Editing Azahar (section)

== Usage ==

The plugin's GUI displays three interactive tabs: Creation, Visualization and Calculations. 
Usage is described by tab:

=== Glycan Creation ===

The Creation tab contains:
 
*Three option menus, two of which are used to specify residues to be connected from a list of predefined templates. And the third one, selects the chemical bond to be used. 

*Three entry boxes, the first one it's called "Repetitions", where the user can enter the number of residues to be connected. The "Position" entry box indicates the index of the residue to which the next bond will be added. On a typical glycan molecule constructed using this plugin, the user would use the "Position" entry box and the bonds menu to specify ramifications. And in the "New Molecule" entry box the user can write the name of the PyMOL object corresponding to the newly created glycan molecule.

*Finally, The "add" button, when clicked, writes a text file containing the connectivity of the glycan molecule to be created. The user can edit this file or provide it as input. The connectivity instructions are also printed in PyMOL's external GUI. When the "create" button is clicked, the molecule is constructed and displayed in the PyMOL's GUI. The "reset" button resets the entry box's parameters. 

=== Visualization ===

On this tab the user will find options to visualize glycans with 3 different ''cartoon-like'' representations. The ''cartoon'' representation is build using PyMOL's [[CGO]] and hence the color of the object has to be define it before creating it. Azahar provides a color menu for that purpose, you can choose from a list of colors or use the ''auto'' option (default), that reads the atom colors from the object. For example if you want to color a glycan cartoon using the b-factors, you should first choose that option from the PyMOL's menu and then tell Azahar to create a cartoon representation with the ''auto'' color option.

You can ''cartoonize'' glycan molecules created by this plugin or loaded from other sources. 

=== Calculations ===

Radius of gyration and Ramachandran Plot are useful tools for the analysis of glycan molecules. Through this plugin's GUI the user can easily select a range of states to compute these calculations, and in case of the RG, the result will be displayed in the PyMOL's external GUI.

=== Monte Carlo ===
This feature is still experimental

A Monte Carlo with Minimization (MCM) is a global optimization method that have proven very efficient to sample the conformational states of complex molecules like proteins, It was first published by [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC299132/ Li and Scheraga], and is some circles is also know as basin hopping. Briefly, the conformational search is done by perturbing a torsional angle (psi, psi, omega or chi), follow by and energy minimization and the new (minimized) conformation is accepted or rejected following the Metropolis-criteria. If the conformation is accepted the next iteration start from the new conformation, otherwise the old conformation is perturbed again.

From the GUI the user can choose the number of iterations to run, whether or not to use a SASA model to take into account the solvent contribution, and whether or not to start from a random conformation.

After the  MCM procedure is completed the user will get:

* one .pdb file for each accepted conformation. 
* one multi-state .pdb file (automatically uploaded at the end of the run)
* one .pdb file for the conformation with the minimum energy.
* a plain text listing the energy of each saved conformation


The internal energy is computed using the MMFF94 force field (as implemented on open-babel) and the contribution of the solvent is approximated using a SASA model (the validity of the SASA model for glycans and the relative weight of the internal and salvation energies needs further test).