Mutate Model to Sequence Dialog Box
In this dialog box, you can mutate all residues in the model to match the sequence and start a side-chain prediction job for the mutated residues.
To open this panel, click Mutate Model to Sequence in the PrimeX Panel.
- Using
- Features
- Additional Resources
Using the Mutate Model to Sequence Dialog Box
If the model lacks residues at either of the termini, some work will be required to refine the newly-placed residues. You may want to perform manual adjustment on these residues, then run a coordinate refinement, for example.
Mutate Model to Sequence Dialog Box Features
- Alignment to reference sequence text area
- Mutate to Match Sequence button
- Place Side Chains button
- Delete residues which align to gaps option
- Alignment to reference sequence text area
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This noneditable text area displays the alignment of the model sequence to the reference sequence. Residues in the model sequence that differ are marked in red. Residues that are missing at the beginning of the model are marked with a tilde.
- Mutate to Match Sequence button
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Perform the residue mutation on the reference sequence. The side chains are placed in a default orientation. A new project entry is created for the mutated structure. After the mutation is finished, the Place Side Chains button is activated. The sequence is not updated unless you re-enter the dialog box.
- Place Side Chains button
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Open the Real-Space Refinement Panel with the Predict side chains task selected and the mutated residues selected for refinement. This button is not available until you have mutated the model to match the sequence.
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Although you could adjust the side chains manually using the Rotamers Dialog Box, and even fit the best of the orientations provided to the density (if you have a map), it is better to do a full optimization of the side chains.
- Delete residues which align to gaps option
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This option deletes the residues that align to gaps in the model, rather than filling them in, when the mutation is performed. You will then have to perform a loop prediction to fill the gaps, but this will produce superior results to the default filling of gaps by the mutation algorithm.