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Hydrogenation is failing to observe coplanar rules. #287

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electronicsbyjulie opened this issue Jun 28, 2023 · 5 comments · Fixed by #302
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Hydrogenation is failing to observe coplanar rules. #287

electronicsbyjulie opened this issue Jun 28, 2023 · 5 comments · Fixed by #302
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CRITICAL Something is very wrong. retest Check if this is still happening.

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@electronicsbyjulie
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This is from the hGNAL PDB:

image
@primaryodors primaryodors added the CRITICAL Something is very wrong. label Jun 28, 2023
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primaryodors commented Jun 28, 2023 •
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This should be fixed right away before continuing with the cron fixes.

Would also be good to create a unit test for hydrogenate() generating coplanar hydrogens in side chains that should have them: Arg, Asn, Gln, His, Phe, Trp, Tyr.

primaryodors added a commit that referenced this issue Jun 28, 2023
@primaryodors
Fix for #282 before work can be done on #287.
1185db8
@primaryodors primaryodors linked a pull request Jun 29, 2023 that will close this issue
More cron stuff. #286
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@electronicsbyjulie electronicsbyjulie linked a pull request Jul 12, 2023 that will close this issue
Coupled Homology #290
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@electronicsbyjulie
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The coupled homology branch has a fix for this one.

primaryodors added a commit that referenced this issue Jul 13, 2023
@primaryodors
282 287 atom positioning (#297)
9c65386 
* Fixed an unrelated segfault that was an obstacle.

* Fix for #282 before work can be done on #287.

* Upgrade of Point class to double precision.

* Test file for coplanar pi hydrogenation.

* Pepteditor script for coplanar pi hydrogen test.

* Test of coplanar pi atoms after hydrogenation.

* Updated tests affected by the Point precision.

* Fixed array deletion before array usage.

* Observe pi coplanarity when hydrogenating.

* Updates to tests.

* Retrying...

* Fixed infinite loop.

* Temporarily increasing limit. See #288.

* Unit test.

* Unit test enhancements.
@primaryodors primaryodors added the retest Check if this is still happening. label Jul 14, 2023
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It looks like the way to test this would be to re-add the hydrogenate_add_missing_heavy_atoms code, enable it, and generate a coupled PDB.

@primaryodors
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Confirmed, still happening, in both the G protein (first image) and the receptor (second image).

image
image

@primaryodors
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There are missing and extra hydrogens, but coplanarity is being observed now.

image
image

This was unlinked from pull requests Jul 14, 2023
More cron stuff. #286
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Coupled Homology #290
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@primaryodors primaryodors linked a pull request Jul 14, 2023 that will close this issue
Retest 287 #302
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Retest 287 primaryodors/primarydock
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