@possumtech/rummy 2.0.1 → 2.2.0

package/audit/sweep/protein-assembly/turns/turn_043.md

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+# turn 043
+
+tokens: prompt=48374 cached=7480 completion=344 reasoning=0 total=48718 cost=0
+created: 2026-05-02 00:07:29
+
+update: status=155 body=getting donor/acceptor FASTA sequences + scanning binders
+
+---
+
+## reasoning (think)
+
+```
+Distillation stage: Prioritize unresolved unknowns critical for fusion protein construction.
+
+Key blockers:
+1. unknown://api/pdb_sequences - Need donor (5JZL/muGFP, Ex~505nm), acceptor (Em~610nm), molecule binder from pdb_ids.txt
+2. unknown://binder/antibody_target - Antigen sequence antibody binds
+3. unknown://api/fpbase_donor/sequence - Confirm 5JZL sequence
+4. unknown://api/fpbase_acceptor/sequence - Red FP from list
+
+Actions:
+- Get 5JZL page for sequence (RCSB often has FASTA links)
+- Search RCSB FASTA API pattern for pdb_ids.txt entries
+- No direct FASTA found yet; check structure pages
+- Scan remaining PDB IDs for red FP (610nm) and benzotriazole binder
+- Antibody target still unresolved
+
+Check token budget before bulk gets.
+```
+
+## assistant emission
+
+```
+<think>
+Distillation stage: Prioritize unresolved unknowns critical for fusion protein construction.
+
+Key blockers:
+1. unknown://api/pdb_sequences - Need donor (5JZL/muGFP, Ex~505nm), acceptor (Em~610nm), molecule binder from pdb_ids.txt
+2. unknown://binder/antibody_target - Antigen sequence antibody binds
+3. unknown://api/fpbase_donor/sequence - Confirm 5JZL sequence
+4. unknown://api/fpbase_acceptor/sequence - Red FP from list
+
+Actions:
+- Get 5JZL page for sequence (RCSB often has FASTA links)
+- Search RCSB FASTA API pattern for pdb_ids.txt entries
+- No direct FASTA found yet; check structure pages
+- Scan remaining PDB IDs for red FP (610nm) and benzotriazole binder
+- Antibody target still unresolved
+
+Check token budget before bulk gets.
+</think>
+
+<get path="https://www.rcsb.org/structure/5JZL" line="-100"/>
+<get path="known://files/pdb_ids_full_list" visibility="visible"/>
+<env>grep -i "5WJ2\|3ADF\|6AA7\|1KFD\|4Q7T\|4KGE\|2IB5" /app/pdb_ids.txt || echo "no acceptor matches"</env>
+<search results="10">PDB REST API "get_fasta" OR "sequence/{id}.fasta" "5JZL" OR "5WJ2" site:rcsb.org OR data.rcsb.org</search>
+
+<update status="155">getting donor/acceptor FASTA sequences + scanning binders</update>
+```
+
+## actions (chronological log entries)
+
+### `log://turn_43/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_43/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_43/env/grep_-i_%225WJ2%5C%7C3ADF%5C%7C6AA7%5C%7C1KFD%5C%7C4Q7T%5C%7C4KGE%5C%7C2IB5%22_/app/pdb_ids.txt_%7C%7C_echo_%22no_`
+scheme=log action=env attrs={"command":"grep -i \"5WJ2\\|3ADF\\|6AA7\\|1KFD\\|4Q7T\\|4KGE\\|2IB5\" /app/pdb_ids.txt || echo \"no acceptor matches\"","summary":"grep -i \"5WJ2\\|3ADF\\|6AA7\\|1KFD\\|4Q7T\\|4KGE\\|2IB5\" /app/pdb_ids.txt || echo \"no acceptor matches\"","action":"env"}
+
+```
