Editing PyANM (section)

= Usage = 
Now that you have PyANM installed, let's build one ANM together!

=== Structure Handling ===
*Type the name of your protein structure under 'Select Structure', this could either be a valid 4-letter PDB (Protein Data Bank) ID or the name of a object you have already loaded into Pymol.
*You could also choose to upload a local file from your system using the 'Browse' button.
*If the check box 'Use only Alpha Carbons' is checked, even if you choose an all-atom structure, PyANM will coarse-grain the structure for you. Otherwise PyANM will build an all-atom ANM if an all-atom structure is used.
*If the check box 'Include HETATMs' is checked, PyANM will include atoms in PDB that starts with HETATM as well.

=== ANM Parameters ===
*So far there are two ANMs available for you to choose in PyANM : the cutoff model as described [http://www.cell.com/biophysj/abstract/S0006-3495%2801%2976033-X here] and the Parameter Free Model described [http://www.pnas.org/content/106/30/12347.short here], where spring constants are adjusted based on distance between two residues.
*If you choose to use <b>Cutoff Model</b>, you will be able to choose your desired cutoff value. The default value is 12 angstroms, personally I would recommend using any value between 7 angstroms to 15 anstroms.
*If you choose to use <b>Parameter Free Model</b>, you will be able to choose the power t for calculating spring constants for all residue pairs, where spring constant k for residue i and j is calculated as 1/distance(i,j) to the power of t. The default value for power t is 6.

=== Build ANM ===
Once you have selected the structure you wish to use as well as the model and its parameters, you should be able to build your ANM simply by clicking 'Build ANM'.A window will pop up telling you your ANM was built successfully once the calculation has finished. For a protein with less than 200 residues, this should take less than 10 seconds.

[[File:Pyanm_example_of_springs.png|400px|thumb|<b>Figure 2</b>: All springs of HIV protease (PDB ID: 1T3R) when cutoff value is set as 12 angstroms]]

=== Show Springs ===
After building your ANM, you will be able to visualize all the springs in Pymol by simply clicking 'Show Springs' in PyANM. 

See Figure 2 for a demonstration of all springs for HIV Protease (PDB ID: 1T3R) using cutoff model with cutoff value set as 12 angstroms.

=== Color by MSFs ===
[[File:Pyanm_example_of_msf.png|400px|thumb|<b>Figure 3</b>: HIV protease (PDB ID: 1T3R) colored by its calculated MSFs]]
One can also calculate the Mean Square Fluctuations (MSF) with all the modes calculated by ANM. ANM has been successful in getting high correlations between its calculated MSFs and experimental b-factors for most cases. Here PyANM allows you to color the structure based on its calculated MSFs just like Pymol colors a structure with its b-factors. Here the spectrum is from blue to red corresponding to from low values to high values.

Figure 3 shows the same HIV protease in figure 2 colored by its calculated MSFs.

=== Make Movies ===
[[File:Pyanm_example_of_arrows.png|400px|thumb|<b>Figure 3</b>: Arrows showing mode motions for HIV Protease (PDB ID: 1T3R)]]
You will be able to make harmonic fluctuation movies for different modes when you click 'Make Movies' after building your ANM. A dialogue will pop up asking for the desired modes you wish to make movies with. Modes are sorted with an ascending frequencies and the first 6 rigid-body modes are already discarded. So modes 1,2,3 will be the first 3 slowest modes. 

=== Draw Arrows ===
Instead of making movies for different modes, you can also draw arrows for each residue for different modes. Each arrow's direction will point to the direction where the residue will move and each arrow's length will indicate the moving scale for each residue.

Figure 4 shows the arrows for mode 2 of HIV protease produced by PyANM.

=== Export Data ===
This will allow you to save data calculated from PyANM to your local system for future processing. You can choose to save eigenvalues (frequencies for modes), eigenvectors (modes), MSFs, contact matrix or hessian matrix from <b>Control Panel</b>.

=== Control Panel ===
This is where PyANM allows you to change the scales (sizes) of the movies (arrows), or change color of the arrows (The color of movie objects could simply be changed like you change colors for other objects in Pymol). You could either predefine scales (sizes) or colors you would like before building your ANM or you could change these settings after you have made movies or arrows and these changes will happen real-time.

You could also select what attributes you would like to export to your local system here inside control panel. These data will be written as text files and Numpy-ready for future processing.