Swap template matching at3 and rln5

Author: Phaips

docs/03-tutorial/04-template-matching/index.md

@@ -74,6 +74,34 @@ relion_image_handler --i input.mrc --o output.mrc --rescale_angpix 7.64 --new_bo
 - **`new_box`** or **`clip`**: Boxsize (in pixels). See [good box sizes](https://blake.bcm.edu/emanwiki/EMAN2/BoxSize).
 - **`force_header_angpix`**: There might be some discrepancy between the desired and actual pixel size from the way RELION scales the image. We force the header to the desired pixel size.
 
+## Running template matching on AreTomo3 tomograms {#at3tm}
+
+Similarly, if you have reconstructed your tomograms using the [AreTomo3 pipeline](/03-tutorial/02-aretomo3/), we have a **[batch_pytom_aretomo3](https://github.com/Phaips/batch_pytom_aretomo3)** script. This will also create submission files for template matching using the tilt and CTF information from the AreTomo3 outputs. Your output folder should look something like:
+
+```
+aretomo3/
+├─ AreTomo3_Session.json
+├─ TiltSeries_Metrics.csv
+├─ TiltSeries_TimeStamp.csv
+├─ Position_1.aln
+├─ Position_1.mrc
+├─ Position_1_ODD.mrc
+├─ Position_1_EVN.mrc
+├─ Position_1_Vol.mrc
+├─ Position_1_CTF.txt
+├─ Position_1_TLT.txt
+├─ Position_1_CTF_Imod.txt
+├─ Position_1_Imod/
+│   ├─ Position_1_st.tlt
+│   ├─ Position_1_st.xf
+│   └─ Position_1_order_list.csv
+├─ Position_2.aln
+├─ Position_2.mrc
+...
+```
+
+The functionality of the batch submission script is basically the same as for the above [RELION5](/03-tutorial/04-template-matching/#rln5tm) one. Make sure to check the `--help` and the [Github README](https://github.com/Phaips/batch_pytom_aretomo3) and feel free to raise any issues or comments directly on the GitHub page. Alternatively, as always, you can run pytom with template matching just using the conventional way. Our scripts are intended to facilitate the batch submission of jobs in case you want to template match hundreds of tomograms.
+
 ### Running template matching on RELION5 tomograms {#rln5tm}
 
 To run template matching in batch (on all the tomograms in your RELION folder), we will use this **[batch_pytom_wRln5](https://github.com/Phaips/batch_pytom_wRln5)** script we wrote. It is intended to create `bash.sh` files for SLURM submission.  It will read all necessary information like the defocus per tilt and exposure values from the `tilt-series.star` files in your RELION `Tomograms/jobXXX/` folder. For each tomogram, those values will be provided to the `pytom_match_template.py` script. Alternatively, as always, you can just run template matching using pytom in the conventional way. Our scripts are intended to facilitate the batch submission of jobs in case you want to template match hundreds of tomograms.
@@ -164,34 +192,6 @@ If you don't have an HPC or don't use SLURM, you can just run the regular [pytom
 You can check the `_scores.mrc` file in IMOD for example to already see if template matching was successful. If you open the `tomogram.mrc` and `_scores.mrc` at the same time you should see bright dots at the center of each of your particles of interest. Later in this section, we'll show you how to visualize your particles first with IMOD, and then more appealingly using ChimeraX & ArtiaX.
 
 
-## Running template matching on AreTomo3 tomograms {#at3tm}
-
-Similarly, if you have reconstructed your tomograms using the [AreTomo3 pipeline](/03-tutorial/02-aretomo3/), we have a **[batch_pytom_aretomo3](https://github.com/Phaips/batch_pytom_aretomo3)** script. This will also create submission files for template matching using the tilt and CTF information from the AreTomo3 outputs. Your output folder should look something like:
-
-```
-aretomo3/
-├─ AreTomo3_Session.json
-├─ TiltSeries_Metrics.csv
-├─ TiltSeries_TimeStamp.csv
-├─ Position_1.aln
-├─ Position_1.mrc
-├─ Position_1_ODD.mrc
-├─ Position_1_EVN.mrc
-├─ Position_1_Vol.mrc
-├─ Position_1_CTF.txt
-├─ Position_1_TLT.txt
-├─ Position_1_CTF_Imod.txt
-├─ Position_1_Imod/
-│   ├─ Position_1_st.tlt
-│   ├─ Position_1_st.xf
-│   └─ Position_1_order_list.csv
-├─ Position_2.aln
-├─ Position_2.mrc
-...
-```
-
-The functionality of the batch submission script is basically the same as for the above [RELION5](/03-tutorial/04-template-matching/#rln5tm) one. Make sure to check the `--help` and the [Github README](https://github.com/Phaips/batch_pytom_aretomo3) and feel free to raise any issues or comments directly on the GitHub page. Alternatively, as always, you can run pytom with template matching just using the conventional way. Our scripts are intended to facilitate the batch submission of jobs in case you want to template match hundreds of tomograms.
-
 ## Extract particles
 
 Once you have succesfully run template matching, you can extract your particles with `pytom_extract_candidates.py`. This will create the `particles.star` in RELION5 format to then use for [subtomogram averaging](/03-tutorial/05-sta-in-relion5/). Again for detailed explanation check the documentation or `--help` of the pytom script.