Merge branch 'master' of https://github.com/RUBi-ZA/pyMODE-TASK

Author: nizamibilal

docs/source/pyMODE-TASK_usage.rst

@@ -21,15 +21,15 @@ Browse to the directory and click ok.
 .. figure:: ../img/conf_page.png
    :align: center
 
-   Fig: Set pyMODE-TASK directory
+   Fig 1: Set pyMODE-TASK directory
 
 3. It should look something like this
 
 
 .. figure:: ../img/conf_page1.png
    :align: center
 
-   Fig: Set pyMODE-TASK directory
+   Fig 2: Set pyMODE-TASK directory
 
 4. Next go to the PCA tab. Read the trajectory, topology and reference PDB by clicking on the respective
 buttons. Next select the appropriate options and click on Run PCA. The results file will be saved in a folder
@@ -38,14 +38,14 @@ within the output directory.
 .. figure:: ../img/pca_page.png
    :align: center
 
-   Fig: PCA 
+   Fig 3: PCA 
 
 5. If the run is successful you will see something like following
 
 .. figure:: ../img/pca_result.png
    :align: center
 
-   Fig: PCA successful 
+   Fig 4: PCA successful 
 
 MDS and t-SNE
 -------------------------------
@@ -58,7 +58,7 @@ under MDS options widget and click on Run MDS.
 .. figure:: ../img/mds_page.png
    :align: center
 
-   Fig: MDS and t-SNE 
+   Fig 5: MDS and t-SNE 
 
 
 Normal mode analysis (NMA)
@@ -69,19 +69,19 @@ Normal mode analysis (NMA)
 .. figure:: ../img/nma1.png
    :align: center
 
-   Fig: NMA set configuration
+   Fig 6: NMA set configuration
 
 2. Perform the coarse graining for large protein molecules.
 
 .. figure:: ../img/nma2.png
    :align: center
 
-   Fig: Coarse graining
+   Fig 7: Coarse graining
 
 .. figure:: ../img/nma3.png
    :align: center
 
-   Fig: Coarse graining results
+   Fig 8: Coarse graining results
 
 3. Perform the coarse graining for second conformation of the protein. 
 This is useful in case if you want to perform "Conformation/ Combination tool analysis" and 
@@ -90,40 +90,40 @@ This is useful in case if you want to perform "Conformation/ Combination tool an
 .. figure:: ../img/nma4.png
    :align: center
 
-   Fig: Coarse graining 2
+   Fig 9: Coarse graining 2
 
 4. Run NMA on each coarse grained PDB using a suitable cutoff. 
 
 .. figure:: ../img/nma5.png
    :align: center
 
-   Fig: NMA for first PDB
+   Fig 10: NMA for first PDB
 
 .. figure:: ../img/nma6.png
    :align: center
 
-   Fig: NMA for second PDB
+   Fig 11: NMA for second PDB
 
 5. Run conformation / combination mode analysis. This require two PDB of different conformation.
 
 .. figure:: ../img/nma7.png
    :align: center
 
-   Fig: conformation/combination mode analysis
+   Fig 12: conformation/combination mode analysis
 
 6. Run MSF. This requires decomposed ANM matrices for comparing the mean square fluctuation between 2 proteins. 
 
 .. figure:: ../img/nma8.png
    :align: center
 
-   Fig: MSF
+   Fig 13: MSF
 
 8. Get an assembly covariance for a specified chain of an asymmetric unit
 
 .. figure:: ../img/nma9.png
    :align: center
 
-   Fig: Get Eigenvectors
+   Fig 14: Get Eigenvectors
 
 9. Generate mode animation for visualization. Afterward use the following command in VMD for visualization
 
@@ -134,7 +134,7 @@ This is useful in case if you want to perform "Conformation/ Combination tool an
 .. figure:: ../img/nma10.png
    :align: center
 
-   Fig: Mode animation
+   Fig 15: Mode animation