Re: [PyMOL] [Help]About indentifying interaction between residues

[Jared S. <jar...@co...>]

Hi Nikita -

To me this looks like the cartoon representation for missing residues,
which is controlled by the cartoon_gap_cutoff
<https://pymolwiki.org/index.php/Cartoon_gap_cutoff> setting.  If you
either `hide cartoon` or `set cartoon_gap_cutoff, 0`, does it go away?

Usually the dashed line would be somewhat curved for a normal gap to mimic
an unmodeled flexible loop, but I can reproduce something similar to your
image by creating a new object containing only with two non-contiguous
residues and showing the cartoon for that object:

```
fetch 1shv
as cartoon

create gap_res, polymer.protein and resi 237+243

show sticks, gap_res

```


Hope that helps.

Cheers,
Jared


On Sat, Feb 17, 2024 at 3:36 AM Maisnam Nikita Chanu <mni...@gm...>
wrote:

> Dear All,
>
> My name is Nikita, I am a graduate student at Academia Sinica, Taiwan.
> This e-mail aims to ask for help in identifying the bond/interaction
> between two residues.
>
> I am currently learning about PyMol to utilize in my project. I used PyMol
> to visualize potential H-bond interactions in specific amino acid residues.
> However, I have just discovered that Arg465 and Ser461 show a distinct
> interaction, as shown in the file.
> Please help identify this interaction.
> I would be grateful for any help or suggestions.
>
> Please don't hesitate to contact me if you have any questions.
> I look forward to hearing from you.
>
> Best regards,
> Nikita Chanu
>
>
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