Visualization
Visualization in BMaps is mostly handled using the mini-menus on the right-side bar. However, there are also a range of style features available by right clicking an atom or residue in the workspace. See the sections below for more info about the capabilities in each.
Visualization Side Bar
In addition to the components discussed below, visualization may also be changed using the Select with query button at the bottom of the Visualization Side Bar. This option is discussed elsewhere.
View
View options change the visualization in the 3D workspace.
In addition to these presets, the view can also be changed in the following ways:
Zoom - scroll wheel/two fingers on the track pad
Rotate - left click and drag
Focused Views
These views are relevant presets that may be useful to you.
Protein View - A full picture of the system with the protein in cartoon ribbon and ligands in ball and stick.
Ligand View - A zoomed in view of the ligand position with ligand as ball and stick and the protein as wire.
Publication View - Adds hot spots to the Ligand View.
Reset - Return the protein to cartoon ribbon and the ligand to ball and stick.
Protein Structural Views
The protein structure views update the protein atoms only by default.
You can also select individual atoms or residues by left clicking on them (turning them pink) once to choose the ligand or residue clicked on, or double left clicking to select the whole entity (compound or protein). You can then use the Protein Structural View options to change only the selected components. This special selection logic works for all options except the Connolly Surface.
Hide Atoms - hide only the protein unless parts of the compound are selected.
Hydrogen Views
The hydrogen views apply to both the protein and the ligand and will adjust what hydrogens are visible. Polar hydrogens are defined as those attached to nitrogen, oxygen, or sulfur.
Interaction Highlights
Interaction highlights visualize various atomic interactions to assist the user in understanding the underlying chemistry.
Hydrogen Bonds
Hydrogen bonds are displayed as bars between the hydrogen and target atom the hydrogen is interacting with.
Strengths of the bonds are color coded as follows:
Lime - weak: 1.2-4 kcal/mol (press W to see these after selecting HBonds)
Cyan - regular: 4-12 kcal/mol
White - strong > 12 kcal/mol
Ligand Desolvation
This interaction is not available until energies have been calculated either through the minimization in the Compound Ellipse Dropdown Menu, or the Energies tab of the Inspector Menu.
Hovering over the desolation spheres will give the free energies of desolvation for that interaction.
Sphere colors refer to:
Green < 3 kcal/mol
Gray 3 > X < 10 kcal/mol
Red > 10 kcal/mol
Protein Desolvation
This interaction is not available until energies have been calculated either through the minimization in the Compound Ellipse Dropdown Menu, or the Energies tab of the Inspector Menu. The visualized globule colors refer to the interaction with the focused compound. As such, only the active site around the compound will be populated with interaction highlights.
Hovering over the desolation globuals will give the free energies of desolvation for that interaction.
Sphere colors refer to:
Green < 3 kcal/mol
Gray 3 > X < 10 kcal/mol
Red > 10 kcal/mol
Protein Hydrophobicity Points
Because of the nature of the definitions of desolvation and hydrophobicity, these two interactions for the protein generally appear as inverses. However this is not really the case. Protein Hydrophobicity is based on a per-residue chart found here.
This interaction is not available until energies have been calculated either through the minimization in the Compound Ellipse Dropdown Menu, or the Energies tab of the Inspector Menu. The visualized globule colors refer to the interaction with the focused compound. As such, only the active site around the compound will be populated with interaction highlights.
Hovering over the desolation globuals will give the free energies of desolvation for that interaction.
Sphere colors refer to:
Green < 3 kcal/mol
Gray 3 > X < 10 kcal/mol
Red > 10 kcal/mol
Hot Spots
Hot spots are points on the target protein where it is on average favorable to replace the solvent with a diverse set of fragments. These hotspots permit draggability analysis and can assist in finding allosteric sites and subpockets in orthosteric sites. Using cluster analysis, the Hot spots determined by BMaps follows three principles:
- The fragment set is diverse
- The fragments strongly bind
- Positions where waters strongly bind are excluded.
The BMaps fragment maps obtained through our Grand Canonical Monte Carlo - Simulated Annealing of Chemical Potentials method have demonstrated accurate predictions of hot spots and druggable sites for protein−ligand, protein−protein, and
protein−DNA/RNA interactions and has been validated with experiment. More details can be found in these papers [9,49].
The fragments used in the average calculation are by default the BMaps Fragment Library, though these can be updated using the fragment manager. Hovering over the hotspot in the 3D workspace will produce a tool tip showing the excess chemical potential for the most favorable fragments for that hotspot, as well as the average. The excess chemical potential shown corresponds to the last favorable excess chemical potential at which the fragment was present in that hotspot during the fragment simulation. The threshold in the Protein tab of the Selector menu allows you to hide hot spots that are less favorable by adjusting the threshold for the excess chemical potential. More details for this can be found in the Menus Section.
Water/Fragment Maps
Crystal Waters
Crystal waters are waters that were imported as part of the pdb or cif file and are therefore assumed to be determined through accepted crystallography.
BMaps Waters
BMaps waters are waters determined through a BMaps water map simulation detailed extensively here. Importantly, these water maps are calculated much quicker, more thoroughly, and discover multi-body interactions not normally discoverable by other free and commercial water mapping technologies.
Waters with magenta spheres around them are strong binders (< -6 kcal/mol, More negative).
Fragment Maps Search
The Fragment Maps Search button is a convenient way to remind yourself how to perform a fragment search, but currently serves no other purpose.
As noted in the pop-up image, fragments from a pre-computed fragment map can be accessed via right clicking any atom I the 3D workspace and selecting "Search Nearby Fragments". If you need to run a fragment map that hasn't already been computed, you instead select "Fragment Data Query" from the right-click dropdown menu, but more on this is discussed in the Maps or Compound Design Sections.
You can also visualize fragment maps by using the Selector Fragments tab and clicking the show button next to the desired fragment name. The fragment energy filter can then be used to adjust which fragments are visible based on excess chemical potential.
Draw/Edit
Draw New Compound
Clicking the Draw New Compound button will pull up the Ketcher compound editor. Instructions for use can be found using the 
button in the upper right or checking the Ketcher documentation.
Edit Active Compound
Pressing this button will bring the focused compound into the Ketcher compound editor. Edited compounds that have valence problems will throw an error but will still be imported. It is normal that edited compounds may clash with the protein and need to be minimized or docked with respect to the protein in order to form a more realistic structure.
Replace Terminal
This button currently just gives the following instructions for replacing a terminal:
Right-click a compound's terminal group or hydrogen in the 3D workspace to view terminal replacement options.
Hold down the R key to view all hydrogens and functional groups available for replacement.
Right-Click Visualization Menu
The options under the Style section of the Right Click Dropdowns permit changing the visual appearance of components in the workspace. For each option of either Protein, Residue, or Compound right-clicked, the components may have only carbon atoms' color changed, all atoms' colors changed, or the visualization style may be changed.
