Thanks Bob, I could make a working function out of your lines.
Luciano
De: Robert Hanson <hans...@stolaf.edu>
Para: Otis Rothenberger <osrot...@chemagic.com>;
"jmol-users@lists.sourceforge.net" <jmol-users@lists.sourceforge.net>
Enviado: Lunes, 19 de enero, 2015 5:21:05
Asunto: Re: [Jmol-users] JSmol: how to put a protein's sequence into a
javascript variable
You can get any "show" data back from "print" using
print show("sequence false")
$ load =1crn
PLANT PROTEIN 30-APR-81 1CRN
WATER STRUCTURE OF A HYDROPHOBIC PROTEIN AT ATOMIC RESOLUTION.
PENTAGON RINGS OF WATER MOLECULES IN CRYSTALS OF CRAMBIN
found biomolecule 1: A
$ show sequence false
Model 1
Chain A:
TTCCPSIVARSNFNVCRLPGTPEAICATYTGCIIIPGATCPGDYAN
$ x = show("sequence false")
$ print x
Model 1
Chain A:
TTCCPSIVARSNFNVCRLPGTPEAICATYTGCIIIPGATCPGDYAN
Thus, in JavaScript, you can get the sequence (of the selected atoms) using:
var seq = Jmol.evaluateVar(jmolApplet, "show('sequence false')")
and then apply a bit of parsing to remove the Model/Chain business.
In addition, note that you can get the cysteine linkages using Jmol bioSMILES:
$ print {*}.find("SMILES",true)
//* Jmol bioSMILES 14.3.11_2015.01.18 2015-01-18 19:26 1 *//
//* chain A protein 1 *// ~p~TTC:1C:2PSIVARSNFNVC:3RLPGTPEAIC:3ATYTGC:2IIIPGA
TC:1PGDYAN //* 46 *//
where C:1 links with C:1, C:2 with C:2, and C:3 with C:3
Finally, there is still one more thing you can do. The .find() function can
return a sequence:
$ print {*}.find("SEQUENCE")
//* chain A protein 1 *// ~p~TTCCPSIVARSNFNVCRLPGTPEAICATYTGCIIIPGATCPGDYAN //*
46 *//
and you can use this along with searching for sequences:
$ select within(SEQUENCE,"EQAC")
58 atoms selected
$ print {within(SEQUENCE,"EQAC")}.find("SEQUENCE")
//* chain A protein 8 *// ~p~EQAC //* 11 *//.
//* chain B protein 8 *// ~p~EQAC //* 11 *//
Bob
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