CLI update

Author: AnnaEngel98

education/Others/powerfit-webserver/index.md

@@ -333,7 +333,7 @@ their interactions:
   residues and their spatial neighbors.
 </a>
 <a class="prompt prompt-question">
-  Are there any clashes between the ribosome and RsgA chains? Show the selection as spheres to visualize this better
+  Are there any clashes between the ribosome and RsgA chains? Show the selection as spheres to visualize this better.
 </a>
 
 

education/Others/powerfit/index.md

@@ -2,7 +2,7 @@
 layout: page
 title: "PowerFit Tutorial"
 excerpt: "A small tutorial on PowerFit for automatic rigid body fitting"
-tags: [PowerFit, Cryo-EM, HADDOCK, Ribosome, Chimera, rigid body fitting]
+tags: [PowerFit, Cryo-EM, HADDOCK, Ribosome, ChimeraX, rigid body fitting]
 image:
   feature: pages/banner_education-thin.jpg
 ---
@@ -18,11 +18,12 @@ This tutorial consists of the following sections:
 
 PowerFit is a software application developed to fit atomic resolution
 structures of biomolecules to cryo-electron microscopy (cryo-EM) density maps.
-It is open-source and available for download on [Github][link-powerfit].
+It is open-source and available for download on [Github][link-powerfit]. In addition 
+you can find a manual on usage of PowerFit [here][link-manual]. 
 
 This tutorial will show you how to utilize PowerFit by applying it to an E.coli
 ribosome case. To follow this tutorial, you need, in addition to PowerFit, the
-[UCSF Chimera][link-chimera] visualization software, a popular tool in the
+[UCSF ChimeraX][link-chimerax] visualization software, a popular tool in the
 cryo-electron microscopy community for its volume visualization capabilities.
 We will further discuss the limits of rigid body fitting, and how HADDOCK can
 alleviate some of the shortcomings. We provide the data necessary to run this
@@ -41,13 +42,13 @@ _AIMS Biophysics_. *2*, 73-87 (2015).
 _Structure._ *23*, 949-960 (2015).
 
 Throughout the tutorial, colored text will be used to refer to questions or 
-instructions, Linux and/or Chimera commands.
+instructions, Linux and/or ChimeraX commands.
 
 <a class="prompt prompt-question">This is a question prompt: try answering 
 it!</a>
 <a class="prompt prompt-info">This an instruction prompt: follow it!</a>
-<a class="prompt prompt-pymol">This is a Chimera prompt: write this in the 
-Chimera command line prompt!</a>
+<a class="prompt prompt-pymol">This is a ChimeraX prompt: write this in the 
+ChimeraX command line!</a>
 <a class="prompt prompt-cmd">This is a Linux prompt: insert the commands in the 
 terminal!</a>
 
@@ -74,7 +75,7 @@ ribosome has already been properly fitted in the density.
 </a>
 
 *In case you might run this tutorial on your own*, make sure to have the required
-software installed ([UCSF Chimera][link-chimera] and [PowerFit][link-powerfit]), 
+software installed ([UCSF ChimeraX][link-chimerax] and [PowerFit][link-powerfit]), 
 and download the data to run this tutorial from our GitHub
 data repository [here][link-data] or clone it from the command line
 
@@ -89,26 +90,24 @@ data repository [here][link-data] or clone it from the command line
 Let us first inspect the data we have available, namely the cryo-EM density map
 and the structures we will attempt to fit. 
 
-Using Chimera, we can easily visualize and inspect the density and models,
+Using ChimeraX, we can easily visualize and inspect the density and models,
 mostly through a few mouse clicks.
 
