From: Robert Campbell <rlc1@po...> - 2004-03-11 16:44:40
I've added a new script to my PyMOL script archive. Have you ever wanted
to highlight in the display a particular sequence and couldn't be
bothered to look up the residue numbers? Me, too. So I wrote a little
script called seq_select.py that creates a named selection of an object
containing a particular sequence.
e.g. seq_select protein, efghi, actsite
will create a selection name 'actsite' from the 'protein' object that
contains the consecutive residues that match the sequence 'Glu Phe Gly
His Ile'. You can then alter the display of that selection by colour or
drawing mode as you wish.
The sequence can be entered in lower or upper case or a mixture thereof
-- it is converted to uppercase internally.
If the sequence 'efghi' happens to occur more than once, then all
instances will be included in the selection. If the sequence happens
to contain an unknown residue (in the 3-letter code stored by PyMOL),
say as part of a bound ligand, then that can be represented by 'X'. So
if you have a ligand that is CBZ-Leu-Tyr you could find it with the
I've written this to import my seq_convert.py script (available under
my "scripts" page as distinct from my PyMOL scripts page) if available,
but it isn't necessary. 'seq_convert.py' does 1-letter to 3-letter code
conversion of sequences as well as extracting sequences from PDB files
(from SEQRES records or from the coordinates themselves).
As always, please let me know if you find any bugs.
Hope this helps someone out there,
Robert L. Campbell, Ph.D. <rlc1@...>
Senior Research Associate phone: 613-533-6821
Dept. of Biochemistry, Queen's University, fax: 613-533-2497
Kingston, ON K7L 3N6 Canada http://adelie.biochem.queensu.ca/~rlc
PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 C0E2