Peptide Sequence: Difference between revisions
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==Other Sources== | ==Other Sources== | ||
Robert Campbell has notified us of [http:// | Robert Campbell has notified us of [http://pldserver1.biochem.queensu.ca/~rlc/work/pymol 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) | 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) | In addition, [[Rotamer Toggle]] can set the sidechains to different rotamers or specific side-chain angle sets. (Dan Kulp) | ||
Revision as of 11:16, 21 January 2009
Building a Peptide Sequence From Hand
There are more than one method in PyMol for building a peptide sequence from hand. First, you may simply hold down the alt (option on Mac) key and type in the one-letter code for the sequence. Secondly, you can write a script like the following
for aa in "DCAHWLGELVWCT": cmd._alt(string.lower(aa))
which will build the amino acid sequence "DCAHWLGELVWCT".
Other Sources
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)