Hi Yufeng, The "Properties" panel can show you which settings got changed with the preset. The "pretty" preset indeed sets "cartoon_side_chain_helper" to "off" for the object. The easiest way to clear this setting is to use the "unset_deep" command.
unset_deep cartoon_side_chain_helper set cartoon_side_chain_helper https://pymolwiki.org/index.php/Unset_deep https://pymolwiki.org/index.php/Properties_Inspector Cheers, Thomas > On Jan 29, 2021, at 6:26 AM, Yufeng Tong <yufeng.t...@gmail.com> wrote: > > Hi Tomas, > > I noticed this setting is not working when > preset.pretty(selection='all') has been invoked, that is, whether > cartoon_side_chain_helper is set to on or off, the side chain is > disconnected. Do you know what is changed when preset.pretty() is > called? > > The reason I want to call preset.pretty() is that if this is not > called, the sticks representation of an isopeptide cannot be properly > displayed (no sticks shown for the isopeptide bond), a bit of a > dilemma. > > Thanks, > > Yufeng > > > On Mon, Jan 18, 2021 at 3:35 AM Tomas Malinauskas > <tomas.malinaus...@gmail.com> wrote: >> >> Hi Emilia, >> >> You might try the following: >> set cartoon_side_chain_helper, on >> >> Hope that helps, >> Tomas >> >> On Mon, Jan 18, 2021 at 7:52 AM Emilia C. Arturo (Emily) >> <ecgart...@gmail.com> wrote: >>> >>> Hi All, >>> >>> I'm wondering if anyone here knows how to represent an amino acid residue >>> side chain that resides within a beta strand in stick representation such >>> that the residue is linked in space with the backbone. This works fine when >>> representing as sticks a residue that is within a loop or helix, but not >>> within a strand; there it just sticks out into space, which looks awful if >>> the figure is not turned 'just so' so that the viewer cannot see the space. >>> I am using version 2.4.0 on my Mac. >>> >>> Regards, >>> Emilia. >>> >>> -- >>> "Study as if you were going to live forever; live as if you were going to >>> die tomorrow." - Maria Mitchell >>> >>> "I'm not afraid of storms for I'm learning to sail my ship." - Louisa May >>> Alcott >>> >>> _______________________________________________ >>> 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 >> >> >> _______________________________________________ >> 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 > > > _______________________________________________ > 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 -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. _______________________________________________ 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
