5.2 Dealing with Molecules
Adding Molecules
As soon as you have opened a membrane (or created a new one) you are able to insert molecule instances into it. Adding Proteins works a differently than adding Lipids; although both have to be done from the tables in the Local Database View.
Adding Proteins
The best way to add a protein is to use drag&drop. Press the left mouse button over the chosen entry and hold it for one second. This will load the file and create its 3D object. Now you can, still holding down the button, drag the protein into the membrane. Releasing the button places the object, or discards it if it was placed outside the valid range.
Adding a protein via drag&drop
An alternative way to add a protein is to use the add button 
located
at the entry's left side. The program will attempt to place it automatically.
In case the added protein contains either OPM or PDBTM alignment data, the protein will be automatically aligned respectively. This feature can be disabled inside the settings dialog
You can change a protein's location any time by moving it with your mouse; just select one and hold down the left mouse button pressed. If you drop it at an invalid position, or if you press the escape button while moving, your protein will snap back to its original place.
If you want to remove a protein from the membrane, press the remove button
located in the upper part of the Membrane
View while it is selected. Or press the right mouse button over a protein
to open a popup menu where you will find an equivalent button.
Handling Molecular Intersections
If you move molecules by hand, multiple intersections may occur. Intersections are always indicated in the lower toolbar by a specific icon:
You may also want to activate a detailed display of the involved members by activating the 'Display' checkbox. This option marks all intersecting members with a red box, but requires more CPU resources.
In case one or more moved proteins intersect with lipids, you can remove the effected lipids by pressing this button:
Adding Lipids
Lipids, unlike proteins, cannot be put directly into the membrane. If you add one, it will only serve as a template. The "physical" placing of the lipids is up to the particular algorithm that is used when generating the bilayer. For this purpose, these algorithms need a composition of lipids that they can refer to, which is defined by the sample lipids that you have previously added.
In order to add a sample lipid, press the add button of its entry.
You will have to decide whether to add it to both, or only to one side of the
layer, consisting of the extra- and the intracellular side.
Note that you can only add one instance (on each side) for each lipid type.
Handling contents
The proteins and sample lipids in your membrane are listed inside the Component View:
Proteins
Proteins are available in the upper part of the view. Single instances are not listed here, instead they are categorized into groups; one group for each type. If you click on a group, you will get some options:
Change amount
Use the number field in order to change the amount of the referring proteins. Increasing the number will add the differentiating number of proteins randomly, decreasing the number will randomly remove them.
Remove
Pressing the remove button will delete all proteins of the group at once.
Inside the submenu:Select Profile
Opens the Molecule Editor in order to apply a predefined molecule profile. See how to use molecule profiles
Change color
Here you can change the presenting color for a protein type here. The colors are irrelevant to any output and are only made to improve your survey.
Use actual Color
This is only relevant if you display your molecules in the atomic mode.
This option switches the atom colors between the originals (like in
Jmol) and the assigned color of the molecule inside this program
Sample Lipids
In the lower part of the Component View is the list of sample lipids. Each of the two membrane sides has its own lipids, so you can set them up differently, if required. You could also generate a monolayer by keeping one side completely empty.
Click on a sample lipid to see its options:
Change percentage
You can change the percental spread of the selected lipid by using the number field.
Remove
Pressing the remove button will remove the sample lipid from the list.
Inside the submenu:
Select Profile
Opens the Molecule Editor in order to apply a predefined molecule profile. See how to use molecule profiles
Change color
You can change the presenting color for a lipid type here. The colors are irrelevant to any output and only made to improve your survey.
Use actual Color
This is only relevant if you display your molecules in atomic mode. This option switches the atom colors between the originals (like in Jmol) and the assigned color of the molecule inside this programChange default Alignment
Enables you to change the default rotation of this sample lipid. See aligning lipids for more information.
Options of the Component View
In the lower left corner of the Component View you can find a button that opens a small menu where you can can enable or disable some features.
Prompt user first
You can choose whether or not you should be prompted before removing molecules from inside the Component View
Auto adjust percentages (lipids only)
If this option is enabled and you are changing the percentage
of one lipid, then the percentages of the other lipids will be adjusted automatically
to a total of 100%.
Note that it is necessary to have them at exactly 100% in order to generate
the layer!
Synchronize Extra- and Intracellular values (lipids only)
This feature synchronizes your editing sample lipid with its counterpart on the other membrane side (if present), including percentages, color, or removal.