Re: [PyMOL] waterbox visulization in pymol

[Matic K. <Mat...@ki...>]

Hi Yeeun,

could it be that you had orthoscopic view (menu Display>Orthoscopic View) enabled in Pymol and not in VMD?

To see the 'grid' I think you usually need Orthoscopic view. I may be wrong. Try the perspective view if that changes things.
So I think this is just a visualisation artefact and does not affect the simulations (if you plan to do that).

Usually all the water molecules are defined in the input file, so I would guess it is not 'several small waterboxes combined into one'.
You can also check by opening the input file in a advanced text editor (Notepad++, Sublime text, ...) and you will be able to count the molecules and see if there is some symmetry defined (probably not).

Best!
Matic


On 22. 10. 23 08:24, 김예은 wrote:
Dear Pymol,
Hello.
I visualized a water box generated by Charmm-gui in pymol.
[image.png]
There is a grid pattern in the waterbox, so I thought several small waterboxes were generated and combined into one.
However, in VMD software, there is no grid pattern in the same waterbox.
[image.png]
Is there any specific visualization method to show the grid pattern in the waterbox in Pymol?
Or, could I think that several small waterboxes were generated and combined into one?

Sincerely,
Yeeun Kim




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