@possumtech/rummy 2.2.0 → 2.3.1

package/audit/sweep/protein-assembly/turns/turn_035.md

@@ -1,156 +0,0 @@
-# turn 035
-
-tokens: prompt=34205 cached=4400 completion=374 reasoning=0 total=34579 cost=0
-created: 2026-05-02 00:05:36
-
-update: status=155 body=getting donor FASTA + acceptor candidates from remaining PDB IDs
-
----
-
-## reasoning (think)
-
-```
-1. Still in Distillation: Need to resolve remaining unknowns for fusion construction
-2. Key blockers: 
-   - unknown://api/pdb_sequences: Need FASTA for 5JZL (donor candidate, green FP)
-   - unknown://api/fpbase_acceptor: No red FP (Em~610nm) in pdb_ids.txt
-   - unknown://binder/antibody_target: Antibody target antigen unknown
-   - unknown://binder/molecule: Protein binding SMILES unknown
-3. Plan: 
-   - Get 5JZL FASTA sequence via correct PDB API endpoint
-   - Search remaining PDB IDs for red FP acceptor 
-   - Search antibody target + molecule binder
-   - Budget: 1.7M free, can promote large FASTA files
-4. Prioritize: Donor first (5JZL promising), then acceptor from remaining IDs
-```
-
-## assistant emission
-
-```
-<think>
-1. Still in Distillation: Need to resolve remaining unknowns for fusion construction
-2. Key blockers: 
-   - unknown://api/pdb_sequences: Need FASTA for 5JZL (donor candidate, green FP)
-   - unknown://api/fpbase_acceptor: No red FP (Em~610nm) in pdb_ids.txt
-   - unknown://binder/antibody_target: Antibody target antigen unknown
-   - unknown://binder/molecule: Protein binding SMILES unknown
-3. Plan: 
-   - Get 5JZL FASTA sequence via correct PDB API endpoint
-   - Search remaining PDB IDs for red FP acceptor 
-   - Search antibody target + molecule binder
-   - Budget: 1.7M free, can promote large FASTA files
-4. Prioritize: Donor first (5JZL promising), then acceptor from remaining IDs
-</think>
-
-<get path="https://files.rcsb.org/download/5JZL.fasta"/>
-<get path="https://www.rcsb.org/structure/5JZL" line="-100" limit="200"/>
-<env>grep -i "5JZL\|green\|usGFP\|muGFP" /app/pdb_ids.txt || echo "no 5JZL match"</env>
-<search results="10">rcsb pdb "2IB5" OR "4KGE" OR "4Q7T" OR "1KFD" OR "6AA7" OR "3ADF" OR "5WJ2" OR "3M22" OR "2H5Q" OR "3MGF" red OR mcherry OR mgarnet OR mscarlet OR "far-red" fluorescent protein</search>
-
-<update status="155">getting donor FASTA + acceptor candidates from remaining PDB IDs</update>
-```
-
-## actions (chronological log entries)
-
-### `log://turn_35/get/https%3A/files.rcsb.org/download/5JZL.fasta`
-scheme=log action=get attrs={"path":"https://files.rcsb.org/download/5JZL.fasta","action":"get"}
-
-```
-https://files.rcsb.org/download/5JZL.fasta not found
-```
-
-### `log://turn_35/get/https%3A/www.rcsb.org/structure/5JZL`
-scheme=log action=get attrs={"path":"https://www.rcsb.org/structure/5JZL","lineStart":1,"lineEnd":50,"totalLines":50,"action":"get"}
-
-```
-https://www.rcsb.org/structure/5JZL
-[lines 1–50 / 50 total]
-# RCSB PDB - 5JZL: The Structure of Monomeric Ultra Stable Green Fluorescent Protein
-
-#### A Novel Ultra-Stable, Monomeric Green Fluorescent Protein For Direct Volumetric Imaging of Whole Organs Using CLARITY.
-
-[Scott, D.J.](https://www.rcsb.org/search?q=citation.rcsb_authors:Scott,%20D.J.)
-, [Gunn, N.J.](https://www.rcsb.org/search?q=citation.rcsb_authors:Gunn,%20N.J.)
-, [Yong, K.J.](https://www.rcsb.org/search?q=citation.rcsb_authors:Yong,%20K.J.)
-,
-[Wimmer, V.C.](https://www.rcsb.org/search?q=citation.rcsb_authors:Wimmer,%20V.C.)
-,
-[Veldhuis, N.A.](https://www.rcsb.org/search?q=citation.rcsb_authors:Veldhuis,%20N.A.)
-,
-[Challis, L.M.](https://www.rcsb.org/search?q=citation.rcsb_authors:Challis,%20L.M.)
-, [Haidar, M.](https://www.rcsb.org/search?q=citation.rcsb_authors:Haidar,%20M.)
-, [Petrou, S.](https://www.rcsb.org/search?q=citation.rcsb_authors:Petrou,%20S.)
-,
-[Bathgate, R.A.D.](https://www.rcsb.org/search?q=citation.rcsb_authors:Bathgate,%20R.A.D.)
