Constructing and Exploring Crystal Contacts
by Eric Martz, March 2000; revised April 2001; revised August 2001.
A resource within Protein Explorer.

Disclaimer: I am not very experienced with this, and am certainly not an authority. There may be errors in this document, or better procedures. Send suggestions to me please. If you know better methods, please tell me!

Overview: Below is a detailed procedure for

  1. Building crystal contacts from a PDB file, using DeepView (formerly called Swiss PDB Viewer).
  2. Selecting just the asymmetric unit plus the contacting shell from the enormous file resulting from the previous step.
  3. Inserting MODEL/ENDMDL records to distinguish, for Protein Explorer, the original asymmetric unit from the contacting portions of adjacent asymmetric units.
  4. Exploring the contacts using Protein Explorer.

    All software employed is freeware.

This document assumes you have some knowledge about PDB files and 3D macromolecular structure. If you need more background in order to understand the procedure below, start at the tutorial for Protein Explorer, and continue with the documentation for DeepView.

Plan to spend at least an hour or two doing this procedure on a single PDB file.

This procedure was written for Windows. Some keyboard shortcuts will differ for Macintosh or unix.

    I. Constructing crystal contacts in SwissPDBViewer

    I.A. Loading your molecule

  1. Install the SwissPDBViewer version 3.6b3. At the time of this writing, the current version is 3.7b2, but it contains bugs in the crystal construction routines -- do not use 3.7b2! (The symptom is that after completion of I.C., the crystal is not symmetrical.)

  2. Run DeepView (hereafter referred to as DV)
  3. Preferences, loading protein, uncheck ignore solvent, OK.
  4. Preferences, Electron density maps, check Draw unit cell (at bottom left), OK.
  5. File, Open PDB to load your PDB file (which should first be downloaded to your local disk).

  6. Press the Ins (Insert) key to center and size the molecule. From here on, use 2nd-4th icons at upper left of main window to zoom and rotate at will.

  7. Optional recommended simplification of display:
    Window, Layers Infos.
    In the Layers Window: In the Control Panel, shift-click the 'side' (sidechain) column to hide sidechains.

  8. Make sure 'Save in original orientation' is checked on the File menu.

  9. Save your work (recommended filename: AU.PDB, for asymmetric unit). File, Save, Layer. (DV "Project" format is a PDB file with additional info saved for DV.) If you run into problems later, close and reopen DV, then load this file.

    I.B. Filling out a single unit cell.

  10. Using the layers window, toggle 'axis' on and off. Zoom till you can see it, and you can find that X=red, Y=green, Z=blue (mnemonic RGB).

  11. Optional: Check out the space group in the PDB file header. Click the little printed page/text icon at the upper left, third row, to right of globe symbol. Scroll down till the atom records begin, and notice a few lines earlier the CRYST1 record containing the space group (for example, P 21 21 2).

  12. Tools, build crystallographic symmetry. The window opens with the correct symmetry group at the top ready to click. (click on red space group, for example P21212). This adds copies of the molecule as needed to fill out the unit cell. Each copy is in a new layer.

    Caution: some PDB files don't work properly. An example is oxyhemoglobin 1HHO. As noted in REMARK records in this file, nonstandard coordinates are used and these confuse DV. Inspect your unit cell carefully to be sure none of the molecules overlap in the same space (physically impossible). It should be possible to check for such clashes using Select, Groups close to another layer, but I'm not sure how to do it reliably.

  13. Use Shift-Click in the Layers Infos and Control Panel to hide everything except the backbone trace, as we did above for the original molecule. In the Control Panel, you select each layer (to uncheck 'side') by clicking on the very top, where a menu of all layers will open, allowing you to select one.

  14. Optional, recommended: Color, Layer. This gives each chain a different color.

  15. Now we need to merge all the current layers into a single layer, save it, and reload the merged layer.
    1. In the control panel, use the pull-down menu of layers to select each layer in turn. For each layer, Select, All (or Shift-Click in the left-most column of the Control Panel). After doing this, in the Layers window, each layer should have the same number of atoms selected (last column).

    2. Edit, Create merged layer from selection. A new layer will be created named _merge_.

    3. Using the pull-down menu at the top of the Control Panel, select the merged layer. File, Save, Layer. A good filename would be UC.PDB (for unit cell).

    I.C. Translating and copying unit cells.

    Our next goal is to rubber stamp the unit cells needed to visualize all crystallographic contacts to the asymmetric unit. These will be additional unit cells at all faces, edges, and vertices of the original central unit cell.

