https://pymolwiki.org/api.php?action=feedcontributions&user=XinYu&feedformat=atomPyMOLWiki - User contributions [en]2024-03-29T11:46:06ZUser contributionsMediaWiki 1.35.7https://pymolwiki.org/index.php?title=Annotate_v&diff=13249Annotate v2020-02-20T16:47:11Z<p>XinYu: </p>
<hr />
<div>{{Infobox script-repo<br />
|type = script<br />
|filename = annotate_v.py<br />
|author = [[User:XinYu|Xin Yu]]<br />
|license = BSD<br />
}}<br />
<br />
== Description ==<br />
<br />
''Version: 1.0''<br />
<br />
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<br />
<br />
== Annotation Schemes == <br />
<br />
Currently supports '''Kabat, Chothia, Contact, IMGT'''<sup>1</sup><br />
<br />
<sup>1</sup>Definitions 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/)<br />
<br />
== Dependencies and Limitations ==<br />
<br />
1. Import '''request''' module<br />
<br />
2. Relies on internet connection to ''Abnum''<br />
<br />
3. Incomplete VH or VL sequence might not be annotated<br />
<br />
== How to use ==<br />
<br />
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. <br />
<br />
<br />
[[Image:Annotate_v_pic1.jpg|center|thumb|800px|Create a selection group for input seq, or use the default sele]]<br />
<br />
2. Copy the entire script and create a `.py` file. Run script. <br />
<br />
3. The general syntax is:<br />
<br />
<source lang="python">annotate_v("selection_group_name", "scheme")</source><br />
<br />
'''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<br />
<br />
'''scheme:''' currently supports Kabat, Chothia, Contact, IMGT. Must be lowercase<br />
<br />
For example: <br />
<br />
<syntaxhighlight lang="python"><br />
annotate_v("VH", "kabat") #input sequence from VH selection group, annotate using "kabat"<br />
annotate_v("sele", "imgt") #input sequence from the default sele group, annotate using "imgt". You can also try "contact", "chothia"<br />
</syntaxhighlight><br />
<br />
<br />
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. <br />
<br />
[[File:Annotate_v_pic2.jpg|center|thumb|400px|example output from command lines]]<br />
<br />
[[File:Annotate_v_pic3.jpg|center|thumb|800px|new FR and CDR selection groups are created]]<br />
<br />
<br />
== Contact ==<br />
For bugs & questions, emai @ xinyu18018@gmail.com. Enjoy!<br />
<br />
[[Category:Script_Library]]<br />
[[Category:ObjSel_Scripts]]<br />
[[Category:Pymol-script-repo]]</div>XinYuhttps://pymolwiki.org/index.php?title=Annotate_v&diff=13246Annotate v2020-02-15T21:10:59Z<p>XinYu: </p>
<hr />
<div>== Description ==<br />
<br />
''Author: Xin Yu''<br />
<br />
''License: BSD, 2020''<br />
<br />
''Version: 1.0''<br />
<br />
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<br />
<br />
== Annotation Schemes == <br />
<br />
Currently supports '''Kabat, Chothia, Contact, IMGT'''<sup>1</sup><br />
<br />
<sup>1</sup>Definitions 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/)<br />
<br />
== Dependencies and Limitations ==<br />
<br />
1. Import '''request''' module<br />
<br />
2. Relies on internet connection to ''Abnum''<br />
<br />
3. Incomplete VH or VL sequence might not be annotated<br />
<br />
== How to use ==<br />
<br />
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. <br />
<br />
<br />
[[Image:Annotate_v_pic1.jpg|center|thumb|800px|Create a selection group for input seq, or use the default sele]]<br />
<br />
2. Copy the entire script and create a `.py` file. Run script. <br />
<br />
3. The general syntax is:<br />
<br />
<source lang="python">annotate_v("selection_group_name", "scheme")</source><br />
<br />
'''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<br />
<br />
'''scheme:''' currently supports Kabat, Chothia, Contact, IMGT. Must be lowercase<br />
<br />
For example: <br />
<br />
<syntaxhighlight lang="python"><br />
annotate_v("VH", "kabat") #input sequence from VH selection group, annotate using "kabat"<br />
annotate_v("sele", "imgt") #input sequence from the default sele group, annotate using "imgt". You can also try "contact", "chothia"<br />