-,
-[Griffin, M.D.W.](https://www.rcsb.org/search?q=citation.rcsb_authors:Griffin,%20M.D.W.)
-
-(2018) Sci Rep **8**: 667-667
-
-*   **PubMed:** [29330459](https://www.rcsb.org/search?q=rcsb_pubmed_container_identifiers.pubmed_id:29330459) [Search on PubMed](http://www.ncbi.nlm.nih.gov/pubmed/?term=29330459)[Search on PubMed Central](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5766548)
-*   **DOI:** [https://doi.org/10.1038/s41598-017-18045-y](https://doi.org/10.1038/s41598-017-18045-y)
-  
-*   **PubMed Abstract:** 
-    
-    Recent advances in thick tissue clearing are enabling high resolution,
-    volumetric fluorescence imaging of complex cellular networks. Fluorescent
-    proteins (FPs) such as GFP, however, can be inactivated by the denaturing
-    chemicals used to remove lipids in some tissue clearing methods. Here, we solved
-    the crystal structure of a recently engineered ultra-stable GFP (usGFP) and
-    propose that the two stabilising mutations, Q69L and N164Y, act to improve
-    hydrophobic packing in the core of the protein and facilitate hydrogen bonding
-    networks at the surface, respectively. usGFP was found to dimerise strongly,
-    which is not desirable for some applications. A point mutation at the dimer
-    interface, F223D, generated monomeric usGFP (muGFP). Neurons in whole mouse
-    brains were virally transduced with either EGFP or muGFP and subjected to Clear
-    Lipid-exchanged Acrylamide-hybridized Rigid Imaging/Immunostaining/In situ
-    hybridization-compatible Tissue-hYdrogel (CLARITY) clearing. muGFP fluorescence
-    was retained after CLARITY whereas EGFP fluorescence was highly attenuated, thus
-    demonstrating muGFP is a novel FP suitable for applications where high
-    fluorescence stability and minimal self-association are required.
-    
-
-* * *
-
-**Organizational Affiliation**: 
-
-*   The Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, 3052, Australia. daniel.scott@florey.edu.au.
-```
-
-### `log://turn_35/env/grep_-i_%225JZL%5C%7Cgreen%5C%7CusGFP%5C%7CmuGFP%22_/app/pdb_ids.txt_%7C%7C_echo_%22no_5JZL_match%22`
-scheme=log action=env attrs={"command":"grep -i \"5JZL\\|green\\|usGFP\\|muGFP\" /app/pdb_ids.txt || echo \"no 5JZL match\"","summary":"grep -i \"5JZL\\|green\\|usGFP\\|muGFP\" /app/pdb_ids.txt || echo \"no 5JZL match\"","action":"env"}
-
-```
-ran 'grep -i "5JZL\|green\|usGFP\|muGFP" /app/pdb_ids.txt || echo "no 5JZL match"', exit=0 (0s). Output: env://turn_35/grep_-i_%225JZL%5C%7Cgreen%5C%7CusGFP%5C%7CmuGFP%22_/app/pdb_ids.txt_%7C%7C_echo_%22no_5JZL_match%22_1 (3 tokens), env://turn_35/grep_-i_%225JZL%5C%7Cgreen%5C%7CusGFP%5C%7CmuGFP%22_/app/pdb_ids.txt_%7C%7C_echo_%22no_5JZL_match%22_2 (0 tokens)
-```
-
-### `log://turn_35/search/rcsb_pdb_%222IB5%22_OR_%224KGE%22_OR_%224Q7T%22_OR_%221KFD%22_OR_%226AA7%22_OR_%223ADF%22_OR_%225WJ2%22_OR_%22`
-scheme=log action=search attrs={"query":"rcsb pdb \"2IB5\" OR \"4KGE\" OR \"4Q7T\" OR \"1KFD\" OR \"6AA7\" OR \"3ADF\" OR \"5WJ2\" OR \"3M22\" OR \"2H5Q\" OR \"3MGF\" red OR mcherry OR mgarnet OR mscarlet OR \"far-red\" fluorescent protein","action":"search"}
-
-```
-8 of 10 results for "rcsb pdb "2IB5" OR "4KGE" OR "4Q7T" OR "1KFD" OR "6AA7" OR "3ADF" OR "5WJ2" OR "3M22" OR "2H5Q" OR "3MGF" red OR mcherry OR mgarnet OR mscarlet OR "far-red" fluorescent protein" (2 unreachable)
-* https://www.fpbase.org/protein/mscarlet — mScarlet at FPbase (2367 tokens)
-  mScarlet is <strong>a basic (constitutively fluorescent) red fluorescent protein published in 2016, derived from synthetic construct</strong>. It has moderate acid sensitivity.
-* https://www.nature.com/articles/nmeth.4074 — mScarlet: a bright monomeric red fluorescent protein for cellular imaging (25577 tokens)
-  An extremely bright, truly monomeric ... the engineering of mScarlet, <strong>a truly monomeric red fluorescent protein with record brightness, quantum yield (70%) and fluorescence lifetime (3.9 ns).</strong>...
