Export a protein and ligand together in one file

What is the purpose of this workflow?

To illustrate to people who want to create a protein-ligand complex molecular format file rather than separate protein and ligand files for use, transfer, or storage outside of BMaps.

Who is this workflow useful for?

  • People who want to transfer a protein-ligand complex as a single file for further analysis or visualization

Current Workflow Requirements

  • Have a protein in the protein selector menu.
  • Have a compound in the compound selector menu.
  • See here for help on accomplishing these pre-requisites.

Workflow - Just the steps

  1. Get all of your systems you wish to export into the 3D workspace.
  2. Use the Selection Query button - Type "select all" and hit enter.
  3. Click the export button to open the export menu.
  4. Select your file format from the dropdown.
  5. Click the download button.

Workflow - Detailed

  1. If your compound and protein are not already visualized in the 3D workspace, then you will need to add them.
    1. From the protein selector menu, which can be accessed using the tab labeled “Protein” on the left hand side of the BMaps window, select the eyeball of the protein not currently in the workspace that you would like to add. Note that a grey eyeball indicates the protein is not visible while a white eyeball indicates the protein is visible. If you select the eyeball associated with the top level protein or chain then you are including every component within that group. Select as many eyeball icons as you want to include protein components in the 3D workspace for export.
    2. From the compound selector menu, which can be accessed using the tab labeled “Compounds” on the left hand side of the BMaps window, select the arrow () next to the compound you wish to include in the 3D workspace. When the compound is selected it’s arrow icon changes to a magnifying glass with either a + (for ligand view) or – (for protein view) inside it. You want to make sure you have a magnifying glass with a + in it for this tutorial’s goal. You can toggle to this icon by clicking the magnifying glass with a – in it or the arrow. If you wish to have multiple compounds exported with your protein then you need to use the pin icon to the left of the compound name you wish to include. Note that the compound with the magnifying glass icon is always being included.
  2. Now that your proteins and compounds you wish to export in a single file are all visualized in the 3D workspace, you can select them all using the selection tool. The selection tool is accessed by clicking the bottom icon on the right hand side menu that looks like a hand clicking on an atom in a molecule . Now in the text box that appears after you click the aforementioned button, type “select all” and hit enter. You will notice after hitting enter that everything in the 3D workspace has turned pink. This pink is the selection color.
  3. Now, with the whole 3D workspace selected, click the “Export” button above the selection button in the right hand side menu to open the export menu. You will know you have done it write because the header text for the menu says “Exporting selected atoms”.
  4. You can now choose to export your selected system in PDB – Protein Data Bank or Mol2 – Tripos Sybyl Molecule format using the “Choose Format” dropdown menu. Selecting either will populate the box beneath the dropdown with the text in the selected format as it will be exported. This is a good time to verify everything you wanted to export is in the file. Note that you are unable to update this text box manually.
  5. With your desired selection, you can now choose to download the file using the download arrow which looks like an arrow pointing down above a horizontal line, or copy the text to paste wherever you like using the double button that looks like two offset pages overlapping. If you click the download button the file will automatically be downloaded to your downloads folder as set by your browser preferences. The default name for the download will be “selected__atoms.”.

 

Developer Reasoning and Comments:

As always, the BMaps development team appreciates feedback on the processes we design. If you have questions or comments on this or other processes, please email support@coniferpoint.com.

Currently, the only available file formats to export selected systems to are PDB and Mol2. The reasoning for this is a mixture of prioritization and intended use (mis)match for different chemical file formats. If you would like native support of this feature for a different file format, please let us know!

Selection can be performed in many ways in BMaps. You can read more about these ways here. Given the many combinations of proteins and compounds a user may end up with throughout their studies in BMaps, it is easiest for users to select their specific export systems up by populating the 3D workspace such that they can see which components will be included. The textbox showing the output for the file before export is another way in which we build in checks for the user to ensure they are exporting their system correctly. If the user wants to save the entire project they are working on for later rather than just the system in the workspace, please remember that a save session button is available on the top right hand side of the BMaps window.