Electrostatic surfac colours are wrong (all blue) - Githubissues

m2ms / fragalysis-frontend

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Electrostatic surfac colours are wrong (all blue) #241

Closed phraenquex closed 4 years ago

phraenquex commented 4 years ago

The electrostatic surface (#228) is not coming up with the right colour. It's all blue, when it should be red-white-blue.
It might be something in the PDB file, e.g. incorrect protonation state defined on upload, or similiar. Might need some expert (e.g. Matteo Ferla) to troubleshoot.

matej-vavrek commented 4 years ago

It could be cause by "colorDomain: [-0.3, 0.3]" setting*, because without this it looks different (not able to upload a screenshot atm, but it is on Slack).

https://fragalysis-matej.apps.xchem.diamond.ac.uk/viewer/react/snapshot/f74b7d69-8951-4b8a-ae0c-ade157cccee7

Settings for surface would be then like

{
  sele: 'polymer',
  colorScheme: 'electrostatic',
  // colorDomain: [-0.3, 0.3],
  surfaceType: 'av',
  radiusType: 'vdw',
  opacity: 0.47,
  colorValue: colour
}

* https://github.com/m2ms/fragalysis-frontend/issues/214#issuecomment-603433002

matej-vavrek commented 4 years ago

It was caused by rendering of surface. Fixed version: https://fragalysis-matej.apps.xchem.diamond.ac.uk/viewer/react/landing

phraenquex commented 4 years ago

Great!
So two details that now become clear: 1) opacity should be 0.74;
2) line thickness of the protein should be higher (4 or 5) - so that it's visible enough through the surface. [ 3) I can't edit the display settings of the *_protein object in the Display Controls]

matej-vavrek commented 4 years ago

Thank you for the feedback.

[x] opacity should be 0.74;
[x] line thickness of the protein should be higher (4 or 5) - so that it's visible enough through the surface.
[x] ~I can't edit the display settings of the *_protein object in the Display Controls]~ objects loaded on first target entry is not possible to edit

matej-vavrek commented 4 years ago

Fixed and ready: https://fragalysis-matej.apps.xchem.diamond.ac.uk/viewer/react/landing

phraenquex commented 4 years ago

Looks great, except now you've lost the waters. The contact lines should end at red crosses, which are the water molecules. I've circled some in red in the image here, and marked in one of them.

matej-vavrek commented 4 years ago

Like these?

phraenquex commented 4 years ago

Okay, starting a new ticket - this one is sorted, please issue pull request.