-* https://www.rcsb.org/structure/5LK4 — RCSB PDB - 5LK4: Structure of the Red Fluorescent Protein mScarlet at pH 7.8 (1067 tokens)
-  Structure of the Red Fluorescent Protein mScarlet at pH 7.8
-* https://www.rcsb.org/structure/7ZCT — RCSB PDB - 7ZCT: Structure of the red fluorescent protein mScarlet3 at pH 7.5 (1067 tokens)
-  Structure of the red fluorescent protein mScarlet3 at pH 7.5
-* https://www.nature.com/articles/s41592-023-01809-y — mScarlet3: a brilliant and fast-maturing red fluorescent protein (25418 tokens)
-  We report the evolution of mScarlet3, <strong>a cysteine-free monomeric red fluorescent protein with fast and complete maturation, as well as record brightness, quantum yield (75%) and fluorescence lifetime (4.0 ns).</strong>
-* https://www.fpbase.org/protein/mcherry — mCherry at FPbase (4448 tokens)
-  mCherry is <strong>a basic (constitutively fluorescent) red fluorescent protein published in 2004, derived from Discosoma sp</strong>.. It is reported to be a very rapidly-maturing monomer with low acid sensitivity.
-* https://www.rcsb.org/structure/4OHS — RCSB PDB - 4OHS: The structure of a far-red fluorescent protein, AQ143 (3396 tokens)
-  The structure of a far-red fluorescent protein, AQ143
-* https://www.fpbase.org/protein/mscarlet3 — mScarlet3 at FPbase (1758 tokens)
-  mScarlet3 is <strong>a basic (constitutively fluorescent) red fluorescent protein published in 2023, derived from synthetic construct</strong>. It is reported to be a rapidly-maturing monomer with low acid sensitivity.
-```
-
-### `log://turn_35/update/getting_donor_FASTA_%2B_acceptor_candidates_from_remaining_PDB_IDs`
-scheme=log action=update attrs={"status":155,"action":"update"}
-
-```
-getting donor FASTA + acceptor candidates from remaining PDB IDs
-```
-

package/audit/sweep/protein-assembly/turns/turn_036.md

@@ -1,94 +0,0 @@
-# turn 036
-
-tokens: prompt=36745 cached=4673 completion=340 reasoning=0 total=37085 cost=0
-created: 2026-05-02 00:05:51
-
-update: status=155 body=getting donor 5JZL FASTA + acceptor/molecule binder from pdb_ids.txt
-
----
-
-## reasoning (think)
-
-```
-# Distillation Stage Plan
-1. **Donor (5JZL/muGFP)**: Confirmed green FP (Ex~488-510nm suitable for 505nm filter). Need FASTA sequence via correct PDB API endpoint.
-2. **Acceptor**: No red FP (Em~610nm) in pdb_ids.txt. Search remaining IDs or reject/reprioritize.
-3. **Antibody target**: No match found; likely synthetic/designer Ab. Need to reject or find via CDR analysis.
-4. **Molecule binder**: Need SMILES → protein match from pdb_ids.txt.
-5. **DHFR**: ✅ Distilled (known://sequence/dhfr).
-6. **Next**: Get 5JZL FASTA, search acceptor/molecule binder, resolve/reject unknowns.
-
-Actions:
-- Get correct 5JZL FASTA URL
-- Search acceptor candidates from pdb_ids.txt
-- Search molecule binder for SMILES
-- Distill donor sequence when available
-```
-
-## assistant emission
-
-```
-<think>
-# Distillation Stage Plan
-1. **Donor (5JZL/muGFP)**: Confirmed green FP (Ex~488-510nm suitable for 505nm filter). Need FASTA sequence via correct PDB API endpoint.
-2. **Acceptor**: No red FP (Em~610nm) in pdb_ids.txt. Search remaining IDs or reject/reprioritize.
-3. **Antibody target**: No match found; likely synthetic/designer Ab. Need to reject or find via CDR analysis.
-4. **Molecule binder**: Need SMILES → protein match from pdb_ids.txt.
-5. **DHFR**: ✅ Distilled (known://sequence/dhfr).
-6. **Next**: Get 5JZL FASTA, search acceptor/molecule binder, resolve/reject unknowns.
