Re: [PyMOL] representation of residue sidechain within a beta strand?

[Thomas H. <tho...@sc...>]

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 <yuf...@gm...> 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
> <tom...@gm...> 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)
>> <ecg...@gm...> 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.
>>> 
>>> --
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>>> 
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--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.