+ran 'grep -i "5WJ2\|3ADF\|6AA7\|1KFD\|4Q7T\|4KGE\|2IB5" /app/pdb_ids.txt || echo "no acceptor matches"', exit=0 (0s). Output: env://turn_43/grep_-i_%225WJ2%5C%7C3ADF%5C%7C6AA7%5C%7C1KFD%5C%7C4Q7T%5C%7C4KGE%5C%7C2IB5%22_/app/pdb_ids.txt_%7C%7C_echo_%22no__1 (18 tokens), env://turn_43/grep_-i_%225WJ2%5C%7C3ADF%5C%7C6AA7%5C%7C1KFD%5C%7C4Q7T%5C%7C4KGE%5C%7C2IB5%22_/app/pdb_ids.txt_%7C%7C_echo_%22no__2 (0 tokens)
+```
+
+### `log://turn_43/search/PDB_REST_API_%22get_fasta%22_OR_%22sequence/%7Bid%7D.fasta%22_%225JZL%22_OR_%225WJ2%22_site%3Arcsb.org`
+scheme=log action=search attrs={"query":"PDB REST API \"get_fasta\" OR \"sequence/{id}.fasta\" \"5JZL\" OR \"5WJ2\" site:rcsb.org OR data.rcsb.org","action":"search"}
+
+```
+5 of 10 results for "PDB REST API "get_fasta" OR "sequence/{id}.fasta" "5JZL" OR "5WJ2" site:rcsb.org OR data.rcsb.org" (5 unreachable)
+* https://data.rcsb.org — data-api – RCSB PDB Data API: Understanding and Using (18075 tokens)
+  RCSB PDB: Data API Documentation · The RCSB PDB offers two ways to access data through application programming interfaces (APIs):
+* https://search.rcsb.org — search-api – RCSB PDB Search API: Understanding and Using (69178 tokens)
+  RCSB PDB: Search API Documentation · Stay current with API announcements by subscribing to the RCSB PDB API mailing list:
+* https://www.rcsb.org/docs/programmatic-access/web-apis-overview — Web APIs Overview (4271 tokens)
+  As a member of the wwPDB, the RCSB PDB curates and annotates PDB data according to agreed upon standards. The RCSB PDB also provides a variety of tools and resources. Users can perform simple and advanced searches based on annotations relating to sequence, structure and function.
+* https://www.rcsb.org — RCSB PDB: Homepage (2023 tokens)
+  As a member of the wwPDB, the RCSB PDB curates and annotates PDB data according to agreed upon standards. The RCSB PDB also provides a variety of tools and resources. Users can perform simple and advanced searches based on annotations relating to sequence, structure and function.
+* https://education.molssi.org/python-scripting-biochemistry/chapters/rcsb_api.html — Retrieving Information from the PDB using the Web API — Python Data and Scripting for Biochemists and Molecular Biologists (10492 tokens)
+  interface = requests.get(&quot;https://data.rcsb.org/rest/v1/core/interface/4hhb/1/1&quot;)
+```
+
+### `log://turn_43/update/getting_donor/acceptor_FASTA_sequences_%2B_scanning_binders`
+scheme=log action=update attrs={"status":155,"action":"update"}
+
+```
+getting donor/acceptor FASTA sequences + scanning binders
+```
+

package/audit/sweep/protein-assembly/turns/turn_044.md

@@ -0,0 +1,168 @@
+# turn 044
+
+tokens: prompt=50781 cached=5692 completion=495 reasoning=0 total=51276 cost=0
+created: 2026-05-02 00:07:46
+
+update: status=155 body=discovering donor/acceptor FASTA + acceptor candidates + antibody target
+
+---
+
+## 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**: From pdb_ids.txt matches (2IB5,4KGE,4Q7T,1KFD,6AA7,3ADF,5WJ2), need red FP Em~610nm. Check RCSB pages.
+3. **Antibody target**: Heavy chain sequence QVQLQQSAA... needs antigen identification.
+4. **Molecule binder**: SMILES Nc3nc(OCc1ccccc1)c2nc[nH]c2n3 (benzotriazole derivative) - check PDBs for binding protein.
+5. **DHFR**: Already distilled ✓
+6. **Resolve unknowns**: Promote RCSB pages for remaining PDB IDs, search correct FASTA API.
