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
_______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
