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In work with typical proteins the template Start1.2.cara should be sufficient. However, in special cases the user may be working with a protein containing unusual amino acids or even with artificial polymers. In this case it becomes necessary to build custom ResidueTypes.

Step-by-step guide to making a ResidueType:

Case I. New ResidueType is similar to one in the template.

  1. If the new ResidueType is similar to an existing ResidueType, right-click on the existing ResidueType and select "duplicate ResidueType" NOTE: this feature is not yet included in Cara 1.5 - use the following workaround:
    1. Right-Click in the ResidueType explorer and select "Import ResidueType".
    2. select any repository derived from Start1.2.cara or Start1.2.cara itself.
    3. From the displayed list select the ResidueType most similar to the one you want to create and click OK.
    4. Enter the Short Name for the new ResidueType which must be unique.
    5. Right-Click on the new ResidueType and select "Rename".
    6. enter the full name of the new ResidueType.
    7. you cannot change the Letter of the new ResidueType within CARA (unfortunately) Do this by editing the repository.
  2. Enter then Name, Short name, and Letter abbreviation for the new residue. The "Short Name" must be unique (if you used above workaround then skip this step).
  3. Right-Click on the new ResidueType and select MoleculeViewer.
  4. Modify the new ResidueType to have the correct structure. See MoleculeViewer for how to do this.
  5. Right-Click on new ResidueType and select "set terminals". Usually these will be correct if the ResidueType you duplicated has the same N- and C-terminal atoms.
  6. Right-Click on new ResidueType and select "set SpinSystemType". Select the SpinSystemType appropriate for the new residue.

Case II. New ResidueType is unrelated to existing ResidueTypes.

  1. Right-click in ResidueType Explorer and select "New ResidueType".
  2. Enter Name, Short Name (unique), Letter of the new ResidueType.
  3. Open MoleculeViewer and create the new ResidueType.
  4. Close MoleculeViewer, Right-click on the new ResidueType and select "Set Terminals".
  5. Enter the name of the atoms which connect to the previous (Nterminal) and following (Cterminal) residue.
  6. If the new ResidueType is the first of its class, you will need to create a new SpinSystemType for the class. See Creating new SpinSystemType.
  7. After creating a SpinSystemType, define the SpinSystemType for the new ResidueType by Right-clicking on the new ResidueType and selecting "Set SpinSystemType". Select the appropriate SpinSystemType.

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