SeeSAR help • BioSolveIT

Possible stumbling blocks

Overall SeeSAR should be quite seamless and easy to use. Here are the few places where we have seen users to be confused:

Different functions in SeeSAR are grouped into different modes. To move from one to another, use the round mode switch button at the top middle. Each mode has its mode-specific menu (top left) and data table. To transfer molecules from one mode to another right-click on them and use the respective "Add to ..." button.

Upon opening a PDB file, all hetero groups (e.g. co-factors) are listed. Select the one which is the bound ligand with the radio button in front of the name and confirm with a click on the green action button

. Note that the selected ligand is extracted from the protein, while any other hetero-groups become a permanent part of the protein.

To work with the binding site around your bound ligand, follow these easy steps: (1^st) right-click on the ligand; (2^nd) click on the "Add to Binding Site mode" button. SeeSAR will automatically switch to the Binding Site Mode. (3^rd) confirm the pre-selected binding-site around your reference ligand using the green arrow button.

Inspirator requires additional files before you can use it. To replace a core of a molecule, please download one of the index files. The growing functionality can be used with a small sample library containing 100 R-groups, included in the installation package. For more options, use one of the SD-files from this zip, containing R-groups in different weight ranges. After the download follow the instructions in the system-settings for the Inspirator.

Mouse-buttons and key-bindings

Note: some keyboards will have [strg] instead of a [ctrl] button. For the Mac, replace [ctrl] by the Apple key. Also [fn]+[back] equals [del] on the Mac keyboard.

general viewing:
right-click	rotate Note: if you click on an object, this is taken as the center of rotation. Otherwise, the rotation is – depending on the viewing mode – either around the center of the entire protein or around the center of the binding site. So don't just click anywhere but close to a ligand atom of interest to rotate around it.
left-click	select
[ctrl] + right-click middle-click	translate
[shift] + right-click	z-rotation
[ctrl] + [shift] + right-click mouse-wheel	zoom
[del]	delete table entries
[up] and [down] arrows	move to the respective next table entry
[space]	center view on selected pose

hot keys:
[d] + left-click, left-click	measure distances
[l] + left-click	label items

editing:
[esc]	exit the editor
[ctrl] + [s]	save the current state in the table
left-click: hold & drag	select all atoms and bonds in a box
[del]	delete the current selection
[ctrl] + [z]	undo
[ctrl] + [shift] + [z]	redo
[ctrl] + [r]	replace core
right-click	context menu to add atom, resp. change bond type
left-click + [c, n, o, s, p, f, i, 1, 2, 3]	change element, resp. change bond type

Hidden beauties

quick-distance measure

While measuring is enabled (either in the utilities or by click-and-hold the 'd'-key on your keyboard), once you select a starting-point to measure, you may simply mouse-over other objects to see their distance to the starting point.

center of rotation

When you right-click to rotate, right-click on a particular atom makes this atom the center of rotation.

move labels

Often times the labels get into the way, you may click-hold and drag the labels to a different location.

upload SDF data

When you load molecules from SDF and they contain, information in the property-fields, you can show them in the table. Check the visible-columns button at the very right end of the table header.

highlight interacting protein atoms

The HYDE atom-score is indicated by the size and color of the translucent sphere surrounding it. When you switch on the label to such an atom, you get the details of the atom-score. Inside the label there is an eye-icon. If you click on it, you'll see the protein atoms contributing to the score.

command line launch

As a jump start, you may launch SeeSAR as follows from the commandline:

seesar.com --protein <pdb-file> --ligand <sd-file>

This will open up the GUI with the protein and the compounds from file already loaded. More command line options are listed via

seesar.com --help

editor hot-keys

Click-select any atom or bond and type either c, n, o, s, p, f, i, 1, 2, 3 on your keyboard to change the element (respectively bond) type.

edit molecule name

Double-click on any cell in the "Name"-column to enable the editing. [enter] saves and finishes the editing, while [esc] cancels and restores the old name.

export to Excel

Upon saving the molecules table to file, you have the choice between .sdf and .xlsx the latter exports the 2D images together with all associated properties.

binding site definition

There are multiple ways to define a common binding site (required to estimate the affinity of a molecule).The fastest is to use a bound ligand for that purpose is right-clicking on it and "Add to Binding Site Mode".

copy from/to clipboard

In the molecules table, [ctrl]+c copies the currently selected molecule to the clipboard and [ctrl]+v pastes any molecule from the clipboard into the molecules table. This is probably the quickest way to get a compound from your favorite drawing program into SeeSAR and vice versa. Note that this trick does not work in the other tables and SDF, MOL, MOL2, SMILES as well as PDB are the only supported molecule formats.

editing in 2D

In the Molecule and Protein Editor mode (as well as in the Inspirator mode), the display of the currently loaded molecule in 2D is a "live image". You can make selections and the hotkeys work. Via click-and-drag you can make a "lasso-style selection".

Possible stumbling blocks

Mouse-buttons and key-bindings

Hidden beauties

How to cite