Modeller PIR Format IO

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fio%2Fmodellerpir.html;h=ec8b39c9242c1bbbd2eb26ea10cea6beda950082;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=c5839ad4fbd67fbe04371f0842d8a60fc547c5c4;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git diff --git a/help/html/io/modellerpir.html b/help/html/io/modellerpir.html index c5839ad..ec8b39c 100755 --- a/help/html/io/modellerpir.html +++ b/help/html/io/modellerpir.html @@ -1,32 +1,40 @@ + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + --> 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
+  
+    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-------------
@@ -37,26 +45,30 @@ structureX:1FER:1:.:105:.:.
 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
+  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.
+  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.