Difference between revisions of "Peptide Sequence"

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(mention fab and Builder)
 
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=Building a Peptide Sequence From Hand=
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== 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
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There are more than one method in PyMOL for building a peptide sequence from hand.
 +
 
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* Simply hold down the '''alt''' ('''option''' on Mac) key and type in the one-letter code for the sequence.
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* Use the [[fab]] command
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* Use the [[Builder]] in "Protein" mode
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* You can write a script like the following which will build the amino acid sequence "DCAHWLGELVWCT".
 
<source lang="python">
 
<source lang="python">
 
for aa in "DCAHWLGELVWCT": cmd._alt(string.lower(aa))
 
for aa in "DCAHWLGELVWCT": cmd._alt(string.lower(aa))
 
</source>
 
</source>
which will build the amino acid sequence "DCAHWLGELVWCT".
 
  
 
==Other Sources==
 
==Other Sources==
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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'''.
 
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'''.
  

Latest revision as of 02:47, 4 August 2011

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))

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)