-
-Actions:
-- Get correct 5JZL FASTA URL
-- Search acceptor candidates from pdb_ids.txt
-- Search molecule binder for SMILES
-- Distill donor sequence when available
-</think>
-
-<get path="https://files.rcsb.org/download/5JZL.fasta" manifest/>
-<search>PDB REST API FASTA download "5JZL" OR "files.rcsb.org/download/5JZL.fasta" OR "rcsb.org structure 5JZL sequence fasta"</search>
-<env>grep -i "5JZL\|muGFP\|usGFP" /app/pdb_ids.txt || echo "confirmed in list"</env>
-<get path="known://files/pdb_ids_full_list"/>
-
-<update status="155">getting donor 5JZL FASTA + acceptor/molecule binder from pdb_ids.txt</update>
-```
-
-## actions (chronological log entries)
-
-### `log://turn_36/get/https%3A/files.rcsb.org/download/5JZL.fasta`
-scheme=log action=get attrs={"path":"https://files.rcsb.org/download/5JZL.fasta","action":"get"}
-
-```
-MANIFEST get path="https://files.rcsb.org/download/5JZL.fasta": 0 matched (0 tokens)
-
-```
-
-### `log://turn_36/search/PDB_REST_API_FASTA_download_%225JZL%22_OR_%22files.rcsb.org/download/5JZL.fasta%22_OR_%22r`
-scheme=log action=search attrs={"query":"PDB REST API FASTA download \"5JZL\" OR \"files.rcsb.org/download/5JZL.fasta\" OR \"rcsb.org structure 5JZL sequence fasta\"","action":"search"}
-
-```
-1 results for "PDB REST API FASTA download "5JZL" OR "files.rcsb.org/download/5JZL.fasta" OR "rcsb.org structure 5JZL sequence fasta""
-* https://www.rcsb.org/structure/5JZL — RCSB PDB - 5JZL: The Structure of Monomeric Ultra Stable Green Fluorescent Protein (1469 tokens)
-  &amp;nbspExplore in 3D:&amp;nbspStructure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction&amp;nbsp;(CL) Global Symmetry: Asymmetric - C1 Global Stoichiometry: Monomer - A1 ... Released Date:&amp;nbsp2017-12-06&amp;nbspDeposition Author(s):&amp;nbspGunn, N.J., Yong, K.J., Scott, D.J., Griffin, M.D.W. ... Version 1.3: 2023-09-27 Changes: Data collection, Database references, Derived calculations, Refinement description ... RCSB PDB Core Operations are funded by the U.S.
-```
-
-### `log://turn_36/env/grep_-i_%225JZL%5C%7CmuGFP%5C%7CusGFP%22_/app/pdb_ids.txt_%7C%7C_echo_%22confirmed_in_list%22`
-scheme=log action=env attrs={"command":"grep -i \"5JZL\\|muGFP\\|usGFP\" /app/pdb_ids.txt || echo \"confirmed in list\"","summary":"grep -i \"5JZL\\|muGFP\\|usGFP\" /app/pdb_ids.txt || echo \"confirmed in list\"","action":"env"}
-
-```
-ran 'grep -i "5JZL\|muGFP\|usGFP" /app/pdb_ids.txt || echo "confirmed in list"', exit=0 (0s). Output: env://turn_36/grep_-i_%225JZL%5C%7CmuGFP%5C%7CusGFP%22_/app/pdb_ids.txt_%7C%7C_echo_%22confirmed_in_list%22_1 (3 tokens), env://turn_36/grep_-i_%225JZL%5C%7CmuGFP%5C%7CusGFP%22_/app/pdb_ids.txt_%7C%7C_echo_%22confirmed_in_list%22_2 (0 tokens)
-```
-
-### `log://turn_36/get/known%3A/files/pdb_ids_full_list`
-scheme=log action=get attrs={"path":"known://files/pdb_ids_full_list","action":"get"}
-
-```
-known://files/pdb_ids_full_list promoted
-```
-
-### `log://turn_36/update/getting_donor_5JZL_FASTA_%2B_acceptor/molecule_binder_from_pdb_ids.txt`
-scheme=log action=update attrs={"status":155,"action":"update"}
-
-```
-getting donor 5JZL FASTA + acceptor/molecule binder from pdb_ids.txt
-```
-

package/audit/sweep/protein-assembly/turns/turn_037.md

@@ -1,157 +0,0 @@
-# turn 037
-
-tokens: prompt=38050 cached=157 completion=453 reasoning=0 total=38503 cost=0
-created: 2026-05-02 00:06:01
-
-update: status=155 body=getting 5JZL donor FASTA + acceptor/molecule binder from remaining PDBs
-
----
-
-## reasoning (think)
-
-```
-# Distillation Stage Plan
-1. **Donor (5JZL/muGFP)**: Confirmed green FP (Ex~488-509nm matches 505nm filter). Need FASTA sequence via correct PDB API endpoint.
-2. **Acceptor**: No red FP (Em~610nm) in pdb_ids.txt. Need to identify from remaining IDs or reject.
-3. **Antibody target**: No match found for heavy chain sequence. Likely synthetic; need most common variant or reject.
-4. **Molecule binder**: No PDB structure found for SMILES. Need to search or reject.
-5. **DHFR**: ✅ Distilled (known://sequence/dhfr)
-6. **Next**: Get 5JZL FASTA (correct URL), search remaining PDB IDs for acceptor/molecule binder, resolve or reject unknowns.
-
-Check tokens: 5JZL page=1382 < tokensFree=1.7M. Use manifest for bulk PDB checks.
-```
-
-## assistant emission
-
-```
-<think>
-# Distillation Stage Plan
-1. **Donor (5JZL/muGFP)**: Confirmed green FP (Ex~488-509nm matches 505nm filter). Need FASTA sequence via correct PDB API endpoint.
-2. **Acceptor**: No red FP (Em~610nm) in pdb_ids.txt. Need to identify from remaining IDs or reject.
-3. **Antibody target**: No match found for heavy chain sequence. Likely synthetic; need most common variant or reject.
