Dear Joel,

Thank you so much for sharing!
Totally answered my question, very much appreciated and I will look into the 
command as well.

Thank you very much for your kind guidance and assistance!

Jessica Lim

From: Joel Tyndall<mailto:joel.tynd...@otago.ac.nz>
Sent: Tuesday, 31 August 2021 5:55 am
To: #JESSICA LIM JIAYING#<mailto:jessicaj...@e.ntu.edu.sg>; 
pymol-users@lists.sourceforge.net<mailto:pymol-users@lists.sourceforge.net>
Subject: RE: [PyMOL] Recognition and Display of Secondary Structure Cartoon

Hi Jessica,

Generally secondary structure is extracted from a pdb file and PyMol would read 
this.

e.g.
HELIX    1   1 GLY A   86  THR A   91  1                                   6
HELIX    2   2 GLY B   86  THR B   91  1                                   6
SHEET    1   A 4 GLN A   2  THR A   4  0
SHEET    2   A 4 THR B  96  ASN B  98 -1  O  LEU B  97   N  ILE A   3
SHEET    3   A 4 THR A  96  ASN A  98 -1  N  THR A  96   O  ASN B  98
SHEET    4   A 4 GLN B   2  ILE B   3 -1  N  ILE B   3   O  LEU A  97


Sometimes the pdb file is incomplete or does not display all secondary 
structure. Using the command dss in Pymol can usually help define/display 
correct ss.

https://www.pymolwiki.org/index.php/Dss

Hope this helps
J

From: #JESSICA LIM JIAYING# <jessicaj...@e.ntu.edu.sg>
Sent: Saturday, 28 August 2021 6:54 pm
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Recognition and Display of Secondary Structure Cartoon

Hi all,

I am wondering how PyMOL recognises and display secondary structure (like alpha 
helix) when selecting the ‘Cartoon’ function. I have attached an image of my 
molecule where only certain regions are displayed in the cartoon representation 
whereas there is helical propensity throughout my molecule as seen in the 
image. Hence, how does PyMOL decide on the secondary structure features?

Thank you so much!
Any suggestions/advice on where to look will be greatly appreciated!

Jessica Lim

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