SeeSAR First Aid

First Aid Remedies

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 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.
  • 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.
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:
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.
select
translate
z-rotation
zoom
delete table entries
move to the respective next table entry
center view on selected pose
hot keys:
measure distances
label items
editing:
exit the editor
save the current state in the table
select all atoms and bonds in a box
delete the current selection
undo
redo
replace core
context menu to add atom, resp. change bond type
change element, resp. change bond type
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.
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.
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".

How to cite

In publications please cite SeeSAR with the respective version number as follows:
SeeSAR version 11.0.2; BioSolveIT GmbH, Sankt Augustin, Germany, 2021, www.biosolveit.de/SeeSAR
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