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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