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SeeSAR: help

Note that this help page is continuously evolving. Instead of a comprehensive user guide, which nobody reads..., we intend to respond here quickly to questions and feedback which we get from users. So, if anything is missing here, please send us a note!

Further note that starting with major release 6 of SeeSAR, help-functions are provided within the tool. Watch out for the lifesaver – it provides context-dependent help! For newcomers to the tool we recommend to watch the few introductory slides, which SeeSAR shows upon starting. No worries, we won't bother you with the silde-show all the time but only if you haven't used SeeSAR for a while.

1.

tutorials

For beginners we recommend to take a look at the tutorial and/or watch one of the tutorial movies.



2.

possible stumbling blocks

For the major part SeeSAR should be quite seamless and easy to use. Here are the few places where we have seen users to be irritated:

  • Some of the functions that SeeSAR provides, lead the user into a specific mode. This should actually help separate the mode-specific actions from more general actions and make the users life easier, once the mechanism is understood. Examples for modes are the editor or the binding site definition. Upon entering a mode, you will notice that the main menu (top left) changes to the mode-specific menu. Other changes may occur too. For example when entering the editor-mode the molecules-table is replaced by the editor table, which makes it easy for you to keep track of all your edited compounds.
    Most importantly: you need to leave any mode in order to get back to the main menu and all general functions (which may not be accessible in the mode).
  • The data in SeeSAR is organized in two main tables the Proteins Table and Molecules Table. One confusing point is that the Proteins Table contains molecules too. These are the bound ligands found in the selected protein. One major difference between these two tables is that the each of the ligands in the Proteins Table has its own binding site, while all molecules in the Molecules Table (up to 50,000) have one common, user-defined binding site. If you just want to visually inspect the bound ligands, you simply stay in the Proteins Table. However if you want to "work" with molecules – e.g. load many more, edit compounds or generate poses – you need to put them in the Molecules Table first. In the vast majority of cases, you will copy a protein ligand to the Molecules Table. You do so by: (1st) selecting the ligand of interest in the Proteins Table; (2nd) opening the ligand menu ; followed by (3rd) a click on the molecule icon .
  • As mentioned before, the molecules in the Molecules Table require the definition of a common binding site. The most common way to do this, is to do it on the basis of a protein ligand. For your convenience we implemented the following shortcut to do so: (1st) select the ligand of interest in the Proteins Table; (2nd) open the ligand menu ; followed by (3rd) a click on the define binding site icon . Once you have done so, you enter the binding site definition mode (cf. above) with the desired binding-site pre-selected (as you can see the binding site is highlighted in pink). All you have to do now is to leave the mode and confirm your choice of binding site on your way out.


3.

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


4.

system requirements

  • Graphics card must support OpenGL 2.1 or greater
    Note: We highly recommend an update of the graphics card driver. In most of the cases this resolves any issue.
  • Supported operating systems:
    • Windows: tested on Windows 7, Windows 8.1, Windows 10
    • Mac: tested on OS X 10.11+
    • Linux: tested on openSUSE Leap 42.1


5.

FAQs

You can find the complete list of frequently asked questions in our knowledge base: FAQs SeeSAR.



6.

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.
editor context menus
Right-click any atom or bond to get the add atom (resp. change bond type) function as a context menu.
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 work with the molecules table), the fastest is to use a bound ligand for that purpose. Just one klick on the respective context menu completes the task.
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 drwaing 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 Editor (as well as the Inspirator), the display of the currently loaded molecule in 2D is a "live image". You can make selections and the hotkeys work. Via klick-and-drag you can make a "lasso-style selection".

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