Editing Annotate v (section)

== How to use ==

1. Create a selection object for the V region, (such as '''VH''' and '''VL''' shown here). Only 1 V-region (VH OR VL) can be annotated each time. Alternatively, simply select the residues into the default '''<sele>''' group. 


[[Image:Annotate_v_pic1.png|center|thumb|800px|Create a selection group for input seq, or use the default sele]]

2. Copy the entire script and create a `.py` file. Run script. 

3. The general syntax is:

<source lang="python">annotate_v("selection_group_name", "scheme")</source>

'''selection_group_name:''' name of the selection group where you have the input sequence. Must be single-letter amino acid coded. Either VH or VL but not both

'''scheme:''' currently supports Kabat, Chothia, Contact, IMGT. Must be lowercase

For example: 

<syntaxhighlight lang="python">
annotate_v("VH", "kabat") #input sequence from VH selection group, annotate using "kabat"
annotate_v("sele", "imgt") #input sequence from the default sele group, annotate using "imgt". You can also try "contact", "chothia"
</syntaxhighlight>


4. In the output window, the script will print the FR and CDR regions (if found). It also automatically creates a selection group for each of the FR and CDR region. 

[[File:Annotate_v_pic2.png|center|thumb|400px|example output from command lines]]

[[File:Annotate_v_pic3.png|center|thumb|800px|new FR and CDR selection groups are created]]