  16. File, Close all layers.

  17. File, Open PDB, open your UC.PDB file.

  18. Tools, Translate layer along unit cell.

  19. Save the project (or subset projects) as a PDB file, which we'll refer to below as the CRYSTAL.PDB file (it may be quite large, between 5 and 100 megabytes!).

    II. Selecting the contact shell.

    Now we need to select only the residues in a shell near the original asymmetric unit, and save the original asymmetric unit with its nearby shell of crystal contacts. This will typically reduce the size of the file about 200-fold!

  20. Load CRYSTAL.PDB or one of the project files that represents a subset of it.

  21. Load the original AU.PDB file as an additional layer.

  22. Deselect everything: Select, Select None; Select, Extend to other layers. (Confirm that the last columns in the Layers window are all 0.)

  23. Select the AU layer, and Select All. (Confirm in the layers window that all layers have 0 selected, except the AU layer.)

  24. Select, Neighbors of selected aa. Check "Add to selection", set the distance to 10. Angstroms, and check "Act on all layers". Click OK and wait. This can take a long time! When the selection is finished, numbers of selected residues will appear in some of the layers in the Layers window (provided any residues in this translated subset of unit cells were within 10 A). If you can open the Windows menu, it has finished the selection, even if there are zero residues selected in all layers except the AU.

  25. If you saved subsets of the crystal, and if 0 residues were selected outside the AU layer, there is nothing to save from this subset. If nonzero counts appear in layers other than AU, save them:

  26. If you were able to save all of the translations in to a single crystal file, go on to Section III. If you saved subsets of the crystal, repeat the steps above in IIA (10 Angstrom selection and saving) for each subset, producing a shell file for each.

  27. If you saved subsets of the crystal, File, Close all layers. File, Open the 10A shell for each subset. File, Save Project (filename SHELL10.PDB). This file should contain the original AU plus all of its crystal contacts.

    III. Inserting model records.

    Separating your SHELL file into NMR-style models will greatly assist your exploration of the crystal contacts in Protein Explorer.

  28. In a text editor (Word, or Wordpad on Windows, or BBEdit on Mac) examine the contents of your AU file, noting the atom serial number of the last atom in the file. (This is the first number in the last ATOM or HETATM line in the file.)

  29. Open the final (merged if necessary) SHELL file in your text editor. Immediately before the CRYST1 record at the top of the file, insert a new line "MODEL 1", being sure to put the "1" in the same column as the element, like this:
    MODEL        1
    CRYST1 ...
    ATOM      1  N   ...

  30. Between the line with the serial number of the original last atom, and the next line, insert ENDMDL and MODEL 2, like this:
    HETATM  461  O   HOH    80      12.095  14.835  35.393  0.81 48.91
    MODEL        2
    ATOM    462  N   MET     1      14.122   1.978  57.372  1.00 15.93

  31. Just before the last line, "END", in the CRYSTAL file, insert the line ENDMDL to end the second model. Save the model-delimited CRYSTAL file.

  32. Optional: You may find it useful to have the contacting piece of each separate chain in a separate model. In this case, scan forward watching the residue numbers. When they decrease, it is a boundary between chains -- insert ENDMDL and a new model number.

    IV. Analysing the contacts in Protein Explorer.

    There are undoubtedly excellent possibilities for analysis within DV but I'm not familiar with them. Here are my suggestions.

  33. If you are interested in whether a particular region of the surface has crystal contacts, this method will help to simplify the image. Load your shell10 file, and go to Advanced Explorer, and then to the NMR Models control panel.
    1. In the slot "Always show model [ ] black", enter 1, then click outside the slot. Now click the [Model] button to click through all models, noting which models are close to the region of interest.
    2. Enter 1 plus numbers of other models of interest in the "Model list" slot, and press the [All] button. This shows only the listed models.
    3. You may wish to delete unwanted models from your SHELL file. If you do, renumber the remaining models to be consecutive. You may find this file useful in the next step below.

  34. A very informative overview is possible with the Contact Surfaces mechanism in PE's QuickViews. Load your SHELL file and go to QuickViews. SELECT All (or, to exclude solvent, SELECT Chains). Scroll the top control frame down to QuickViews Plus, and check Include all models in contact surfaces. Now, DISPLAY Contacts.

    The Contact Surfaces options in the middle frame enable a wide variety of views.

  35. A more detailed, bond-by-bond analysis is possible using your SHELL file in the Noncovalent Bond Finder, accessed in Advanced Explorer. Again, the trick is to select model=1 before starting the Finder. Alternatively, if you are interested in only a specific region of model 1, select that before starting the Finder.
Please send suggestions for improvement of this document to yours truly.