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natedey / RINRUS

Residue Interaction Network ResidUe Selector
MIT License
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if a lone glycine CA is tagged by probe, we can have a free glycine unit trimmed to CH4? #39

Closed natedey closed 11 months ago

natedey commented 11 months ago

I thought we fixed this a long time ago?

tsantaloci commented 11 months ago

I am so confused. I need a path of an example of this issue so I can try to solve

tsantaloci commented 11 months ago

/home/tjsntlci/chem/tj_problem/test/free_glycine I created a customized case and this seemed to create a free glycine as CH4 if the res atom file just has CA for glycine

natedey commented 11 months ago

That is a HUGE problem that I thought had been solved a VERY long time ago

tsantaloci commented 11 months ago

Do you want it trimmed to CH4 or no?

natedey commented 11 months ago

no. never. That chemically makes no sense. Even worse with alanine being trimmed to an ethane because it can rotate totally out of the active site

tsantaloci commented 11 months ago

What should it be? what about CA O?

tsantaloci commented 11 months ago

For my case, Rinrus wouldn't be able to trim the CA because my pdb file is super small. I kinda hacked It badly so I wouldn't mind an actual example

tsantaloci commented 11 months ago

Solve

tsantaloci commented 11 months ago

The issue was solved by editing rinrus_trim python file.