fd1-4834-414a-9330-37015514fe09">
create volume list</label><div class="sd-tab-content docutils">
<p>The volume list manager can create volume list (<code class="docutils literal notranslate"><span class="pre">.vll</span></code>) files containing the information needed for cropping particles.</p>
<p>Open the volume list manager from the <code class="docutils literal notranslate"><span class="pre">Crop</span> <span class="pre">particles</span></code> menu at the top of the <code class="docutils literal notranslate"><span class="pre">dcm</span></code> window.</p>
Expand All @@ -977,8 +977,8 @@ <h2>The procedure<a class="headerlink" href="#the-procedure" title="Permalink to
</ul>
<p><img alt="create volume list file" src="../../_images/create-volume-list.gif" /></p>
</div>
<input id="483caec9-2c35-4588-a8ae-d0783151898f" name="f208cac7-28f0-4db9-ab48-2ad6101405c5" type="radio">
</input><label class="sd-tab-label" for="483caec9-2c35-4588-a8ae-d0783151898f">
<input id="d58474ec-9128-4e4d-a7c3-9afc29fb4f14" name="18875686-0668-45b6-a8f8-93b432e9289a" type="radio">
</input><label class="sd-tab-label" for="d58474ec-9128-4e4d-a7c3-9afc29fb4f14">
extract particles</label><div class="sd-tab-content docutils">
<aside class="margin sidebar">
<p class="sidebar-title"></p>
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32 changes: 16 additions & 16 deletions mini-tutorials/dynamo/interactive-mask-creation.html
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Expand Up @@ -968,32 +968,32 @@ <h2>Loading our data into mapview<a class="headerlink" href="#loading-our-data-i
<h2>Getting comfortable with the viewer<a class="headerlink" href="#getting-comfortable-with-the-viewer" title="Permalink to this headline">#</a></h2>
<p>Here we go over some of the controls available in this viewer, you might have noticed there are a lot!</p>
<div class="sd-tab-set docutils">
<input checked="checked" id="f08a1b71-df29-4f0b-9623-170ce1f4e0e8" name="449332ea-a10d-49cb-a029-6d48d8fa25df" type="radio">
</input><label class="sd-tab-label" for="f08a1b71-df29-4f0b-9623-170ce1f4e0e8">
<input checked="checked" id="edbed25b-57c7-4384-8468-057a4a96b1cb" name="d64b2ac6-287b-475f-904d-869cbecb32ea" type="radio">
</input><label class="sd-tab-label" for="edbed25b-57c7-4384-8468-057a4a96b1cb">
x/y/z view</label><div class="sd-tab-content docutils">
<p>You can switch between viewing x-, y- or z-slices with the <code class="docutils literal notranslate"><span class="pre">x</span></code>, <code class="docutils literal notranslate"><span class="pre">y</span></code> and <code class="docutils literal notranslate"><span class="pre">z</span></code> buttons.</p>
<p><img alt="xyz switching image" src="../../_images/xyz.gif" /></p>
</div>
<input id="33be7aa7-a77e-4c93-91dc-94bfdbd107d0" name="449332ea-a10d-49cb-a029-6d48d8fa25df" type="radio">
</input><label class="sd-tab-label" for="33be7aa7-a77e-4c93-91dc-94bfdbd107d0">
<input id="524e570b-ca06-447d-89a1-5621f4731432" name="d64b2ac6-287b-475f-904d-869cbecb32ea" type="radio">
</input><label class="sd-tab-label" for="524e570b-ca06-447d-89a1-5621f4731432">
slice mode</label><div class="sd-tab-content docutils">
<p>You can switch between viewing either a single projection or a set of slices</p>
<p><img alt="singleproj image" src="../../_images/singleproj.gif" /></p>
</div>
<input id="eb6d1afa-450b-4bd8-a2db-a930cfe3b49d" name="449332ea-a10d-49cb-a029-6d48d8fa25df" type="radio">
</input><label class="sd-tab-label" for="eb6d1afa-450b-4bd8-a2db-a930cfe3b49d">
<input id="bc33ece7-216d-4d77-bb93-32bd39e9ed1c" name="d64b2ac6-287b-475f-904d-869cbecb32ea" type="radio">
</input><label class="sd-tab-label" for="bc33ece7-216d-4d77-bb93-32bd39e9ed1c">
Fourier filters</label><div class="sd-tab-content docutils">
<p>Bandpass filters can be applied from the GUI by setting the <code class="docutils literal notranslate"><span class="pre">band</span></code> parameters then hitting the <code class="docutils literal notranslate"><span class="pre">band</span></code> button. The filter frequencies are set in Fourier pixels.</p>
