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.
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 project
save the current molecule in the molecule editor mode
select all atoms and bonds in a box
delete the current selection
undo
redo
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".
Our software is license key protected. To generate your license, we need the Host-ID of the machine on which the software shall run.
In case of a server license, we need the Host-ID of the server machine.

There are several options to determine the Host-ID:

License menu
  1. Open the System setting in the top right and select "License"
  2. Click on "Request license"
  3. Choose "individual assistance" in the now open website and submit your machine ID.

Systemlog
  1. Open the System settings in the top right and choose “Systemlog”
  2. You find the Host-IDs when you scroll all the way down, and search for the line "Host-ID" a few lines above.
  3. You can either send us the complete Systemlog (copy and paste it into an email) or reduce the copied content to the HostID(s)

System terminal/Commandline
  1. Open a system terminal/commandline (Windows: cmd, Mac: Terminal)
  2. Change to the directory of the software executable
  3. Call the app with --license-info, e.g. "seesar --license-info" or “infinisee --license-info”
  4. Send us the complete output of this call
Follow these steps to manually enter a license file:
  1. Click on the System settings icon in the top right corner.
  2. Click the key icon (License) to open the license management interface.
  3. Select the license file or drag&drop it in this window.
If the license key is valid, the license period will be updated in the info line.
Alternatively, you can place the license file into the directory of the software executable.
In case you want to add or update a server (floating) license file, please check the corresponding "server license" FAQ entry.
Our software is license key protected. A license can either be bound to a single node or to a dedicated license server.

A server license (als called "floating license") allows a flexible administration and usage as it is hosted by a server and distributed to compute clients on demand. Such a server may manage the license requests for hundreds or thousands of software clients.

How to set up the license server
  1. First, please download the BioSolveIT flexlm package from our download page. Select the suitable package corresponding to your operating system.
  2. Login to the computer, where you want to run the license server. Flexera Software strongly discourages running the license servers with elevated privileges. However, to install the license server as a system service, you might need elevated privileges during installation.
  3. Extract the package on the license server computer.
  4. Follow the installation notes in the chapter License Server Manager “lmadmin” in package file license /doc/fnp_LicAdmin.pdf
  5. Copy the BIOSOLVE vendor daemon from the package directory license/bin to the new lmadmin installation directory. On linux, make sure that BIOSOLVE has executable rights - if in doubt, just execute chmod +x BIOSOLVE.

Making the server license available to local software installations
When you have fed the server with the license file, you have different options to make the license available to local software installations.
No matter which option you choose, if your license needs to be renewed, you only have to feed the license server with the updated file. The local installations don’t need the license again.
  1. Installation directory
    • Just copy the license file into the directory of the software application, right beside the executable.
    • If you are using non-standard ports for the license server communication, you have to enter these ports into the license file.
  2. Environment variable
    • Set the environment variable BIOSOLVE_LICENSE_FILE to point to the server name prepended by "@", e.g. BIOSOLVE_LICENSE_FILE=@my_server
    • If you are using non-standard ports, you have to specify the port number in front of "@", e.g. BIOSOLVE_LICENSE_FILE=12345@my_server
To find out why your license is not working, we need your help:
Please send us the systemlog (open the System settings in the top right, then choose Systemlog). Also, screenshots may be helpful, and errors/warnings in the exact wording.

The most frequent issues are:
  • cannot connect to license server - check:
    • firewall and DNS configuration, any blocked ports?
  • the key cannot be found - check:
    • key expiration (open the System settings in the top right, then choose License)
    • is the “.lic” file extension still there or has the mailer modified the file?
    • old license keys have to be removed
      • go to the software directory and delete outdated or invalid licenses files
      • if you are unsure about the software directory, look into the Systemlog (open the System settings in the top right and choose “Systemlog”, then scroll all the way down)

How to cite

In publications please cite SeeSAR with the respective version number as follows:
SeeSAR version 12.1.0; BioSolveIT GmbH, Sankt Augustin, Germany, 2022, www.biosolveit.de/SeeSAR