</syntaxhighlight><br />
<br />
<br />
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. <br />
<br />
[[File:Annotate_v_pic2.jpg|center|thumb|400px|example output from command lines]]<br />
<br />
[[File:Annotate_v_pic3.jpg|center|thumb|800px|new FR and CDR selection groups are created]]<br />
<br />
<br />
== Source code ==<br />
<br />
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<br />
<br />
== Contact ==<br />
Bugs? Questions? Email Xin Yu @ xinyu18018@gmail.com. Enjoy!<br />
<br />
[[Category:Script_Library]]<br />
[[Category:ObjSel_Scripts]]<br />
[[Category:Pymol-script-repo]]</div>XinYuhttps://pymolwiki.org/index.php?title=Annotate_v&diff=13245Annotate v2020-02-15T21:06:44Z<p>XinYu: </p>
<hr />
<div>== Description ==<br />
<br />
''Author: Xin Yu, 2020''<br />
''Version: 1.0''<br />
<br />
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<br />
<br />
<br />
<br />
== Annotation Schemes == <br />
<br />
Currently supports '''Kabat, Chothia, Contact, IMGT'''<sup>1</sup><br />
<br />
<sup>1</sup>Definitions 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/)<br />
<br />
== Dependencies and Limitations ==<br />
<br />
1. Import '''request''' module<br />
<br />
2. Relies on internet connection to ''Abnum''<br />
<br />
3. Incomplete VH or VL sequence might not be annotated<br />
<br />
== How to use ==<br />
<br />
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. <br />
<br />
<br />
[[Image:Annotate_v_pic1.jpg|center|thumb|800px|Create a selection group for input seq, or use the default sele]]<br />
<br />
2. Copy the entire script and create a `.py` file. Run script. <br />
<br />
3. The general syntax is:<br />
<br />
<source lang="python">annotate_v("selection_group_name", "scheme")</source><br />
<br />
'''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<br />
<br />
'''scheme:''' currently supports Kabat, Chothia, Contact, IMGT. Must be lowercase<br />
<br />
For example: <br />
<br />
<syntaxhighlight lang="python"><br />
annotate_v("VH", "kabat") #input sequence from VH selection group, annotate using "kabat"<br />
annotate_v("sele", "imgt") #input sequence from the default sele group, annotate using "imgt". You can also try "contact", "chothia"<br />
</syntaxhighlight><br />
<br />
<br />
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. <br />
<br />
[[File:Annotate_v_pic2.jpg|center|thumb|400px|example output from command lines]]<br />
<br />
[[File:Annotate_v_pic3.jpg|center|thumb|800px|new FR and CDR selection groups are created]]<br />
<br />
<br />
== Source code ==<br />
<br />
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<br />
<br />
== Contact ==<br />
Bugs? Questions? Email Xin Yu @ xinyu18018@gmail.com. Enjoy!<br />
<br />
[[Category:Script_Library]]<br />
[[Category:ObjSel_Scripts]]<br />
[[Category:Pymol-script-repo]]</div>XinYuhttps://pymolwiki.org/index.php?title=Annotate_v&diff=13244Annotate v2020-02-15T21:05:43Z<p>XinYu: </p>
<hr />
<div>== Description ==<br />
<br />
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<br />
<br />
Author: Xin Yu, 2020<br />
<br />
== Annotation Schemes == <br />
<br />
Currently supports '''Kabat, Chothia, Contact, IMGT'''<sup>1</sup><br />
<br />
<sup>1</sup>Definitions 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/)<br />
<br />
== Dependencies and Limitations ==<br />
<br />
1. Import '''request''' module<br />
<br />
2. Relies on internet connection to ''Abnum''<br />
<br />
3. Incomplete VH or VL sequence might not be annotated<br />
<br />
== How to use ==<br />
<br />
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. <br />
<br />
<br />
[[Image:Annotate_v_pic1.jpg|center|thumb|800px|Create a selection group for input seq, or use the default sele]]<br />
<br />
2. Copy the entire script and create a `.py` file. Run script. <br />
<br />
3. The general syntax is:<br />
<br />
<source lang="python">annotate_v("selection_group_name", "scheme")</source><br />
<br />