<p><img alt="bandpass image" src="../../_images/bandpass.gif" /></p>
</div>
<input id="56cc0ef5-5492-4652-93b1-73ee3d668229" name="449332ea-a10d-49cb-a029-6d48d8fa25df" type="radio">
</input><label class="sd-tab-label" for="56cc0ef5-5492-4652-93b1-73ee3d668229">
<input id="d3511992-557b-4376-9927-21324ed82b42" name="d64b2ac6-287b-475f-904d-869cbecb32ea" type="radio">
</input><label class="sd-tab-label" for="d3511992-557b-4376-9927-21324ed82b42">
symmetry</label><div class="sd-tab-content docutils">
<p>Symmetry can be applied from the GUI. Symmetry is applied along the z-axis of the volume.</p>
<p><img alt="symmetry image" src="../../_images/sym.gif" /></p>
</div>
<input id="eb871282-3909-4b25-bf72-c54ce0ee1f1a" name="449332ea-a10d-49cb-a029-6d48d8fa25df" type="radio">
</input><label class="sd-tab-label" for="eb871282-3909-4b25-bf72-c54ce0ee1f1a">
<input id="1d1a2b18-a684-491c-a1c2-74ecd4760989" name="d64b2ac6-287b-475f-904d-869cbecb32ea" type="radio">
</input><label class="sd-tab-label" for="1d1a2b18-a684-491c-a1c2-74ecd4760989">
reset</label><div class="sd-tab-content docutils">
<p>The volume visualised can be reset to its original state at any time with the <code class="docutils literal notranslate"><span class="pre">reset</span></code> button.</p>
<p><img alt="reset button image" src="../../_images/reset.gif" /></p>
Expand All @@ -1004,8 +1004,8 @@ <h2>Getting comfortable with the viewer<a class="headerlink" href="#getting-comf
<h2>Mask creation<a class="headerlink" href="#mask-creation" title="Permalink to this headline">#</a></h2>
<p>This section covers the basics of mask creation in <code class="docutils literal notranslate"><span class="pre">dpkdev.legacy.dynamo_mapview()</span></code></p>
<div class="sd-tab-set docutils">
<input checked="checked" id="a25d12d6-2513-4c28-84cf-ba45ac02fab2" name="4915beb6-1077-49ff-9d31-ad51e5d3143e" type="radio">
</input><label class="sd-tab-label" for="a25d12d6-2513-4c28-84cf-ba45ac02fab2">
<input checked="checked" id="02cc42c6-0f29-454b-b728-474ce3450388" name="f94e6467-1775-4bbd-8d33-40c1d2103677" type="radio">
</input><label class="sd-tab-label" for="02cc42c6-0f29-454b-b728-474ce3450388">
mask creation</label><div class="sd-tab-content docutils">
<p>You can create a shaped mask by</p>
<ul class="simple">
Expand All @@ -1016,14 +1016,14 @@ <h2>Mask creation<a class="headerlink" href="#mask-creation" title="Permalink to
<p>hit the <code class="docutils literal notranslate"><span class="pre">layer</span></code> button to bring up a visualisation of the mask on the currently depicted slices.
<img alt="interactive mask creation image" src="../../_images/masking.gif" /></p>
</div>
<input id="23aac763-f6dc-4da5-ab10-85103dbcad20" name="4915beb6-1077-49ff-9d31-ad51e5d3143e" type="radio">
</input><label class="sd-tab-label" for="23aac763-f6dc-4da5-ab10-85103dbcad20">
<input id="7a7592cc-05a4-4635-abf4-6c63600b545e" name="f94e6467-1775-4bbd-8d33-40c1d2103677" type="radio">
</input><label class="sd-tab-label" for="7a7592cc-05a4-4635-abf4-6c63600b545e">
saving a mask</label><div class="sd-tab-content docutils">
<p>You can save a mask by setting a filename in the <code class="docutils literal notranslate"><span class="pre">Mask</span></code> section and hitting <code class="docutils literal notranslate"><span class="pre">save</span></code>
<img alt="save mask image" src="../../_images/savemask.gif" /></p>
</div>
<input id="d848cbfc-28ad-4b8d-9a09-8a2b7d630420" name="4915beb6-1077-49ff-9d31-ad51e5d3143e" type="radio">
</input><label class="sd-tab-label" for="d848cbfc-28ad-4b8d-9a09-8a2b7d630420">
<input id="d33e9a10-c9df-4af9-94df-7fd63b7f7786" name="f94e6467-1775-4bbd-8d33-40c1d2103677" type="radio">
</input><label class="sd-tab-label" for="d33e9a10-c9df-4af9-94df-7fd63b7f7786">
saving a masked volume</label><div class="sd-tab-content docutils">
<p>You can apply a mask onto a volume and save the volume in the <code class="docutils literal notranslate"><span class="pre">File</span> <span class="pre">I/O</span></code> section
<img alt="" src="../../_images/save_masked_vol.gif" /></p>
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