Building a Peptide Sequence From Hand
There are more than one method in PyMOL for building a peptide sequence from hand.
- Simply hold down the alt (option on Mac) key and type in the one-letter code for the sequence.
- Use the fab command
- Use the Builder in "Protein" mode
- You can write a script like the following which will build the amino acid sequence "DCAHWLGELVWCT".
for aa in "DCAHWLGELVWCT": cmd._alt(string.lower(aa))
Robert Campbell has notified us of his two scripts to solve the problem. You can apparently specify phi/psi angles, too. Look for build_seq.py and build_seq_phi_psi.py.
Also check out CreateSecondaryStructure , which you can build repeating units of different types of secondary structure (a-helix,b-sheets, loops,etc) (Dan Kulp)
In addition, Rotamer Toggle can set the sidechains to different rotamers or specific side-chain angle sets. (Dan Kulp)