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23 <title>Modeller PIR Format IO</title>
27 <strong>Modeller PIR Format IO</strong>
30 The homology modelling program, <a
31 href="http://salilab.org/modeller/"
32 >Modeller</a> uses a special form of the PIR format where information
33 about sequence numbering and chain codes are written into the
34 'description' line between the PIR protein tag and the protein
37 <pre>>P1;Q93Z60_ARATH
38 sequence:Q93Z60_ARATH:1:.:118:.:.
39 ----MASTALSSAIVSTSFLRRQQTPISLRSLPFANT-QSLFGLKS-STARGGRVTAMATYKVKFITPEGEQ
40 EVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSD------QSFLD-D-------------
41 ---------------------*
43 structureX:1FER:1:.:105:.:.
44 ----------------------------------------------------AFVVTDNCIKCKY---TDCV
45 EV-CPVDCFY----EGPNFLVIHPDECIDCALCEPECPAQAIFSEDEVPEDMQEFIQLNAELAEVWPNITEK
46 KDPLPDAEDWDGVKGKLQHLE*
48 <p>Jalview will attempt to parse any PIR entries conforming to the
49 Modeller/PIR format, in order to extract the sequence start and end
50 numbering and (possibly) a PDB file reference. The description line
51 information is always stored in the sequence description string - so
52 no information is lost if this parsing process fails.</p>
54 The 'Modeller Output' flag in the 'Output' tab of the Jalview <a
55 href="../features/preferences.html"
56 >Preferences dialog box</a> controls whether Jalview will also output
57 MODELLER style PIR files. In this case, any existing 'non-modeller
58 PIR' header information in the description string of an alignment is
59 appended to an automatically generated modeller description line for
62 <p>The general format used for generating the Modeller/PIR
63 sequence description line is shown below :
64 <pre>>P1;<em>Primary_Sequence_ID</em>
65 <em>sequence or structureX</em>:<em>pdb-reference if
66 available</em>:<em>start residue</em>:<em>start chain code</em>:<em>end
67 residue</em>:<em>end chain code</em>:. <em>description text</em>
69 The first field is either sequence or structureX, depending upon the
70 presence of a PDB database ID for the sequence. If the protein has no
71 PDB reference, then the chain code is not specified, unless one
72 already existed when the sequence was imported into Jalview.