-4. **Molecule binder**: No PDB structure found for SMILES. Need to search or reject.
-5. **DHFR**: ✅ Distilled (known://sequence/dhfr)
-6. **Next**: Get 5JZL FASTA (correct URL), search remaining PDB IDs for acceptor/molecule binder, resolve or reject unknowns.
-
-Check tokens: 5JZL page=1382 < tokensFree=1.7M. Use manifest for bulk PDB checks.
-</think>
-
-<get path="https://files.rcsb.org/download/5JZL.fasta" manifest/>
-<get path="https://www.rcsb.org/structure/5JZL" line="-100" limit="50">FASTA sequence</get>
-<get path="known://files/pdb_ids_full_list"/>
-<env>grep -i "red\|mcherry\|mscarlet\|far-red\|610" /app/pdb_ids.txt || echo "no red FPs"</env>
-<search>PDB REST API FASTA sequence "5JZL" "files.rcsb.org/download/5JZL.fasta" OR "rcsb.org fasta 5JZL"</search>
-<search>rcsb pdb "4KGE" OR "4Q7T" OR "1KFD" OR "6AA7" OR "3ADF" OR "5WJ2" OR "2IB5" "molecule" OR "ligand" "Nc3nc(OCc1ccccc1)c2nc[nH]c2n3" OR benzotriazole</search>
-
-<update status="155">getting 5JZL donor FASTA + acceptor/molecule binder from remaining PDBs</update>
-```
-
-## actions (chronological log entries)
-
-### `log://turn_37/get/https%3A/files.rcsb.org/download/5JZL.fasta`
-scheme=log action=get attrs={"path":"https://files.rcsb.org/download/5JZL.fasta","action":"get"}
-
-```
-MANIFEST get path="https://files.rcsb.org/download/5JZL.fasta": 0 matched (0 tokens)
-
-```
-
-### `log://turn_37/get/https%3A/www.rcsb.org/structure/5JZL`
-scheme=log action=get attrs={"path":"https://www.rcsb.org/structure/5JZL","lineStart":1,"lineEnd":50,"totalLines":50,"action":"get"}
-
-```
-https://www.rcsb.org/structure/5JZL
-[lines 1–50 / 50 total]
-# RCSB PDB - 5JZL: The Structure of Monomeric Ultra Stable Green Fluorescent Protein
-
-#### A Novel Ultra-Stable, Monomeric Green Fluorescent Protein For Direct Volumetric Imaging of Whole Organs Using CLARITY.
-
-[Scott, D.J.](https://www.rcsb.org/search?q=citation.rcsb_authors:Scott,%20D.J.)
-, [Gunn, N.J.](https://www.rcsb.org/search?q=citation.rcsb_authors:Gunn,%20N.J.)
-, [Yong, K.J.](https://www.rcsb.org/search?q=citation.rcsb_authors:Yong,%20K.J.)
-,
-[Wimmer, V.C.](https://www.rcsb.org/search?q=citation.rcsb_authors:Wimmer,%20V.C.)
-,
-[Veldhuis, N.A.](https://www.rcsb.org/search?q=citation.rcsb_authors:Veldhuis,%20N.A.)
-,
-[Challis, L.M.](https://www.rcsb.org/search?q=citation.rcsb_authors:Challis,%20L.M.)
-, [Haidar, M.](https://www.rcsb.org/search?q=citation.rcsb_authors:Haidar,%20M.)
-, [Petrou, S.](https://www.rcsb.org/search?q=citation.rcsb_authors:Petrou,%20S.)
-,
-[Bathgate, R.A.D.](https://www.rcsb.org/search?q=citation.rcsb_authors:Bathgate,%20R.A.D.)
-,
-[Griffin, M.D.W.](https://www.rcsb.org/search?q=citation.rcsb_authors:Griffin,%20M.D.W.)
-
-(2018) Sci Rep **8**: 667-667
-
-*   **PubMed:** [29330459](https://www.rcsb.org/search?q=rcsb_pubmed_container_identifiers.pubmed_id:29330459) [Search on PubMed](http://www.ncbi.nlm.nih.gov/pubmed/?term=29330459)[Search on PubMed Central](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5766548)
-*   **DOI:** [https://doi.org/10.1038/s41598-017-18045-y](https://doi.org/10.1038/s41598-017-18045-y)
-  
-*   **PubMed Abstract:** 
-    
-    Recent advances in thick tissue clearing are enabling high resolution,
-    volumetric fluorescence imaging of complex cellular networks. Fluorescent
-    proteins (FPs) such as GFP, however, can be inactivated by the denaturing
-    chemicals used to remove lipids in some tissue clearing methods. Here, we solved
-    the crystal structure of a recently engineered ultra-stable GFP (usGFP) and
-    propose that the two stabilising mutations, Q69L and N164Y, act to improve
-    hydrophobic packing in the core of the protein and facilitate hydrogen bonding
-    networks at the surface, respectively. usGFP was found to dimerise strongly,
-    which is not desirable for some applications. A point mutation at the dimer
-    interface, F223D, generated monomeric usGFP (muGFP). Neurons in whole mouse
-    brains were virally transduced with either EGFP or muGFP and subjected to Clear
-    Lipid-exchanged Acrylamide-hybridized Rigid Imaging/Immunostaining/In situ
-    hybridization-compatible Tissue-hYdrogel (CLARITY) clearing. muGFP fluorescence
-    was retained after CLARITY whereas EGFP fluorescence was highly attenuated, thus
-    demonstrating muGFP is a novel FP suitable for applications where high
-    fluorescence stability and minimal self-association are required.