+
+Key actions:
+- Get RCSB FASTA download info from https://www.rcsb.org/downloads/fasta (already partially promoted)
+- Bulk check acceptor candidates: get RCSB pages for 2IB5,4KGE,4Q7T,1KFD,6AA7,3ADF,5WJ2
+- Antibody target search refinement
+- Use manifest to check token costs before bulk promotion
+```
+
+## 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**: From pdb_ids.txt matches (2IB5,4KGE,4Q7T,1KFD,6AA7,3ADF,5WJ2), need red FP Em~610nm. Check RCSB pages.
+3. **Antibody target**: Heavy chain sequence QVQLQQSAA... needs antigen identification.
+4. **Molecule binder**: SMILES Nc3nc(OCc1ccccc1)c2nc[nH]c2n3 (benzotriazole derivative) - check PDBs for binding protein.
+5. **DHFR**: Already distilled ✓
+6. **Resolve unknowns**: Promote RCSB pages for remaining PDB IDs, search correct FASTA API.
+
+Key actions:
+- Get RCSB FASTA download info from https://www.rcsb.org/downloads/fasta (already partially promoted)
+- Bulk check acceptor candidates: get RCSB pages for 2IB5,4KGE,4Q7T,1KFD,6AA7,3ADF,5WJ2
+- Antibody target search refinement
+- Use manifest to check token costs before bulk promotion
+</think>
+
+<get path="https://www.rcsb.org/structure/2IB5" manifest/>
+<get path="https://www.rcsb.org/structure/4KGE" manifest/>
+<get path="https://www.rcsb.org/structure/4Q7T" manifest/>
+<get path="https://www.rcsb.org/structure/1KFD" manifest/>
+<get path="https://www.rcsb.org/structure/6AA7" manifest/>
+<get path="https://www.rcsb.org/structure/3ADF" manifest/>
+<get path="https://www.rcsb.org/structure/5WJ2" manifest/>
+
+<get path="https://www.rcsb.org/downloads/fasta" line="1" limit="20"/>
+
+<search>PDB REST API exact FASTA endpoint rcsb "5JZL" OR "sequence.fasta" OR "download/5JZL.fasta" data.rcsb.org</search>
+
+<update status="155">discovering donor/acceptor FASTA + acceptor candidates + antibody target</update>
+```
+
+## actions (chronological log entries)
+
+### `log://turn_44/get/https%3A/www.rcsb.org/structure/2IB5`
+scheme=log action=get attrs={"path":"https://www.rcsb.org/structure/2IB5","action":"get"}
+
+```
+MANIFEST get path="https://www.rcsb.org/structure/2IB5": 1 matched (1506 tokens)
+https://www.rcsb.org/structure/2IB5 (1506)
+```
+
+### `log://turn_44/get/https%3A/www.rcsb.org/structure/4KGE`
+scheme=log action=get attrs={"path":"https://www.rcsb.org/structure/4KGE","action":"get"}
+
+```
+MANIFEST get path="https://www.rcsb.org/structure/4KGE": 1 matched (580 tokens)
+https://www.rcsb.org/structure/4KGE (580)
+```
+
+### `log://turn_44/get/https%3A/www.rcsb.org/structure/4Q7T`
+scheme=log action=get attrs={"path":"https://www.rcsb.org/structure/4Q7T","action":"get"}
+
+```
+MANIFEST get path="https://www.rcsb.org/structure/4Q7T": 1 matched (1539 tokens)
+https://www.rcsb.org/structure/4Q7T (1539)
+```
+
+### `log://turn_44/get/https%3A/www.rcsb.org/structure/1KFD`
+scheme=log action=get attrs={"path":"https://www.rcsb.org/structure/1KFD","action":"get"}
+
+```
+MANIFEST get path="https://www.rcsb.org/structure/1KFD": 1 matched (716 tokens)
+https://www.rcsb.org/structure/1KFD (716)
+```
+
+### `log://turn_44/get/https%3A/www.rcsb.org/structure/6AA7`
+scheme=log action=get attrs={"path":"https://www.rcsb.org/structure/6AA7","action":"get"}
+
+```
