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For the complete documentation index, see llms.txt. This page is also available as Markdown.

Example Run

An example of running LCModel on a test data set

0. Make sure you have installed LCModel

Every user must install LCModel for their own user. If you haven't, please refer to the Installation Guide

1. Start a VNC session

To run LCModel's GUI you will need to start Oscar's VNC Client. LCModel is not very resource intensive so you can request a basic session

2. Launch Terminal

  • Inside your VNC session, open a Terminal window.

  • Navigate to LCModel's hidden directory cd ~/.lcmodel

Example terminal in a VNC session (Oscar). The user navigated into the directory called “.lcmodel” and listed its contents with the “ls” command. Notably, “lcmgui” is listed in the directory.
Sample Terminal Window inside Oscar's VNC

3. Launch lcmgui

  • To launch the lcmgui, simply type ./lcmgui from the current directory (~/.lcmodel)

  • Accept license agreement

4. Select sample Siemens data

  • Select Siemens at the data type prompt

A LC Model pop up window with the title, “Select your data type”. Users should select “Siemens”.
Sample Data Type Window

  • Search for the share data: /oscar/data/bnc/shared/lcmodel/TestData.rda

In the pop up titled “Select your Siemens file.”, enter your path and RDA file. In this example, the path is: “/oscar/data/bnc/shared/lcmodel/“ and the file is: “TestData.rda”. Then press “Ok”.
Sample Data Browser Window

5. Select Basis

During installation, the basis-set was installed under the LCModels' hidden directory in your home. i.e., $HOME/.lcmodel/basis-set which is equivalent to /oscar/home/$USER/.lcmodel/basis-set

  • Change the basis file to: $HOME/.lcmodel/basis-sets/press_te30_3t_gsh_v3.basis

In the “Control Parameters” pop up, there is a section titled "BASIS file:". In the text box, enter: $HOME/.lcmodel/basis-sets/press_te30_3t_gsh_v3.basis. $HOME should be the path to your individual home directory.
Sample Control Parameters Window

6. Add License Key to Control Parameters

You will need to add a key to the Control Parameters. We do so as follows:

  1. Open Advanced Setting Dialog

    In the “Control Parameters” pop up, select the “Advanced Settings” button.

  2. Select View/Edit Control Parameters. A dialog will open

  3. Add key to Control Parameters Add key= 210387309 to the control parameters as shown in the figure below. Be careful to match spaces. When done, press OK

    In the “View/Edit Control Parameters” pop up, a new line was added to the text box, which states: “key= 210387309”.

  4. Save parameters file (optional) LCModel will ask you if you want to save the new parameters to a new file. You can do so. If you do, the next time you can select the saved file from Advanced Settings -> Change Control-Defaults file

7. Run LCModel

After pressing Run LCModel, a two page PDF will appear, which looks as follows

Page 1 of the LC Model PDF, which depicts the metabolite spectra and a table of metabolite values from the dataset.
LCModel Result PDF - Page 1
Page 2 of the LC Model PDF, which depicts the same table of metabolite values, without the spectra. Additionally, there are sections on “MISCELLANEOUS OUTPUT” and “INPUT CHANGES”.
LCModel Result PDF - Page 2
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