'''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<br />
<br />
'''scheme:''' currently supports Kabat, Chothia, Contact, IMGT. Must be lowercase<br />
<br />
For example: <br />
<br />
<syntaxhighlight lang="python"><br />
annotate_v("VH", "kabat") #input sequence from VH selection group, annotate using "kabat"<br />
annotate_v("sele", "imgt") #input sequence from the default sele group, annotate using "imgt". You can also try "contact", "chothia"<br />
</syntaxhighlight><br />
<br />
<br />
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. <br />
<br />
[[File:Annotate_v_pic2.jpg|center|thumb|400px|example output from command lines]]<br />
<br />
[[File:Annotate_v_pic3.jpg|center|thumb|800px|new FR and CDR selection groups are created]]<br />
<br />
<br />
== Source code ==<br />
<br />
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<br />
<br />
== Contact ==<br />
Bugs? Questions? Email Xin Yu @ xinyu18018@gmail.com. Enjoy!<br />
<br />
[[Category:Script_Library]]<br />
[[Category:ObjSel_Scripts]]<br />
[[Category:Pymol-script-repo]]</div>XinYuhttps://pymolwiki.org/index.php?title=Annotate_v&diff=13241Annotate v2020-02-09T00:19:44Z<p>XinYu: </p>
<hr />
<div>== Description ==<br />
<br />
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<br />
<br />
== Annotation Schemes == <br />
<br />
Currently supports '''Kabat, Chothia, Contact, IMGT'''<sup>1</sup><br />
<br />
<sup>1</sup>Definitions 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/)<br />
<br />
== Dependencies and Limitations ==<br />
<br />
1. Import '''request''' module<br />
<br />
2. Relies on internet connection to ''Abnum''<br />
<br />
3. Incomplete VH or VL sequence might not be annotated<br />
<br />
== How to use ==<br />
<br />
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. <br />
<br />
<br />
[[Image:Annotate_v_pic1.jpg|center|thumb|800px|Create a selection group for input seq, or use the default sele]]<br />
<br />
2. Copy the entire script and create a `.py` file. Run script. <br />
<br />
3. The general syntax is:<br />
<br />
<source lang="python">annotate_v("selection_group_name", "scheme")</source><br />
<br />
'''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<br />
<br />
'''scheme:''' currently supports Kabat, Chothia, Contact, IMGT. Must be lowercase<br />
<br />
For example: <br />
<br />
<syntaxhighlight lang="python"><br />
annotate_v("VH", "kabat") #input sequence from VH selection group, annotate using "kabat"<br />
annotate_v("sele", "imgt") #input sequence from the default sele group, annotate using "imgt". You can also try "contact", "chothia"<br />
</syntaxhighlight><br />
<br />
<br />
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. <br />
<br />
[[File:Annotate_v_pic2.jpg|center|thumb|400px|example output from command lines]]<br />
<br />
[[File:Annotate_v_pic3.jpg|center|thumb|800px|new FR and CDR selection groups are created]]<br />
<br />
<br />
== Source code ==<br />
<br />
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<br />
<br />
== Contact ==<br />
Bugs? Questions? Email xinyu18018@gmail.com. Enjoy!<br />
<br />
[[Category:Script_Library]]<br />
[[Category:ObjSel_Scripts]]<br />
[[Category:Pymol-script-repo]]</div>XinYuhttps://pymolwiki.org/index.php?title=Annotate_v&diff=13240Annotate v2020-02-08T04:36:55Z<p>XinYu: /* Contact */</p>
<hr />
<div>{{Infobox script-repo<br />
|type = script<br />
|filename = annotate_v.py<br />
|author = [[User:Inchoate|Xin Yu]]<br />
|license = BSD<br />
}}<br />
<br />
<br />
== Description ==<br />
<br />
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<br />
<br />
== Annotation Schemes == <br />
<br />
Currently supports '''Kabat, Chothia, Contact, IMGT'''<sup>1</sup><br />
<br />
<sup>1</sup>Definitions 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/)<br />
<br />
== Dependencies and Limitations ==<br />
<br />
1. Import '''request''' module<br />
<br />
2. Relies on internet connection to ''Abnum''<br />
<br />