+MANIFEST get path="https://www.rcsb.org/structure/6AA7": 1 matched (3469 tokens)
+https://www.rcsb.org/structure/6AA7 (3469)
+```
+
+### `log://turn_44/get/https%3A/www.rcsb.org/structure/3ADF`
+scheme=log action=get attrs={"path":"https://www.rcsb.org/structure/3ADF","action":"get"}
+
+```
+MANIFEST get path="https://www.rcsb.org/structure/3ADF": 1 matched (1469 tokens)
+https://www.rcsb.org/structure/3ADF (1469)
+```
+
+### `log://turn_44/get/https%3A/www.rcsb.org/structure/5WJ2`
+scheme=log action=get attrs={"path":"https://www.rcsb.org/structure/5WJ2","action":"get"}
+
+```
+MANIFEST get path="https://www.rcsb.org/structure/5WJ2": 1 matched (622 tokens)
+https://www.rcsb.org/structure/5WJ2 (622)
+```
+
+### `log://turn_44/get/https%3A/www.rcsb.org/downloads/fasta`
+scheme=log action=get attrs={"path":"https://www.rcsb.org/downloads/fasta","lineStart":1,"lineEnd":13,"totalLines":13,"action":"get"}
+
+```
+https://www.rcsb.org/downloads/fasta
+[lines 1–13 / 13 total]
+# RCSB PDB - Downloads - FASTA
+
+RCSB PDB Core Operations are funded by the
+[U.S. National Science Foundation](http://www.nsf.gov/) (DBI-2321666), the
+[US Department of Energy](http://science.energy.gov/) (DE-SC0019749), and the
+[National Cancer Institute](http://www.cancer.gov/) ,
+[National Institute of Allergy and Infectious Diseases](http://www.niaid.nih.gov/)
+, and
+[National Institute of General Medical Sciences](http://www.nigms.nih.gov/) of
+the [National Institutes of Health](http://www.nih.gov/) under grant
+R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific
+Computing Center ([NERSC](https://www.nersc.gov/)), a Department of Energy User
+Facility.
+```
+
+### `log://turn_44/search/PDB_REST_API_exact_FASTA_endpoint_rcsb_%225JZL%22_OR_%22sequence.fasta%22_OR_%22download/5`
+scheme=log action=search attrs={"query":"PDB REST API exact FASTA endpoint rcsb \"5JZL\" OR \"sequence.fasta\" OR \"download/5JZL.fasta\" data.rcsb.org","action":"search"}
+
+```
+7 of 12 results for "PDB REST API exact FASTA endpoint rcsb "5JZL" OR "sequence.fasta" OR "download/5JZL.fasta" data.rcsb.org" (5 unreachable)
+* https://data.rcsb.org — data-api – RCSB PDB Data API: Understanding and Using (18075 tokens)
+  GraphQL endpoints require to explicitly specify ID(s) for the requested data objects, there are no endpoints to request all data objects. The Repository Holdings Service REST API current entries endpoint provides a full list of current PDB IDs.
+* https://www.rcsb.org/downloads/fasta — RCSB PDB - Downloads - FASTA (344 tokens)
+  Download a file containing sequences in FASTA format for all entries in the PDB archive
+* https://www.rcsb.org/docs/programmatic-access/file-download-services — File Download Services (10600 tokens)
+  Please note these are to be discontinued when the PDB transitions to extended PDB IDs. Small molecule files, including the ligands/chemical components maintained in the Chemical Component Dictionary and the Biologically Interesting Molecule Reference Dictionary (BIRD) are available in multiple formats. This table includes structure factors, NMR constraints, chemical shifts, electron density maps and map coefficient files. Sequence data in FASTA format (full deposited sequence as in SEQRES records).
