From: jprocter Date: Mon, 10 Apr 2006 13:59:34 +0000 (+0000) Subject: describing the Modeller/PIR output. X-Git-Tag: Release_2_08~17 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=bf019e15f5d4f7894ddb015574be8ebf31e583da;p=jalview.git describing the Modeller/PIR output. --- diff --git a/help/html/features/modellerpir.html b/help/html/features/modellerpir.html new file mode 100755 index 0000000..942b081 --- /dev/null +++ b/help/html/features/modellerpir.html @@ -0,0 +1,45 @@ + + +Modeller PIR Format IO + + +

Modeller PIR Format IO

+

The homology modelling program, Modeller uses a special form +of the PIR format where information about sequence numbering and chain +codes are written into the 'description' line between the PIR protein +tag and the protein alignment entry:

+
>P1;Q93Z60_ARATH
+sequence:Q93Z60_ARATH:1:.:118:.:.
+----MASTALSSAIVSTSFLRRQQTPISLRSLPFANT-QSLFGLKS-STARGGRVTAMATYKVKFITPEGEQ
+EVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSD------QSFLD-D-------------
+---------------------*
+>P1;PDB|1FER|_
+structureX:1FER:1:.:105:.:.
+----------------------------------------------------AFVVTDNCIKCKY---TDCV
+EV-CPVDCFY----EGPNFLVIHPDECIDCALCEPECPAQAIFSEDEVPEDMQEFIQLNAELAEVWPNITEK
+KDPLPDAEDWDGVKGKLQHLE*
+
+

Jalview will attempt to parse any PIR entries conforming to the +Modeller/PIR format, in order to extract the sequence start and end +numbering and (possibly) a PDB file reference. The description line +information is always stored in the sequence description string - so +no information is lost if this parsing process fails.

+

The 'Modeller Output' flag in the 'Output' tab of the Jalview Preferences dialog +box controls whether Jalview will also output MODELLER style PIR +files. In this case, any existing 'non-modeller PIR' header +information in the description string of an alignment is appended to +an automatically generated modeller description line for that +sequence.

+

The general format used for generating the Modeller/PIR sequence +description line is shown below : +

>P1;Primary_Sequence_ID
+sequence or structureX:pdb-reference if
+  available:start residue:start chain code:end
+  residue:end chain code:. description text
+The first field is either sequence or structureX, depending upon the +presence of a PDB database ID for the sequence. If the protein has no +PDB reference, then the chain code is not specified, unless one +already existed when the sequence was imported into Jalview. + +