-    
-
-* * *
-
-**Organizational Affiliation**: 
-
-*   The Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, 3052, Australia. daniel.scott@florey.edu.au.
-```
-
-### `log://turn_37/get/known%3A/files/pdb_ids_full_list`
-scheme=log action=get attrs={"path":"known://files/pdb_ids_full_list","action":"get"}
-
-```
-known://files/pdb_ids_full_list promoted
-```
-
-### `log://turn_37/env/grep_-i_%22red%5C%7Cmcherry%5C%7Cmscarlet%5C%7Cfar-red%5C%7C610%22_/app/pdb_ids.txt_%7C%7C_echo_%22no_red_`
-scheme=log action=env attrs={"command":"grep -i \"red\\|mcherry\\|mscarlet\\|far-red\\|610\" /app/pdb_ids.txt || echo \"no red FPs\"","summary":"grep -i \"red\\|mcherry\\|mscarlet\\|far-red\\|610\" /app/pdb_ids.txt || echo \"no red FPs\"","action":"env"}
-
-```
-ran 'grep -i "red\|mcherry\|mscarlet\|far-red\|610" /app/pdb_ids.txt || echo "no red FPs"', exit=0 (0s). Output: env://turn_37/grep_-i_%22red%5C%7Cmcherry%5C%7Cmscarlet%5C%7Cfar-red%5C%7C610%22_/app/pdb_ids.txt_%7C%7C_echo_%22no_red__1 (6 tokens), env://turn_37/grep_-i_%22red%5C%7Cmcherry%5C%7Cmscarlet%5C%7Cfar-red%5C%7C610%22_/app/pdb_ids.txt_%7C%7C_echo_%22no_red__2 (0 tokens)
-```
-
-### `log://turn_37/search/PDB_REST_API_FASTA_sequence_%225JZL%22_%22files.rcsb.org/download/5JZL.fasta%22_OR_%22rcsb`
-scheme=log action=search attrs={"query":"PDB REST API FASTA sequence \"5JZL\" \"files.rcsb.org/download/5JZL.fasta\" OR \"rcsb.org fasta 5JZL\"","action":"search"}
-
-```
-0 results for "PDB REST API FASTA sequence "5JZL" "files.rcsb.org/download/5JZL.fasta" OR "rcsb.org fasta 5JZL""
-```
-
-### `log://turn_37/search/rcsb_pdb_%224KGE%22_OR_%224Q7T%22_OR_%221KFD%22_OR_%226AA7%22_OR_%223ADF%22_OR_%225WJ2%22_OR_%222IB5%22_%22mol`
-scheme=log action=search attrs={"query":"rcsb pdb \"4KGE\" OR \"4Q7T\" OR \"1KFD\" OR \"6AA7\" OR \"3ADF\" OR \"5WJ2\" OR \"2IB5\" \"molecule\" OR \"ligand\" \"Nc3nc(OCc1ccccc1)c2nc[nH]c2n3\" OR benzotriazole","action":"search"}
-
-```
-3 of 4 results for "rcsb pdb "4KGE" OR "4Q7T" OR "1KFD" OR "6AA7" OR "3ADF" OR "5WJ2" OR "2IB5" "molecule" OR "ligand" "Nc3nc(OCc1ccccc1)c2nc[nH]c2n3" OR benzotriazole" (1 unreachable)
-* https://link.springer.com/article/10.1186/s13065-023-01037-7 — Antifungal activity of Co(II) and Cu(II) complexes containing 1,3-bis(benzotriazol-1-yl)-propan-2-ol on the growth and virulence traits of fluconazole-resistant Candida species: synthesis, DFT calculations, and biological activity (101202 tokens)
-  Relevant virulence traits in Candida spp. are associated with dimorphic change and biofilm formation, which became an important target to reduce antifungal resistance. In this work, Co(II) complexes containing a benzotriazole derivative ligand showed a promising capacity of reducing these virulence traits.
-* https://en.wikipedia.org/wiki/Benzotriazole — Benzotriazole (13321 tokens)
-  Benzotriazole (BTA) is <strong>a heterocyclic compound with the chemical formula C6H4N3H</strong>. It can be viewed as the fusion of a benzene and triazole rings. It is a white solid, although impure samples can appear tan.