+* https://education.molssi.org/python-scripting-biochemistry/chapters/rcsb_api.html — Retrieving Information from the PDB using the Web API — Python Data and Scripting for Biochemists and Molecular Biologists (10555 tokens)
+  interface = requests.get(&quot;https://data.rcsb.org/rest/v1/core/interface/4hhb/1/1&quot;)
+* https://search.rcsb.org — search-api – RCSB PDB Search API: Understanding and Using (69208 tokens)
+  <strong>The simplest query requires specifying only return_type parameter and query context</strong>. With unspecified parameters property in the query object, a query matches all documents, returning PDB IDs if the return_type property is set to &quot;entry&quot;.
+* https://www.rcsb.org/downloads — RCSB PDB Batch Download Service (359 tokens)
+  As a member of the wwPDB, the RCSB PDB curates and annotates PDB data according to agreed upon standards. The RCSB PDB also provides a variety of tools and resources. Users can perform simple and advanced searches based on annotations relating to sequence, structure and function.
+* https://www.rcsb.org/docs/programmatic-access/web-apis-overview — Web APIs Overview (4282 tokens)
+  As a member of the wwPDB, the RCSB PDB curates and annotates PDB data according to agreed upon standards. The RCSB PDB also provides a variety of tools and resources. Users can perform simple and advanced searches based on annotations relating to sequence, structure and function.
+```
+
+### `log://turn_44/update/discovering_donor/acceptor_FASTA_%2B_acceptor_candidates_%2B_antibody_target`
+scheme=log action=update attrs={"status":155,"action":"update"}
+
+```
+discovering donor/acceptor FASTA + acceptor candidates + antibody target
+```
+

package/audit/sweep/protein-assembly/turns/turn_045.md

@@ -0,0 +1,105 @@
+# turn 045
+
+tokens: prompt=53082 cached=6335 completion=435 reasoning=0 total=53517 cost=0
+created: 2026-05-02 00:08:17
+
+update: status=155 body=discovering exact PDB FASTA API + acceptor/molecule binder candidates
+
+---
+
+## reasoning (think)
+
+```
+# Distillation Stage Plan
+1. **Donor (5JZL - muGFP/usGFP, Ex~505nm)**: Promote RCSB page, search exact FASTA API endpoint (data.rcsb.org/rest/v1/core/sequence/5JZL/1)
+2. **Acceptor candidates**: Prioritize from promoted RCSB pages (2IB5 yellow chromoprotein mutant, 4KGE NIR, 6AA7 coral FP, 3ADF mAG green, 5WJ2 Clover green, 4Q7T PSmOrange) - find Em~610nm red/far-red
+3. **Molecule binder**: Check PDB pages for SMILES Nc3nc(OCc1ccccc1)c2nc[nH]c2n3 (benzotriazole derivative) ligand binding
+4. **Antibody target**: No direct hit; likely synthetic/demo - reject or use DHFR as placeholder
+5. **Distill sequences** into known:// once FASTA found, resolve unknowns
+
+Key: Need exact FASTA URLs/REST API for sequences matching pdb_ids.txt requirement.
+```
+
+## assistant emission
+
+```
+<think>
+# Distillation Stage Plan
+1. **Donor (5JZL - muGFP/usGFP, Ex~505nm)**: Promote RCSB page, search exact FASTA API endpoint (data.rcsb.org/rest/v1/core/sequence/5JZL/1)
+2. **Acceptor candidates**: Prioritize from promoted RCSB pages (2IB5 yellow chromoprotein mutant, 4KGE NIR, 6AA7 coral FP, 3ADF mAG green, 5WJ2 Clover green, 4Q7T PSmOrange) - find Em~610nm red/far-red
+3. **Molecule binder**: Check PDB pages for SMILES Nc3nc(OCc1ccccc1)c2nc[nH]c2n3 (benzotriazole derivative) ligand binding
+4. **Antibody target**: No direct hit; likely synthetic/demo - reject or use DHFR as placeholder
+5. **Distill sequences** into known:// once FASTA found, resolve unknowns
+
+Key: Need exact FASTA URLs/REST API for sequences matching pdb_ids.txt requirement.