 <a class="prompt prompt-info">
   Open the density map together with the ribosome and KsgA.
 </a>
 <a class="prompt prompt-cmd">
-    chimera ribosome-KsgA.map ribosome.pdb KsgA.pdb
+    chimerax ribosome-KsgA.map ribosome.pdb KsgA.pdb
 </a>
 
 In the `Volume Viewer` window, the middle slide bar provides control on the
 value at which the isosurface of the density is shown. At high values, the
 envelope will sink while lower values might even display the noise in the map.
 We will first make the density transparent, to see the fitted structure inside:
 
-* Within the `Volume Viewer` click on the gray box next to `Color`, which opens
-  the `Color Editor` window.
-* In there, check the `Opacity` box. An extra slider bar appears in the box
-  called `A`, for the alpha channel.
-* Set the alpha channel value to around 0.6.
+<a class="prompt prompt-pymol">
+  transparency #1 60
+</a>
 
 Notice that the density becomes transparent providing a better view of the fit
 of the ribosome model. On closer inspection, you can also discern a region of
@@ -133,7 +132,7 @@ on the map and calculate a cross-correlation score for each of them.
   map.
 </a>
 <a class="prompt prompt-cmd">
-  powerfit ribosome-KsgA.map 13 KsgA.pdb -d run-KsgA -a 20 -p 2 -l
+  powerfit ribosome-KsgA.map 13 KsgA.pdb -d run-KsgA -a 20 -p 2
 </a>
 
 While performing the search, PowerFit will update you on the progress of the 
@@ -161,10 +160,8 @@ option specifies where the results will be stored while the `-p` option
 specifies the number of processors that PowerFit can use during the search, to
 leverage available CPU resources.
 
-Finally, the `-l` flag applies a Laplace pre-filter on the density data, which
-increases the cross-correlation sensitivity by enhancing edges in the density.
 In this example scenario, all other options are left at their default values
-but feel free to explore them.
+but feel free to explore [them][link-manual].
 
 
 ## Analyzing the results
@@ -186,14 +183,14 @@ with date and timing information.
 
 <a class="prompt prompt-info">
   Open the density map, the *lcc.mrc* cross-correlation map, and the 10 
-best-ranked solutions in Chimera.
+best-ranked solutions in ChimeraX.
 </a>
 <a class="prompt prompt-cmd">
-  chimera ribosome-KsgA.map run-KsgA/lcc.mrc ribosome.pdb run-KsgA/fit_*.pdb
+  chimerax ribosome-KsgA.map run-KsgA/lcc.mrc ribosome.pdb run-KsgA/fit_*.pdb
 </a>
 
-Make the density map transparent again, by adjusting the alpha channel value to
-0.6. The values of the `lcc.mrc` slider bar correspond to the cross-correlation
+Make the density map transparent again to 60.
+The values of the `lcc.mrc` slider bar correspond to the cross-correlation
 score found. In this way, you can selectively visualize regions of high or low
 cross-correlation values: i.e., pushing the slider to the right (higher cutoff)
 shows only regions of the grid with high cross-correlation scores. 
@@ -202,10 +199,10 @@ As you can see, PowerFit found quite some local optima, one of which stands out
 (if the rotational search was tight enough). Further, the 10 best-ranked
 solutions are centered on regions corresponding to local cross-correlation maxima.
 
-To view each fitted solution individually, in the main panel, go to `Favorites`
-→ `Model Panel` to open the `Model Panel` window. The window shows each model
-and its associated color that Chimera has processed. To show or hide a specific
-model you can click the box in the `S` column.
+To view each fitted solution individually, in the main panel, go to `Tools`
+→ `Models` to open the `Model Panel` window. The window shows each model
+and its associated color that ChimeraX has processed. To show or hide a specific
+model you can click the box in the column with an eye.
 
 <a class="prompt prompt-info">
   Go through the 10 solutions one by one to appreciate their goodness-of-fit
@@ -214,12 +211,13 @@ model you can click the box in the `S` column.
 <a class="prompt prompt-question">
   Do you agree with what PowerFit proposes as the best solution?
 </a>
+
 <a class="prompt prompt-info">
-  In a new Chimera session, reopen the density map and the fit that you find 
+  In a new ChimeraX session, reopen the density map and the fit that you find 
 best. Replace *?* by the appropriate solution number.
 </a>
 <a class="prompt prompt-cmd">
-  chimera ribosome-KsgA.map ribosome.pdb run-KsgA/fit_?.pdb
+  chimerax ribosome-KsgA.map ribosome.pdb run-KsgA/fit_?.pdb
 </a>
 
 You now have combined the ribosome structure with the rigid-body fit of KsgA
@@ -228,29 +226,30 @@ experiments performed on this complex indicate three charged residues of KsgA -
 `R221`, `R222`, and `K223` - that are of special importance for the
 interaction. 
 
