Get fastastr

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get_fastastr is an API-only function which returns the one-letter amino acid sequence in FASTA format.

PyMOL API

cmd.get_fastastr(string selection='all', int state=-1, int quiet=1)

Example

fetch 1ubq, async=0
print cmd.get_fastastr('all')
>1ubq
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLV
LRLRGG

Known Issues

  • Due to a bug this function currently only works for selections from a single object (see #3466472)
  • The sequences of different chains are just concatenated and returned as a single sequence

See Also