3. Incomplete VH or VL sequence might not be annotated<br />
<br />
== How to use ==<br />
<br />
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. <br />
<br />
<br />
[[Image:Annotate_v_pic1.jpg|center|thumb|800px|Create a selection group for input seq, or use the default sele]]<br />
<br />
2. Copy the entire script and create a `.py` file. Run script. <br />
<br />
3. The general syntax is:<br />
<br />
<source lang="python">annotate_v("selection_group_name", "scheme")</source><br />
<br />
'''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<br />
<br />
'''scheme:''' currently supports Kabat, Chothia, Contact, IMGT. Must be lowercase<br />
<br />
For example: <br />
<br />
<syntaxhighlight lang="python"><br />
annotate_v("VH", "kabat") #input sequence from VH selection group, annotate using "kabat"<br />
annotate_v("sele", "imgt") #input sequence from the default sele group, annotate using "imgt". You can also try "contact", "chothia"<br />
</syntaxhighlight><br />
<br />
<br />
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. <br />
<br />
[[File:Annotate_v_pic2.jpg|center|thumb|400px|example output from command lines]]<br />
<br />
[[File:Annotate_v_pic3.jpg|center|thumb|800px|new FR and CDR selection groups are created]]<br />
<br />
<br />
== Contact ==<br />
Bugs? Questions? Email xinyu18018@gmail.com. Enjoy!<br />
<br />
[[Category:Script_Library]]<br />
[[Category:ObjSel_Scripts]]<br />
[[Category:Pymol-script-repo]]</div>XinYuhttps://pymolwiki.org/index.php?title=Annotate_v&diff=13239Annotate v2020-02-08T04:36:27Z<p>XinYu: </p>
<hr />
<div>{{Infobox script-repo<br />
|type = script<br />
|filename = annotate_v.py<br />
|author = [[User:Inchoate|Xin Yu]]<br />
|license = BSD<br />
}}<br />
<br />
<br />
== Description ==<br />
<br />
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<br />
<br />
== Annotation Schemes == <br />
<br />
Currently supports '''Kabat, Chothia, Contact, IMGT'''<sup>1</sup><br />
<br />
<sup>1</sup>Definitions 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/)<br />
<br />
== Dependencies and Limitations ==<br />
<br />
1. Import '''request''' module<br />
<br />
2. Relies on internet connection to ''Abnum''<br />
<br />
3. Incomplete VH or VL sequence might not be annotated<br />
<br />
== How to use ==<br />
<br />
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. <br />
<br />
<br />
[[Image:Annotate_v_pic1.jpg|center|thumb|800px|Create a selection group for input seq, or use the default sele]]<br />
<br />
2. Copy the entire script and create a `.py` file. Run script. <br />
<br />
3. The general syntax is:<br />
<br />
<source lang="python">annotate_v("selection_group_name", "scheme")</source><br />
<br />
'''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<br />
<br />
'''scheme:''' currently supports Kabat, Chothia, Contact, IMGT. Must be lowercase<br />
<br />
For example: <br />
<br />
<syntaxhighlight lang="python"><br />
annotate_v("VH", "kabat") #input sequence from VH selection group, annotate using "kabat"<br />
annotate_v("sele", "imgt") #input sequence from the default sele group, annotate using "imgt". You can also try "contact", "chothia"<br />
</syntaxhighlight><br />
<br />
<br />
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. <br />
<br />
[[File:Annotate_v_pic2.jpg|center|thumb|400px|example output from command lines]]<br />
<br />
[[File:Annotate_v_pic3.jpg|center|thumb|800px|new FR and CDR selection groups are created]]<br />
<br />
<br />
== Contact ==<br />
Bugs? Questions? Email xinyu18018@gmail.com <br />
<br />
[[Category:Script_Library]]<br />
[[Category:ObjSel_Scripts]]<br />
[[Category:Pymol-script-repo]]</div>XinYuhttps://pymolwiki.org/index.php?title=Annotate_v&diff=13238Annotate v2020-02-08T04:32:24Z<p>XinYu: A simple-to-use script for annotation of VH or VL sequence of an antibody.</p>
<hr />
<div>{{Infobox script-repo<br />
|type = script<br />
|filename = annotate_v.py<br />
|author = [[User:Inchoate|Xin Yu]]<br />
|license = BSD<br />
}}<br />
<br />
