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PF6 problem #155

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victorlarignon opened this issue Feb 14, 2024 · 2 comments
Open

PF6 problem #155

victorlarignon opened this issue Feb 14, 2024 · 2 comments
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enhancement New feature or request question Further information is requested

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@victorlarignon
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We currently have a problem with the way we draw PF6 counter ions. I thought it was a problem with the display of the error red line, but it's actually a problem with PF6 as every other ions are displayed correctly.
The problem is that we are not drawing it correctly right now, we put the negative charge on the P whereas it should be delocalized on all the F. Ketcher draws an error line because P shouldn't have 6 bonds. One way to fix it would be to make 5 covalent PF bonds and a sixth non covalent, with the negative charge on F. Or it would be great if we could simply write text like in ChemDraw (ie. PF6-), but then it means Ketcher has to modify their program.

example of the error line (you can cycle through all molecules by refreshing the home page, you will only see red lines for PF6):
http://chemwiki.scc.kit.edu/main/mediawiki/Molecule:100695

possible fixes:
image

how it should look like:
https://en.wikipedia.org/wiki/Hexafluorophosphate#/media/File:PF6partialcharge.png

@victorlarignon victorlarignon added enhancement New feature or request question Further information is requested labels Feb 14, 2024
@victorlarignon
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I checked on PubChem, whether it is PF6 or BF4, it's always drawn with negative charge on P or B (the way we did up until now), so I think we can stick with this.
@kkthek, is it possible to not display the red error line in the chem forms?
(For the preview in the yellow window I guess it's also on the third party app that we use, right?)

image

@kkthek
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kkthek commented Apr 12, 2024

Hello Pierre,

I have a question about the molecule rendering service. In Ketcher it is
possible to suppress red underlining in case of warnings/errors. Is it
possible to suppress that in the rendered image as well? Could you
adjust the service so that this is always suppressed?

Pierre will take care of this:

Sorry for the late reply
I'll see what I can do. We are also interested in updating the service, but unfortunately it will probably take me another week or two to accomplish this.

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