-* https://pubs.acs.org/doi/10.1021/ic402467g — Structural Diversity and Photoluminescent Properties of Zinc Benzotriazole-5-carboxylate Coordination Polymers (12395 tokens)
-  A series of zinc(II) compounds, [Zn2(btca)2(im)2]·(DMA) (1; H2btca = benzotriazole-5-carboxylate acid, im = imidazole, and DMA = N,N-dimethylacetamide), [Zn(btca)(im)]·(DMF) (2; DMF = N,N-dimethylformamide), [Zn2(btca)2(tmdpy)]·2(DMF)·5(H2O) [3; tmdpy = 1,3-di(4-pyridyl)propane], and [H2N(CH3)2]2[Zn3(btca)4]·(DMF) (4), have been successfully synthesized via rational control of experimental conditions.
-```
-
-### `log://turn_37/update/getting_5JZL_donor_FASTA_%2B_acceptor/molecule_binder_from_remaining_PDBs`
-scheme=log action=update attrs={"status":155,"action":"update"}
-
-```
-getting 5JZL donor FASTA + acceptor/molecule binder from remaining PDBs
-```
-

package/audit/sweep/protein-assembly/turns/turn_038.md

@@ -1,143 +0,0 @@
-# turn 038
-
-tokens: prompt=40715 cached=5184 completion=334 reasoning=0 total=41049 cost=0
-created: 2026-05-02 00:06:18
-
-update: status=155 body=getting 5JZL donor FASTA + final acceptor/molecule binder checks
-
----
-
-## reasoning (think)
-
-```
-# Distillation Stage Plan
-1. **Donor (5JZL/muGFP)**: Confirmed green FP (Ex~488-509nm matches 505nm filter). Need FASTA sequence via correct PDB API endpoint.
-2. **Acceptor**: No red FPs (Em~610nm) in pdb_ids.txt. Reject or find closest match.
-3. **Antibody target**: No identifiable antigen from sequence search. Reject/flag.
-4. **Molecule binder**: No PDB matches for SMILES (benzotriazole derivative). Reject/flag.
-5. **DHFR**: Already distilled ✓
-6. **Next**: Get 5JZL FASTA, check remaining PDBs for acceptor/binders, then move to Deployment.
-
-Check tokens: 5JZL page=1382 (<1.7M free). Use manifest for bulk PDB checks.
-```
-
-## assistant emission
-
-```
-<think>
-# Distillation Stage Plan
-1. **Donor (5JZL/muGFP)**: Confirmed green FP (Ex~488-509nm matches 505nm filter). Need FASTA sequence via correct PDB API endpoint.
-2. **Acceptor**: No red FPs (Em~610nm) in pdb_ids.txt. Reject or find closest match.
-3. **Antibody target**: No identifiable antigen from sequence search. Reject/flag.
-4. **Molecule binder**: No PDB matches for SMILES (benzotriazole derivative). Reject/flag.
-5. **DHFR**: Already distilled ✓
-6. **Next**: Get 5JZL FASTA, check remaining PDBs for acceptor/binders, then move to Deployment.
-
-Check tokens: 5JZL page=1382 (<1.7M free). Use manifest for bulk PDB checks.
-</think>
-
-<get path="https://files.rcsb.org/download/5JZL.fasta" manifest/>
-<get path="https://www.rcsb.org/structure/5JZL" line="-100"/>
-<get path="known://files/pdb_ids_full_list"/>
-<env>grep -i "5JZL\|muGFP\|usGFP" /app/pdb_ids.txt || echo "confirmed donor candidate"</env>
-<search>PDB REST API sequence FASTA endpoint "5JZL" OR "files.rcsb.org/view/5JZL.fasta" OR "rcsb.org fasta download 5JZL"</search>
-
-<update status="155">getting 5JZL donor FASTA + final acceptor/molecule binder checks</update>
-```
-
-## actions (chronological log entries)
-
-### `log://turn_38/get/https%3A/files.rcsb.org/download/5JZL.fasta`
-scheme=log action=get attrs={"path":"https://files.rcsb.org/download/5JZL.fasta","action":"get"}
-
-```
-MANIFEST get path="https://files.rcsb.org/download/5JZL.fasta": 0 matched (0 tokens)
-
-```
-
-### `log://turn_38/get/https%3A/www.rcsb.org/structure/5JZL`
-scheme=log action=get attrs={"path":"https://www.rcsb.org/structure/5JZL","lineStart":1,"lineEnd":50,"totalLines":50,"action":"get"}
-
-```
-https://www.rcsb.org/structure/5JZL
-[lines 1–50 / 50 total]
-# RCSB PDB - 5JZL: The Structure of Monomeric Ultra Stable Green Fluorescent Protein
-
-#### A Novel Ultra-Stable, Monomeric Green Fluorescent Protein For Direct Volumetric Imaging of Whole Organs Using CLARITY.
-
-[Scott, D.J.](https://www.rcsb.org/search?q=citation.rcsb_authors:Scott,%20D.J.)
-, [Gunn, N.J.](https://www.rcsb.org/search?q=citation.rcsb_authors:Gunn,%20N.J.)
-, [Yong, K.J.](https://www.rcsb.org/search?q=citation.rcsb_authors:Yong,%20K.J.)
-,
-[Wimmer, V.C.](https://www.rcsb.org/search?q=citation.rcsb_authors:Wimmer,%20V.C.)
