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Scripting: add ability to coordinate a metal or attach a prosthetic group to the protein. #76

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electronicsbyjulie opened this issue Jun 27, 2022 · 3 comments
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Scripting: add ability to coordinate a metal or attach a prosthetic group to the protein. #76

electronicsbyjulie opened this issue Jun 27, 2022 · 3 comments
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medium priority This should be made working as soon as time permits.

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@electronicsbyjulie
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electronicsbyjulie commented Jun 27, 2022 •
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  1. Create a command to be able to coordinate metals. ✅
  2. Allow a string variable for the metal ion.
  3. Get the thiolation feature working.
  4. Create a command to add a prosthetic group to the protein, using a SMILES string.
  5. Allow specifying which atoms of the side chain to replace which atoms of the prosthetic with, and vice versa.
@electronicsbyjulie electronicsbyjulie added medium priority This should be made working as soon as time permits. focus labels Jun 27, 2022
@electronicsbyjulie electronicsbyjulie self-assigned this Jun 27, 2022
electronicsbyjulie pushed a commit that referenced this issue Jul 3, 2022
Metal coordination, but without proper flexion of the side chains. #76
43fbe72
electronicsbyjulie pushed a commit that referenced this issue Jul 3, 2022
Scripting: Metal coordination command. #76 Also corrected alphabetiza…
7c47902 
…tion of the scripting readme. (What do I look like I know my ABCs? I'm only 41!)
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electronicsbyjulie commented Jul 4, 2022 •
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Currently, if binding to a pi helix, the coordination side chains are positioned strangely and the metal ion is clashing with the backbone.

HELIX PI %sr %er
LET %c1 = %hyxxce
LET %c2 = %hyxxce + 4
LET %c3 = %hyxxce + 5
MCOORD Zn 2 %c1 %c2 %c3

clashy_metal1
clashy_metal

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Whatever changed since this issue was last updated, the metal coordination feature is working now.

@primaryodors
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#246 is a duplicate of this issue. However, since work for this issue is being obsoleted, we are opting to close this and keep the newer issue.

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