From: jprocter Date: Mon, 10 Apr 2006 14:00:46 +0000 (+0000) Subject: moved modellerpir to io X-Git-Tag: Release_2_08~16 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=e6b0389bf7b855616d21b1121eb35627c776a847;p=jalview.git moved modellerpir to io --- diff --git a/help/html/features/modellerpir.html b/help/html/features/modellerpir.html deleted file mode 100755 index 942b081..0000000 --- a/help/html/features/modellerpir.html +++ /dev/null @@ -1,45 +0,0 @@ - - -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. - -