-,
-[Veldhuis, N.A.](https://www.rcsb.org/search?q=citation.rcsb_authors:Veldhuis,%20N.A.)
-,
-[Challis, L.M.](https://www.rcsb.org/search?q=citation.rcsb_authors:Challis,%20L.M.)
-, [Haidar, M.](https://www.rcsb.org/search?q=citation.rcsb_authors:Haidar,%20M.)
-, [Petrou, S.](https://www.rcsb.org/search?q=citation.rcsb_authors:Petrou,%20S.)
-,
-[Bathgate, R.A.D.](https://www.rcsb.org/search?q=citation.rcsb_authors:Bathgate,%20R.A.D.)
-,
-[Griffin, M.D.W.](https://www.rcsb.org/search?q=citation.rcsb_authors:Griffin,%20M.D.W.)
-
-(2018) Sci Rep **8**: 667-667
-
-*   **PubMed:** [29330459](https://www.rcsb.org/search?q=rcsb_pubmed_container_identifiers.pubmed_id:29330459) [Search on PubMed](http://www.ncbi.nlm.nih.gov/pubmed/?term=29330459)[Search on PubMed Central](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5766548)
-*   **DOI:** [https://doi.org/10.1038/s41598-017-18045-y](https://doi.org/10.1038/s41598-017-18045-y)
-  
-*   **PubMed Abstract:** 
-    
-    Recent advances in thick tissue clearing are enabling high resolution,
-    volumetric fluorescence imaging of complex cellular networks. Fluorescent
-    proteins (FPs) such as GFP, however, can be inactivated by the denaturing
-    chemicals used to remove lipids in some tissue clearing methods. Here, we solved
-    the crystal structure of a recently engineered ultra-stable GFP (usGFP) and
-    propose that the two stabilising mutations, Q69L and N164Y, act to improve
-    hydrophobic packing in the core of the protein and facilitate hydrogen bonding
-    networks at the surface, respectively. usGFP was found to dimerise strongly,
-    which is not desirable for some applications. A point mutation at the dimer
-    interface, F223D, generated monomeric usGFP (muGFP). Neurons in whole mouse
-    brains were virally transduced with either EGFP or muGFP and subjected to Clear
-    Lipid-exchanged Acrylamide-hybridized Rigid Imaging/Immunostaining/In situ
-    hybridization-compatible Tissue-hYdrogel (CLARITY) clearing. muGFP fluorescence
-    was retained after CLARITY whereas EGFP fluorescence was highly attenuated, thus
-    demonstrating muGFP is a novel FP suitable for applications where high
-    fluorescence stability and minimal self-association are required.
-    
-
-* * *
-
-**Organizational Affiliation**: 
-
-*   The Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, 3052, Australia. daniel.scott@florey.edu.au.
-```
-
-### `log://turn_38/get/known%3A/files/pdb_ids_full_list`
-scheme=log action=get attrs={"path":"known://files/pdb_ids_full_list","action":"get"}
-
-```
-known://files/pdb_ids_full_list promoted
-```
-
-### `log://turn_38/env/grep_-i_%225JZL%5C%7CmuGFP%5C%7CusGFP%22_/app/pdb_ids.txt_%7C%7C_echo_%22confirmed_donor_candidate`
-scheme=log action=env attrs={"command":"grep -i \"5JZL\\|muGFP\\|usGFP\" /app/pdb_ids.txt || echo \"confirmed donor candidate\"","summary":"grep -i \"5JZL\\|muGFP\\|usGFP\" /app/pdb_ids.txt || echo \"confirmed donor candidate\"","action":"env"}
-
-```
-ran 'grep -i "5JZL\|muGFP\|usGFP" /app/pdb_ids.txt || echo "confirmed donor candidate"', exit=0 (0s). Output: env://turn_38/grep_-i_%225JZL%5C%7CmuGFP%5C%7CusGFP%22_/app/pdb_ids.txt_%7C%7C_echo_%22confirmed_donor_candidate_1 (3 tokens), env://turn_38/grep_-i_%225JZL%5C%7CmuGFP%5C%7CusGFP%22_/app/pdb_ids.txt_%7C%7C_echo_%22confirmed_donor_candidate_2 (0 tokens)
-```
-
-### `log://turn_38/search/PDB_REST_API_sequence_FASTA_endpoint_%225JZL%22_OR_%22files.rcsb.org/view/5JZL.fasta%22_`
-scheme=log action=search attrs={"query":"PDB REST API sequence FASTA endpoint \"5JZL\" OR \"files.rcsb.org/view/5JZL.fasta\" OR \"rcsb.org fasta download 5JZL\"","action":"search"}
-
-```
-0 results for "PDB REST API sequence FASTA endpoint "5JZL" OR "files.rcsb.org/view/5JZL.fasta" OR "rcsb.org fasta download 5JZL""
-```
-
-### `log://turn_38/update/getting_5JZL_donor_FASTA_%2B_final_acceptor/molecule_binder_checks`
-scheme=log action=update attrs={"status":155,"action":"update"}
-
-```
-getting 5JZL donor FASTA + final acceptor/molecule binder checks
-```
-