Images for README.md

patonlab · Dec 1, 2020 · a2b3fce · a2b3fce
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diff --git a/Example1.png b/Example1.png
diff --git a/Example2.png b/Example2.png
diff --git a/Example3.png b/Example3.png
diff --git a/README.md b/README.md
@@ -92,22 +92,33 @@ H	2.03	0.76	-1.25
 H	0.76	2.03	-1.25
 ```
 
+A visualization of these parameters can be shown in the program PyMOL using the two output files created by DBSTEP, showing the L parameter in blue, Bmin parameter in green and Bmax parameter in red. 
+
+![Example1](Example1.png)
 
 2. Sterimol2Vec Parameters for Ph
 
     The `--scan` argument is formatted as `rmin:rmax:interval` where rmin is the distance from the center along the L axis to start measurements, rmax dictates when to stop measurements, and interval is the frequency of measurements. In this case the length of the molecule (~6A) is measured in 1.0A intervals
+
 ```
->>>python -m dbstep examples/Ph.xyz --sterimol --atom1 2 --atom2 5 --scan 0.0:6.0:1.0
-
-     Ph.xyz / R:  0.00 / Bmin:  1.65 / Bmax:  3.16 
-     Ph.xyz / R:  1.00 / Bmin:  1.65 / Bmax:  3.16 
-     Ph.xyz / R:  2.00 / Bmin:  1.65 / Bmax:  3.16 
-     Ph.xyz / R:  3.00 / Bmin:  1.65 / Bmax:  3.16 
-     Ph.xyz / R:  4.00 / Bmin:  1.65 / Bmax:  3.16 
-     Ph.xyz / R:  5.00 / Bmin:  1.65 / Bmax:  3.11 
-     Ph.xyz / R:  6.00 / Bmin:  1.15 / Bmax:  1.17 
+>>>python -m dbstep examples/Ph.xyz --sterimol --atom1 1 --atom2 2 --scan 0.0:6.0:1.0
+
+    Ph.xyz / R:  0.00 / Bmin:  1.55 / Bmax:  2.86 
+    Ph.xyz / R:  0.50 / Bmin:  1.65 / Bmax:  3.16 
+    Ph.xyz / R:  1.00 / Bmin:  1.65 / Bmax:  3.16 
+    Ph.xyz / R:  1.50 / Bmin:  1.65 / Bmax:  3.16 
+    Ph.xyz / R:  2.00 / Bmin:  1.65 / Bmax:  3.15 
+    Ph.xyz / R:  2.50 / Bmin:  1.65 / Bmax:  2.91 
+    Ph.xyz / R:  3.00 / Bmin:  1.65 / Bmax:  3.16 
+
+    L parameter is  5.95 Ang
+
 ```
 
+ Displayed in PyMOL, each new Bmin and Bmax axis is added along the L axis. 
+ ![Example2](Example2.png)
+
+
 3. Percent Buried Volume 
 
     %Vb is measured by constructing a sphere (typically with a 3.5A radius) around the center atom and measuring how much of the sphere is occupied by the molecule. Output will include the sphere radius, percent buried volume (%V_Bur) and percent buried shell volume (%S_Bur) (zero in all cases unless a scan is being done simultaneously).
@@ -118,6 +129,9 @@ H	0.76	2.03	-1.25
      3.50      41.77       0.00
  ```
 
+ For percent buried volume, the PyMOL script will overlay an appropriate sized sphere where measurement took place.
+  ![Example3](Example3.png)
+
 4. Vol2Vec Parameters
 
     When invoking the --volume and --scan parameters simultaneously, vol2vec parameters can be obtained. In this case, a scan is performed using spheres with radii from 2.0A to 4.0A in 0.5A increments.