Editing CMPyMOL (section)

== Software ==

Clicking (left) and dragging a selection of contact points on the displayed contact map will highlight the corresponding residues in the PyMOL window (as red and blue colored atoms in spheres representation). In addition, several structural/biochemical properties can be overlaid on top of the contact map. The contact-map data can also be plotted in other representations. The calculated contact-map, heat-map and contact density information is stored in a local SQL database. Any subsequent access of the same PDB with matching parameters will be read from the database for fast access. The code for calculating contact map for trajectory files is parallelized for efficiency.

=== Inputs ===
* Single-frame PDB files (local)
* Multi-frame PDB trajectory files (local)
* Multi-frame trajectory files should have the following format.

<source lang="bash">
MODEL X
.
.
.
ATOM ...
ATOM ...
.
.
.
ENDMDL
</source>

NOTE: The PDB can include REMARKS, CRYST and other standard PDB information entries. The MODEL line is essential for the software to work properly (ENDMDL is optional).

=== Overlays ===
* Secondary structure of the protein is overlaid as translucent strips over the contact map. This button won't be active if secondary structure calculation program stride is not found in the system path ($PATH). (Button: Secondary Structure)
* Contact points where a Charge-Charge interaction occurs are highlighted. (Button: Charged Interactions)
* Residues that interact via hydrophobic interaction are highlighted. (Button: Hydrophobic Interactions)
* Contact regions that have a B-factor that is higher than a certain cutoff are highlighted (Button: B-factor). The b-factor cutoff can be varied using a slider (Slider).
* Highlights a contact point/region where the pair of selected residues are in contact (selected by checking the checkboxes). If only one aminoacid is selected from the list, interaction site of the selected aminoacid with another one of the same type is highlighted. (List of checkboxes for each aminoacid)

===  Plots ===
* Pairwise Heat Map - Plots a 20x20 matrix of pairwise aminoacid interaction count.
* Contacts Histogram - Plots the number of contacts around a given residue. Selecting a particular bar highlights the corresponding residue in the PyMOL window.
* Variance Contact Map - For Multi-frame PDB files (trajectory), this button toggles the displays the variance contact map starting from the initial frame until the current frame. This view can be used to identifying the dynamic regions in a protein.

=== Word of Caution ===
When using a multi-frame PDB file, the contact-map for the next frame(s) are being pre-calculated in the background (depending on the number of free CPU cores available). Clicking on "Next Frame" in rapid succession may lead to undesired results and/or a crash.

In the event of a crash, delete the database that is created in the working directory and relaunch the program.