<br />
== Description ==<br />
<br />
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<br />
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== Annotation Schemes == <br />
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Currently supports '''Kabat, Chothia, Contact, IMGT'''<sup>1</sup><br />
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<sup>1</sup>Definitions 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/)<br />
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== Dependencies and Limitations ==<br />
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1. Import '''request''' module<br />
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2. Relies on internet connection to ''Abnum''<br />
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3. Incomplete VH or VL sequence might not be annotated<br />
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== How to use ==<br />
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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. <br />
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[[Image:Annotate_v_pic1.jpg|center|thumb|800px|Create a selection group for input seq, or use the default sele]]<br />
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2. Copy the entire script and create a `.py` file. Run script. <br />
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3. The general syntax is:<br />
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<source lang="python">annotate_v("selection_group_name", "scheme")</source><br />
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'''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<br />
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'''scheme:''' currently supports Kabat, Chothia, Contact, IMGT. Must be lowercase<br />
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For example: <br />
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<syntaxhighlight lang="python"><br />
annotate_v("VH", "kabat") #input sequence from VH selection group, annotate using "kabat"<br />
annotate_v("sele", "imgt") #input sequence from the default sele group, annotate using "imgt". You can also try "contact", "chothia"<br />
</syntaxhighlight><br />
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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. <br />
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[[File:Annotate_v_pic2.jpg|center|thumb|400px|example output from command lines]]<br />
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[[File:Annotate_v_pic3.jpg|center|thumb|800px|new FR and CDR selection groups are created]]<br />
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[[Category:Script_Library]]<br />
[[Category:ObjSel_Scripts]]<br />
[[Category:Pymol-script-repo]]</div>XinYuhttps://pymolwiki.org/index.php?title=File:Annotate_v_pic3.jpg&diff=13237File:Annotate v pic3.jpg2020-02-08T04:24:07Z<p>XinYu: example output</p>
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<div>== Summary ==<br />
example output</div>XinYuhttps://pymolwiki.org/index.php?title=File:Annotate_v_pic2.jpg&diff=13236File:Annotate v pic2.jpg2020-02-08T04:11:55Z<p>XinYu: Print out of the FR and CDR regions</p>
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<div>== Summary ==<br />
Print out of the FR and CDR regions</div>XinYuhttps://pymolwiki.org/index.php?title=File:Annotate_v_pic1.jpg&diff=13235File:Annotate v pic1.jpg2020-02-08T03:48:14Z<p>XinYu: Create VH and VL groups. Alternatively, click-select the VH and VL sequence so that they're in the `sele` group</p>
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<div>== Summary ==<br />
Create VH and VL groups. Alternatively, click-select the VH and VL sequence so that they're in the `sele` group</div>XinYuhttps://pymolwiki.org/index.php?title=User:XinYu&diff=13234User:XinYu2020-02-07T23:38:16Z<p>XinYu: Created page with " == Title =="</p>
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<div><br />
== Title ==</div>XinYu