3 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
4 * Copyright (C) $$Year-Rel$$ The Jalview Authors
6 * This file is part of Jalview.
8 * Jalview is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU General Public License
10 * as published by the Free Software Foundation, either version 3
11 * of the License, or (at your option) any later version.
13 * Jalview is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty
15 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
16 * PURPOSE. See the GNU General Public License for more details.
18 * You should have received a copy of the GNU General Public License
19 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
20 * The Jalview Authors are detailed in the 'AUTHORS' file.
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/">Modeller</a> uses a
32 special form of the PIR format where information about sequence
33 numbering and chain codes are written into the 'description' line
34 between the PIR protein tag and the protein alignment entry:
36 <pre>>P1;Q93Z60_ARATH
37 sequence:Q93Z60_ARATH:1:.:118:.:.
38 ----MASTALSSAIVSTSFLRRQQTPISLRSLPFANT-QSLFGLKS-STARGGRVTAMATYKVKFITPEGEQ
39 EVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSD------QSFLD-D-------------
40 ---------------------*
42 structureX:1FER:1:.:105:.:.
43 ----------------------------------------------------AFVVTDNCIKCKY---TDCV
44 EV-CPVDCFY----EGPNFLVIHPDECIDCALCEPECPAQAIFSEDEVPEDMQEFIQLNAELAEVWPNITEK
45 KDPLPDAEDWDGVKGKLQHLE*
47 <p>Jalview will attempt to parse any PIR entries conforming to the
48 Modeller/PIR format, in order to extract the sequence start and end
49 numbering and (possibly) a PDB file reference. The description line
50 information is always stored in the sequence description string - so
51 no information is lost if this parsing process fails.</p>
53 The 'Modeller Output' flag in the 'Output' tab of the Jalview <a
54 href="../features/preferences.html">Preferences dialog
55 box</a> controls whether Jalview will also output MODELLER style PIR
56 files. In this case, any existing 'non-modeller PIR' header
57 information in the description string of an alignment is appended to
58 an automatically generated modeller description line for that
61 <p>The general format used for generating the Modeller/PIR
62 sequence description line is shown below :
63 <pre>>P1;<em>Primary_Sequence_ID</em>
64 <em>sequence or structureX</em>:<em>pdb-reference if
65 available</em>:<em>start residue</em>:<em>start chain code</em>:<em>end
66 residue</em>:<em>end chain code</em>:. <em>description text</em>
68 The first field is either sequence or structureX, depending upon the
69 presence of a PDB database ID for the sequence. If the protein has no
70 PDB reference, then the chain code is not specified, unless one
71 already existed when the sequence was imported into Jalview.