+</think>
+
+<get path="https://data.rcsb.org/rest/v1/core/sequence/5JZL/1"/>
+<get path="https://www.rcsb.org/structure/5WJ2"/>
+<get path="https://data.rcsb.org/rest/v1/core/sequence/2IB5/1"/>
+<get path="https://data.rcsb.org/rest/v1/core/sequence/4KGE/1"/>
+<get path="https://data.rcsb.org/rest/v1/core/sequence/6AA7/1"/>
+<get path="https://data.rcsb.org/rest/v1/core/sequence/3ADF/1"/>
+<search results="5">PDB REST API "sequence/{id}/1" OR "data.rcsb.org/rest/v1/core/sequence" FASTA 5JZL 2IB5 4KGE 6AA7</search>
+
+<update status="155">discovering exact PDB FASTA API + acceptor/molecule binder candidates</update>
+```
+
+## actions (chronological log entries)
+
+### `log://turn_45/get/https%3A/data.rcsb.org/rest/v1/core/sequence/5JZL/1`
+scheme=log action=get attrs={"path":"https://data.rcsb.org/rest/v1/core/sequence/5JZL/1","action":"get"}
+
+```
+https://data.rcsb.org/rest/v1/core/sequence/5JZL/1 not found
+```
+
+### `log://turn_45/get/https%3A/www.rcsb.org/structure/5WJ2`
+scheme=log action=get attrs={"path":"https://www.rcsb.org/structure/5WJ2","action":"get"}
+
+```
+https://www.rcsb.org/structure/5WJ2 promoted
+```
+
+### `log://turn_45/get/https%3A/data.rcsb.org/rest/v1/core/sequence/2IB5/1`
+scheme=log action=get attrs={"path":"https://data.rcsb.org/rest/v1/core/sequence/2IB5/1","action":"get"}
+
+```
+https://data.rcsb.org/rest/v1/core/sequence/2IB5/1 not found
+```
+
+### `log://turn_45/get/https%3A/data.rcsb.org/rest/v1/core/sequence/4KGE/1`
+scheme=log action=get attrs={"path":"https://data.rcsb.org/rest/v1/core/sequence/4KGE/1","action":"get"}
+
+```
+https://data.rcsb.org/rest/v1/core/sequence/4KGE/1 not found
+```
+
+### `log://turn_45/get/https%3A/data.rcsb.org/rest/v1/core/sequence/6AA7/1`
+scheme=log action=get attrs={"path":"https://data.rcsb.org/rest/v1/core/sequence/6AA7/1","action":"get"}
+
+```
+https://data.rcsb.org/rest/v1/core/sequence/6AA7/1 not found
+```
+
+### `log://turn_45/get/https%3A/data.rcsb.org/rest/v1/core/sequence/3ADF/1`
+scheme=log action=get attrs={"path":"https://data.rcsb.org/rest/v1/core/sequence/3ADF/1","action":"get"}
+
+```
+https://data.rcsb.org/rest/v1/core/sequence/3ADF/1 not found
+```
+
+### `log://turn_45/search/PDB_REST_API_%22sequence/%7Bid%7D/1%22_OR_%22data.rcsb.org/rest/v1/core/sequence%22_FASTA_5J`
+scheme=log action=search attrs={"query":"PDB REST API \"sequence/{id}/1\" OR \"data.rcsb.org/rest/v1/core/sequence\" FASTA 5JZL 2IB5 4KGE 6AA7","action":"search"}
+
+```
+0 results for "PDB REST API "sequence/{id}/1" OR "data.rcsb.org/rest/v1/core/sequence" FASTA 5JZL 2IB5 4KGE 6AA7"
+```
+
+### `log://turn_45/update/discovering_exact_PDB_FASTA_API_%2B_acceptor/molecule_binder_candidates`
+scheme=log action=update attrs={"status":155,"action":"update"}
+
+```
+discovering exact PDB FASTA API + acceptor/molecule binder candidates
+```
+

package/audit/sweep/protein-assembly/turns/turn_046.md

@@ -0,0 +1,193 @@
+# turn 046
+
+tokens: prompt=54302 cached=6870 completion=498 reasoning=0 total=54800 cost=0
+created: 2026-05-02 00:08:28
+
+update: status=155 body=discovering donor/acceptor FASTA sequences + binder candidates from RCSB pages
+
+---
+
+## reasoning (think)
+
+```
+# Distillation Stage Plan
+1. **Donor (5JZL - green FP, Ex~505nm)**: Confirmed from RCSB page as monomeric ultra-stable GFP (muGFP). Need FASTA sequence - searches show https://files.rcsb.org/download/5JZL.fasta exists but <get> fails. Try direct promote + check PDB API endpoints from search results.
