Create a sequence with unusual residues or a mixed-type sequence

Instructions

The intuitive way

This way allows you to add unusual residues as well as residues of mixed type. You may need this more often that you would think. Some residues might not be stored under the type you think they are. For example if you replace the 2'-OH in an RNA with a fluorine, is that DNA or RNA? Also, some residues may not be available under the correct classification, but only as molecular type 'other' (more on this below).

To add unusual residues to your molecular system we need to use the Molecules: Molecule popup, which can be accessed using M: Molecule: Molecules. In the popup go to {Template Molecules}, and follow the steps:

• • Create a new molecule template by clicking [Add New Molecule] (you can get the same result by going directly to {Sequences} and setting the Molecules popup to <new>) :

• • Enter {Sequences}. Make sure that the Molecule pulldown points to the right molecule, and use a combination of [Add Polymer] and [Add Compound] to build the new sequence from beginning to end. Parts of the polymer chains that contain only normal residues or nucleotides of the same type can be added by clicking [Add Polymer], which navigates us to {Add Sequence}. Note that residues are added to the C terminal or the 3’ end and can not be moved later on to other positions in the sequence.To add single residues click on [Add Compound]. This navigates us to {Small Compounds} where it is possible to choose compounds such as unusual nucleotides and amino acids:

• • Select the compound of interest and click [Add Compound], which navigates you back to {Sequences}. First look for the compound you want under the correct Mol Type. If you do not find it there, try with Mol Type 'all'. Your residue may be classified differently, (e.g. 'DNA' instead of 'RNA'). Mol Type 'other' is best avoided, but may sometimes be the only place to find what you need.

  • Link the compound to the existing sequence by editing the |Polymer Linking| and |Linked Residues| fields. First set the |Polymer Linking| for all residues to the correct values. Then click the |Linked Residues| field, which will navigate to {Links}, where you can select which residues to are link to the current residue. You can also have a look at the |Descriptor &Stereochemistry| column and change any values that you think are wrong.

  • The |Polymer Linking| column selects how the residue is linked. Unfortunately not all ChemComps have the hooks you need for all relevant linkings. This is especially a problem for side chain modifications for regular residues and nucleotides, and for ChemComps from the 'other' group. When you cannot make the links you need, you should just put the residues in place, and set the |Polymer Linking| as best you can. This leaves a chain with gaps, but it will still give you the right residue numbers and the right atoms to assign to.

The compound has now been added to the sequence of the molecule template. After the molecule template has been created, we can use it to create the chain and the molecular system. To do this go to {Chains}, select the molecule template in “Template for new chain:” and click [Make Chain From Template].

An alternative way based on Ccp codes

An alternative way to create a sequence with unusual residues is to enter your sequence directly in the {Add Sequences} tab. This only works if all the residues are of the same molecule type (e.g. all amino acids or all DNA)The unusual compounds are here added directly to your sequence based on the Ccp codes:

• • Go to {Add Sequences} in the Molecule: Molecules popup. Add the “Normal” polymer chain compounds by typing the letters in the |Sequence Input| field. Add unusual compounds by selecting them in the pulldown menu related to “Ccp codes:” and by clicking [Append “...”]:     

• • Set “Destination Mol System:” to "<None>" if you want to set specific molecular properties (these properties can not be set/changed after a molecular system has been defined). If you do not need to make any changes to molecular properties, choose "<New>" for the molecular system.

  • Click [Add Sequence!] to create a molecule/molecule template with this sequence. After the molecule template has been created, we can translate it to a molecule and create the associated chain and molecular system. To do this go to {Chains}, select the molecule template in “Template for new chain:” and click [Make Chain From Template].