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Pepteditor: Helix function is warping side chains. #282

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electronicsbyjulie opened this issue Jun 24, 2023 · 2 comments
Open

Pepteditor: Helix function is warping side chains. #282

electronicsbyjulie opened this issue Jun 24, 2023 · 2 comments
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high priority Above average priority.

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@electronicsbyjulie
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From this script:

GEN "ARNDCEQGHIKLMFPSTWYV"
HELIX ALPHA 1 20
SAVE "test/received/all20.pdb"

all20.pdb.txt

Can't seem to attach a PDB extension, but if rename the attachment from .pdb.txt to .pdb, can see in the viewer just how much it's distorting certain side chains, e.g. arginine, leucine, all four of the aromatics...

Doesn't happen if no HELIX command.
@primaryodors primaryodors added CRITICAL Something is very wrong. on hold Waiting for something else to be working first. labels Jun 24, 2023
@primaryodors
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Since our predictions use ready-made PDBs, and therefore do not involve creating helices, this issue is not urgent.

@primaryodors primaryodors added high priority Above average priority. and removed CRITICAL Something is very wrong. on hold Waiting for something else to be working first. labels Jun 24, 2023
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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It is happening even without helixing them.

This was unlinked from pull requests Jul 12, 2023
More cron stuff. #286
Closed
Coupled Homology #290
Closed
@electronicsbyjulie electronicsbyjulie mentioned this issue Jul 12, 2023
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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.
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