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.
HELIX1 1 GLY A 86 THR A 91 1 6
HELIX2 2 GLY B 86 THR B 91 1 6
SHEET1 A 4 GLN A 2 THR A 4 0
SHEET2 A 4 THR B 96 ASN B 98 -1 O LEU B 97 N ILE A 3
SHEET3 A 4 THR A 96 ASN A 98 -1 N THR A 96 O ASN B 98
SHEET4 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#
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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