Describe loading of .dcd trajectories in the docs

Remove the directory with .pdb files and use .dcd trajectory instead
Fluorescence-Tools · Sep 8, 2020 · 7955f7c · 7955f7c
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diff --git a/doc/FRET pair selection tutorial/FRET pair selection tutorial.md b/doc/FRET pair selection tutorial/FRET pair selection tutorial.md
@@ -16,20 +16,25 @@ We use T4 lysozyme (T4L) protein as an example. It is recommended go through the
 ## FRET pair selection
 1. Start Olga software (`Olga.exe` executable).
 
-2. Press "Import structures from directory" button to load a set of PDB files. Select the directory that contains files you need to screen. In this example we use a [trajectory](../data/T4L/3GUN_NMSim_1.8.zip), which contains structural models of T4L protein generated by [NMSim](http://nmsim.de/) software from the 3GUN crystal structure. The trajectory was clustered using RMSD as the distance metric and a threshold of 1.8 Angstrom. You will need to extract the [.zip archive](../data/T4L/3GUN_NMSim_1.8.zip) first.
-
-     ![Import Structures](import%20directory.png)
+2. Choose "Import trajectory" menu item to load a trajectory. Select the trajectory and topology files you need to screen. In this example we use a [trajectory](../data/T4L/3GUN_NMSim_cl-rep_894.dcd) and the corresponding [topology](../data/T4L/3GUN_NMSim_cl-rep-001.pdb), which contains structural models of T4L protein generated by [NMSim](http://nmsim.de/) software from the 3GUN crystal structure. The trajectory was clustered using RMSD as the distance metric and a threshold of 1.8 Angstrom. 
 
+     ![Import trajectory](import_trajectory.png)
+
+     ![Specify trajectory files](specify_trajectory_files.png)
+
 3. Now we need to create a labelling position evaluator that will serve as a template for other positions. In this tutorial we use the same template for donor and acceptor labels, but this is not mandatory. Select "Position" option from the dropdown menu, then press the "+" button.
 
      ![Create Evaluator](create%20evaluator.png)
 
      New labelling position will appear in the evaluators panel. Unfold it to see its settings.
 
 4. Now Labelling Position properties can be filled out. In this tutorial parameters are chosen to represent both Alexa 488 and Alexa 647 dyes. First one has to choose the simulation type (here AV1 is selected). Chromophore moiety approximated by a sphere with the radius of 3.5 Angstrom (`radius1 = 3.5`). It's linker has length of 21 Angstrom at maximum extension (`linker_length = 21`). We use linker width of 2 Angstrom; digitization step is set to 0.9 Angstrom (`simulation_grid_resolution = 0.9`). For the template chain ID (`chain_identifier`), residue ID (`residue_seq_number`), residue name (`residue_name`) should not be changed, they will be set automatically later.  In experiment, typically, labelled residue is mutated to cysteine and then the dye is covalently bound to it by maleimide linker. To mimic that, we use Cβ atom as the attachment point (`atom_name = CB`). User can specify `allowed_sphere_radius` option, which tells algorithm to ignore obstacles in the given radius in AV simulation. For example, side chain atoms would not exist in experiment, but they are present in the PDB files and can be disregarded for AV simulations.
-    We can rename evaluator from default `new LP`  to, e.g. `template_LP` by double-clicking on its name. Activate the template labelling position draft by pressing "save" button.  ![Template labelling position settings](template%20LP.png)
+    We can rename evaluator from default `new LP`  to, e.g. `template_LP` by double-clicking on its name. Activate the template labelling position draft by pressing "save" button.  
+
+    ![Template labelling position settings](template%20LP.png)
 
 5. Next, we will use `Wizards -> Add multiple labeling positions` from the top menu bar to automatically populate the labelling positions list with all residues of interest. Normally one would select almost all positions in this dialog. Positions can be omitted if corresponding mutations could affect structure or function of the protein or for any other reason. For the sake of demonstration and to save time we include only residues 35-50, 85-95 and 115-120. Time needed to calculate FRET efficiencies is proportional to the number of pairs added (next step).
+
     ![Add labelling positions menu](add%20LPs.png)
 
     You can use `Ctrl + A` combination to select all residues and `Space` to toggle the check boxes.

diff --git a/doc/FRET pair selection tutorial/import directory.png b/doc/FRET pair selection tutorial/import directory.png
diff --git a/doc/FRET pair selection tutorial/import_trajectory.png b/doc/FRET pair selection tutorial/import_trajectory.png
diff --git a/doc/FRET pair selection tutorial/specify_trajectory_files.png b/doc/FRET pair selection tutorial/specify_trajectory_files.png
diff --git a/doc/data/T4L/3GUN_NMSim_1.8.zip b/doc/data/T4L/3GUN_NMSim_1.8.zip
diff --git a/doc/screening tutorial/import directory.png b/doc/screening tutorial/import directory.png
diff --git a/doc/screening tutorial/import_trajectory.png b/doc/screening tutorial/import_trajectory.png
diff --git a/doc/screening tutorial/screening tutorial.md b/doc/screening tutorial/screening tutorial.md
@@ -16,15 +16,16 @@ In this tutorial we walk through the calculation of FRET-average inter-dye dista
 Additional information is available in the [article by Kalinin et al](https://doi.org/10.1038/nmeth.2222):
 > Kalinin S, Peulen T, Sindbert S, Rothwell PJ, Berger S, Restle T, Goody RS, Gohlke H, Seidel CA. A toolkit and benchmark study for FRET-restrained high-precision structural modeling. Nature methods. 2012 Dec;9(12):1218.
 
-![AV clouds](/home/dimura/workspace/Olga/doc/screening tutorial/DNA_AVs.jpg)
+![AV clouds](DNA_AVs.jpg)
 
 ## Screening
 
 1. Start Olga software (`Olga.exe` executable).
 
-2. Press "Import structures from directory" button to load a set of PDB files. Select the directory that contains files you need to screen. In this example we use a [trajectory](../data/T4L/3GUN_NMSim_1.8.zip), which contains structural models of T4L protein generated by [NMSim](http://nmsim.de/) software from the 3GUN crystal structure. The trajectory was clustered using RMSD as the distance metric and a threshold of 1.8 Angstrom. You will need to extract the [.zip archive](../data/T4L/3GUN_NMSim_1.8.zip) first.
+2. Choose "Import trajectory" menu item to load a trajectory. Select the trajectory and topology files you need to screen. In this example we use a [trajectory](../data/T4L/3GUN_NMSim_cl-rep_894.dcd) and the corresponding [topology](../data/T4L/3GUN_NMSim_cl-rep-001.pdb), which contains structural models of T4L protein generated by [NMSim](http://nmsim.de/) software from the 3GUN crystal structure. The trajectory was clustered using RMSD as the distance metric and a threshold of 1.8 Angstrom. 
 
-   ![Import Structures](import%20directory.png)
+   ![Import trajectory](import_trajectory.png)
+   ![Specify trajectory files](specify_trajectory_files.png)
 
 3. In this example we are calculating FRET-average distance between the dyes attached to residue #36 (SER, donor) and #132 (ASN, acceptor). First, we create a labelling position evaluator for the donor. Select "Position" option from the dropdown menu, then press the "+" button.
 

diff --git a/doc/screening tutorial/specify_trajectory_files.png b/doc/screening tutorial/specify_trajectory_files.png