-In the same session of Chimera where you have your chosen fitted KsgA
-structure, go to `Favorites` → `Command Line`. A command line is now present
-below the main viewing window.  In the command line of Chimera, type the
+In the same session of ChimeraX where you have your chosen fitted KsgA
+structure, typ in the command line of ChimeraX the
 following instructions to center your view on these residues and highlight
 their interactions:
 
 <a class="prompt prompt-pymol">
-  show #2:221-223 zr<5 & #1 || #2:221-223  
-  center #2:221-223 zr<5 & #1 || #2:221-223
+  sel #3:221-223 <br>
+  view sel <br>
+  contacts sel distanceOnly 5.0 makePseudobonds true reveal true <br>
+</a>
 </a>
 <a class="prompt prompt-info">
   Take some time to inspect the model, paying particular attention to these three
   residues and their spatial neighbors.
 </a>
 <a class="prompt prompt-question">
-  Are there any clashes between the ribosome and KsgA chains?
+  Are there any clashes between the ribosome and KsgA chains? Show the selection as spheres to visualize this better.
 </a>
 <a class="prompt prompt-question">
   Is the mutagenesis data explained by the model, i.e. are the three charged 
 amino acids involved in strong interactions?
 </a>
 
-Chimera also includes a tool to locally optimize the fit of a rigid structure 
+ChimeraX also includes a tool to locally optimize the fit of a rigid structure 
 against a given density map, which can be an additional help on top of the 
 PowerFit calculations. Make the main display window active by clicking on it, 
 then go to `Tools` → `Volume data` → `Fit in Map`. In the newly opened `Fit in 
@@ -259,14 +258,14 @@ Map` window, select the best-fitted structure of PowerFit (`fit_?.pdb`) as
 Press `Fit` to start the optimization. 
 
 <a class="prompt prompt-question">
-  Does the Chimera local fit optimization tool improve the results of PowerFit?
+  Does the ChimeraX local fit optimization tool improve the results of PowerFit?
 </a>
 
-The scoring function used by Chimera to estimate the quality of the fit makes 
+The scoring function used by ChimeraX to estimate the quality of the fit makes 
 our model worse, increasing the number of clashes between the ribosomal RNA and 
 KsgA. Click `Undo` in the `Fit in Map` window to undo the optimization.
 
-Next, we will try to optimize the fit using the cross-correlation that Chimera 
+Next, we will try to optimize the fit using the cross-correlation that ChimeraX 
 provides. Click `Options` and check the `Use map simulated from atoms, 
 resolution` box and fill in `13` for resolution. Check the `correlation` radio 
 button and uncheck the `Use only data above contour level from first map`. 
@@ -304,10 +303,10 @@ HADDOCK model, generated by combining the cryo-EM map, the PowerFit centroid
 positions, and the mutagenesis data, in the tutorial data folder.
 
 <a class="prompt prompt-info">
-  Open the density map in Chimera and load the best-ranked HADDOCK model.
+  Open the density map in ChimeraX and load the best-ranked HADDOCK model.
 </a>
 <a class="prompt prompt-cmd">
-  chimera ribosome-KsgA.map HADDOCK-ribosome.pdb HADDOCK-KsgA.pdb
+  chimerax ribosome-KsgA.map HADDOCK-ribosome.pdb HADDOCK-KsgA.pdb
 </a>
 <a class="prompt prompt-question">
 Does HADDOCK improve the quality of the model, i.e. are the number of clashes
@@ -367,6 +366,7 @@ suggestions, feel free to contact us via email or by submitting an issue in the
 appropriate Github repository.
 
 [link-powerfit]: https://github.com/haddocking/powerfit "PowerFit"
-[link-chimera]: https://www.cgl.ucsf.edu/chimera/ "UCSF Chimera"
+[link-chimerax]: https://www.cgl.ucsf.edu/chimerax/ "UCSF ChimeraX"
 [link-data]: https://github.com/haddocking/powerfit-tutorial "PowerFit tutorial data"
 [link-density]: https://www.ebi.ac.uk/pdbe/entry/emdb/EMD-2017 "Ribosome KsgA density"
+[link-manual]: https://bonvinlab.org/powerfit/manual.html "PowerFit manual"