Tutorials

Importing a structure

You can import a structure by:

• providing the files from your local machine
  1. Open the Home panel on the left-hand side.
  2. Open the Open Local Files menu in the Home panel.
  3. Select Select files… to choose which of the files you have stored locally to upload.
     • You can import multiple files at once.
     • If you are importing multiple files at once, that do not have the same format, the Format option should be set to Auto.
     • If you are importing only one file at a time, or if all files have the same format, you can also specify the format of the file. However, in most cases, this is not necessary.
  4. Select the Apply button.

• using one of the common public servers (like PDB)
  1. Open the Home panel on the left-hand side.
  2. Open the Open Remote Structure menu in the Home panel.
  3. Select the server you want to download the structure from as the Source.
  4. Enter the ID of the structure or trajectory you want to import from the selected server.
  5. Select the Apply button.

• using the URL of a structure file that is publicly available on another server:
  1. Open the Home panel on the left-hand side.
  2. Open the Open Remote File menu in the Home panel.
  3. Enter the URL of the file.
  4. Select the correct format of the file for the Format parameter.
  5. Set the Binary parameter to On, if the file is binary.
  6. Select the Apply button.
     • Note: If you have deployed the client on your local machine, you can also import files that are available on your local network.

Importing a trajectory

You can import a trajectory by:

• providing the files from your local machine
  1. Open the Home panel on the left-hand side.
  2. Open the Load Trajectory menu in the Home panel.
  3. Select File as the Source parameter.
  4. Select Selec a file… for
     • Model: The file containing the structure (e.g. a .pdb).
     • Coordinates: A file containing the coordinates of the trajectory you want to match to the structure.
  5. After selecing the two files, select Apply to import the trajectory.

• using the URL of a structure and coordinate file that are publicly available on another server:
  1. Open the Home panel on the left-hand side.
  2. Open the Load Trajectory menu in the Home panel.
  3. Select URL as the Source parameter.
  4. Select Selec a file… for
     • Model: The URL pointing to the file of the structure.
     • Coordinates: The URL pointing to the file of the coordinates of the trajectory you want to match to the structure.
  5. Specify the format for each file in the Format parameter underneath it.
  6. Specify, if the Model file is Binary.
  7. After selecing the two files and setting their parameters, select Apply to import the trajectory.
     • Note: If you have deployed the client on your local machine, you can also import files that are available on your local network.

Playing a trajectory

You first need to import your trajectory:

• Importing a trajectory or
• Stream a trajectory from the MDsrv

After you imported your trajectory, a play button will appear in the top left corner of the white canvas where the structure is displayed.

When you imported your trajectory by streaming it from the MDsrv, you need to clean up the visualization:

1. Open the State Tree panel on the left-hand side.
2. Toggle the visibility for the imported structure (same name as the original file).
   • The visibility toggle is the outermost button on the right side and has an eye symbol.

Now only the matched result is visible in the representation.

Sharing a session

You can share your your in two ways:

• Through our server:
  1. Import the structures and trajectories you want to share.
     See Tutorials:
     • Importing a structure
     • Importing a trajectory
     • Stream a trajectory from the MDsrv
  2. Prepare your session as desired.
  3. Open the Remote Session menu in the Extensions panel at the bottom.
  4. Name your session.
     • Optional: Change the server address.
     • Optional: Enter a description.
     • Optional: Enter a source for the data in the session.
  5. Select the Upload button.
  6. A message is displayed next to the Upload button if the upload was successful.
  7. Open the Home panel on the left side.
  8. Refresh the server url where the session was saved.
  9. The session will now appear in the list.
  10. To share your session with others, right-click your session to open it in a new tab with its URL.
  11. Share this URL.

• Setting up your own MDsrv, see How do I install a MDsrv server on my machine (Setting up your own server and viewer)?.

Upload a trajectory to the MDsrv

You can save a trajectory to our streaming server if it is too large to visualize in your computer’s memory. When you save the trajectory on the streaming server, you can stream it frame by frame, which allows you to visualize the trajectory, which would not be possible otherwise.

The trajectory you want to store on our streaming server must be publicly available on another server.

1. Open the Extensions panel at the bottom.
2. Open the Add Trajectory to Stream Server menu.
3. Optionally, if you want to upload the trajectory to another MDsrv instance, adjust the Server parameter accordingly.
4. Enter the URL of the trajectory file.
5. Name the trajectory. (If there is already a trajectory with the same name, a message will appear in the Log panel. Please change the name.)
6. Add a more detailed description for your trajectory.
7. Select the Upload Trajectory to Server button.
8. When the trajectory is successfully uploaded, a message appears in the Log panel.
9. To visualize the uploaded trajectory, see the Tutorial Stream a trajectory from the MDsrv.

Currently, only trajectories in the XTC format can be uploaded.

Stream a trajectory from the MDsrv

1. Open the Extensions panel at the bottom.
2. Open the Match Trajectory Stream menu.
3. Enter the Server URL where the trajectory is stored (Must be an MDsrv instance).
4. Import the structure corresponding to the trajectory (see Tutorial Importing a structure).
5. Turn off the visibility for the structure.
6. Select this structure via the Model parameter.
7. Select the trajectory you want to stream via the Trajectory parameter.
8. Select Add Stream Trajectory.
9. You can now play your trajectory.

Superpose structures based on a sequence alignment

1. Import a Clustal alignment (.aln) using the Open Local Files menu.
2. Import the structures corresponding to the sequences in the alignment.
3. Match the sequences of the alignment with the structures using the Match Sequence Alignment menu in the Extension panel at the bottom.
   • For each sequence in the alignment, you must specify which sequence of the structure should be matched to it.
   • Each sequence needs its own structure.
   • Match the following parameters for each sequence in the alignment:
     • Structure
     • Entity
     • Chain
     • Instance (if available)
4. Select the Apply Matching button.
   • If the structures are correctly matched, they will be superposed according to the alignment.
   • If the matching is not correct, it is indicated which sequences of the alignment were not matched correctly in the Log at the bottom.

Add a time-trace plot of a measurement for a trajectory

1. Import the trajectory you want to calculate the measurement for. See Tutorials
   • Importing a trajectory.
   • Stream a trajectory from the MDsrv.
2. If needed, clean up the visualization by toggling the visibility for the importet files in the State Tree panel on the left side.
3. Open the Structure Tools panel on the right side.
4. Open the Measurements menu in the Structure Tools panel.
5. Select the Add button in the Measurements menu.
6. Activate the selection mode by clicking on the mouse pointer icon on the top right side of the white canvas where the structure is displayed (Toggle Selection Mode).
7. An additional menu appears at the top of the white canvas.
8. Select the button labeled Residue to change the granularity of the selection.
9. Select the desired elements to add a measurement (two for distance, three for angle, four for area angle). The selected elements will be displayed in a list in the Measurements menu on the right side.
10. Select the desired measurement in the Measurements menu to add it.
11. Click the Toggle Selection Mode button again, to exit the selection mode.
12. Open the Extensions panel at the bottom.
13. Open the Time-trace Plot menu.
14. Select the measurement you just added to display its plot throughout the trajectory.

There are various interaction possible:

• Skipping to a specific frame by clicking on the value
• Sorting the values by frame, ascending, and descending
• Filtering the values
• Switching the display to RMSD for the whole model
  • Instead of a filter, it is now possible to change he comparison frame for the RMSD