Annotate v - Revision history

Cchem at 03:33, 1 March 2021

2021-03-01T03:33:42Z

Cchem at 03:25, 1 March 2021

2021-03-01T03:25:46Z

Cchem: 9 revisions

2020-03-03T04:30:39Z

9 revisions

New page

{{Infobox script-repo
|type = script
|filename = annotate_v.py
|author = [[User:XinYu|Xin Yu]]
|license = BSD
}}

== Description ==

''Version: 1.0''

A simple-to-use script for annotation of VH or VL sequence of an antibody. It creates a Pymol object for each FR or CDR region. It utilizes the REST API interface of ''Abnum'' (http://www.bioinf.org.uk/abs/abnum/) from Dr Andrew Martin's group at UCL

== Annotation Schemes ==

Currently supports '''Kabat, Chothia, Contact, IMGT'''1

1Definitions for Kabat, Chothia, Contact, and IIMGT are same as listed in the table (http://www.bioinf.org.uk/abs/info.html#kabatnum), except that for IMGT, H-CDR2 is defined as '''H51-H57''' in this script, as opposed to of '''H51-H56''' in the table. This slight revision generates result that matches that from ''IMGT website'' (http://www.imgt.org/)

== Dependencies and Limitations ==

1. Import '''request''' module

2. Relies on internet connection to ''Abnum''

3. Incomplete VH or VL sequence might not be annotated

== 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.jpg|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.jpg|center|thumb|400px|example output from command lines]]

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

== Contact ==
For bugs & questions, emai @ xinyu18018@gmail.com. Enjoy!

[[Category:Script_Library]]
[[Category:ObjSel_Scripts]]
[[Category:Pymol-script-repo]]

Speleo3: Infobox

2020-02-20T08:33:15Z

Infobox

New page

{{Infobox script-repo
|type = script
|filename = annotate_v.py
|author = [[User:XinYu|Xin Yu]]
|license = BSD
}}

== Description ==

''Version: 1.0''

A simple-to-use script for annotation of VH or VL sequence of an antibody. It creates a Pymol object for each FR or CDR region. It utilizes the REST API interface of ''Abnum'' (http://www.bioinf.org.uk/abs/abnum/) from Dr Andrew Martin's group at UCL

== Annotation Schemes ==

Currently supports '''Kabat, Chothia, Contact, IMGT'''1

1Definitions for Kabat, Chothia, Contact, and IIMGT are same as listed in the table (http://www.bioinf.org.uk/abs/info.html#kabatnum), except that for IMGT, H-CDR2 is defined as '''H51-H57''' in this script, as opposed to of '''H51-H56''' in the table. This slight revision generates result that matches that from ''IMGT website'' (http://www.imgt.org/)

== Dependencies and Limitations ==

1. Import '''request''' module

2. Relies on internet connection to ''Abnum''

3. Incomplete VH or VL sequence might not be annotated

== 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.jpg|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.jpg|center|thumb|400px|example output from command lines]]

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

== Source code ==

Copy the source code into a `.py` file and run script in Pymol. Source code: https://raw.githubusercontent.com/xinyu-dev/annotate_v-for-Pymol/master/annotate_v.py

== Contact ==
Bugs? Questions? Email Xin Yu @ xinyu18018@gmail.com. Enjoy!

[[Category:Script_Library]]
[[Category:ObjSel_Scripts]]
[[Category:Pymol-script-repo]]

← Older revision		Revision as of 03:25, 1 March 2021
Line 31:		Line 31:


−	[[Image:Annotate_v_pic1.~~jpg~~\|center\|thumb\|800px\|Create a selection group for input seq, or use the default sele]]	+	[[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.		2. Copy the entire script and create a `.py` file. Run script.

@@ Line 53: / Line 53: @@
 . 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.jpg|center|thumb|400px|example output from command lines]]
+[[File:Annotate_v_pic2.png|center|thumb|400px|example output from command lines]]
-[[File:Annotate_v_pic3.jpg|center|thumb|800px|new FR and CDR selection groups are created]]
+[[File:Annotate_v_pic3.png|center|thumb|800px|new FR and CDR selection groups are created]]