+
+2. **Acceptor candidates from pdb_ids.txt**: Prioritize based on RCSB descriptions for Em~610nm (red/far-red):
+   - 4KGE: "near-infrared fluorescent protein with extended Stokes shift"
+   - 2IB5: "blue chromoprotein and yellow mutant" 
+   - 6AA7: "Fluorescent protein from Acropora digitifera" (likely red)
+   - Promote remaining RCSB pages if needed, then FASTA.
+
+3. **Resolve remaining unknowns**:
+   - unknown://api/pdb_sequences: Distill sequences once FASTA obtained
+   - unknown://binder/antibody_target: No sequence found despite searches; reject or use placeholder
+   - unknown://binder/molecule: No PDB match for SMILES; reject or scan ligands in promoted RCSB pages
+   - unknown://files/pdb_ids, files/plasmid_gb: Already distilled
+
+4. **Budget check**: tokensFree=1.7M, promote RCSB pages (~1-3k each) + FASTA files safe.
+
+5. **Next**: Promote key acceptor RCSB pages + search exact PDB FASTA API syntax from data.rcsb.org results.
+```
+
+## assistant emission
+
+```
+<think>
+# Distillation Stage Plan
+1. **Donor (5JZL - green FP, Ex~505nm)**: Confirmed from RCSB page as monomeric ultra-stable GFP (muGFP). Need FASTA sequence - searches show https://files.rcsb.org/download/5JZL.fasta exists but <get> fails. Try direct promote + check PDB API endpoints from search results.
+
+2. **Acceptor candidates from pdb_ids.txt**: Prioritize based on RCSB descriptions for Em~610nm (red/far-red):
+   - 4KGE: "near-infrared fluorescent protein with extended Stokes shift"
+   - 2IB5: "blue chromoprotein and yellow mutant" 
+   - 6AA7: "Fluorescent protein from Acropora digitifera" (likely red)
+   - Promote remaining RCSB pages if needed, then FASTA.
+
+3. **Resolve remaining unknowns**:
+   - unknown://api/pdb_sequences: Distill sequences once FASTA obtained
+   - unknown://binder/antibody_target: No sequence found despite searches; reject or use placeholder
+   - unknown://binder/molecule: No PDB match for SMILES; reject or scan ligands in promoted RCSB pages
+   - unknown://files/pdb_ids, files/plasmid_gb: Already distilled
+
+4. **Budget check**: tokensFree=1.7M, promote RCSB pages (~1-3k each) + FASTA files safe.
+
+5. **Next**: Promote key acceptor RCSB pages + search exact PDB FASTA API syntax from data.rcsb.org results.
+</think>
+
+<get path="https://www.rcsb.org/structure/6AA7"/>
+<get path="https://www.rcsb.org/structure/2IB5" line="1" limit="200"/>
+<get path="https://files.rcsb.org/download/5JZL.fasta"/>
+<get path="https://files.rcsb.org/download/6AA7.fasta"/>
+<get path="https://data.rcsb.org/rest/v1/core/polymer_entity/5JZL/1"/>
+<get path="known://files/pdb_ids_full_list"/>
+
+<search>PDB REST API FASTA exact endpoint data.rcsb.org "5JZL" OR "sequence fasta" OR "polymer_entity/sequence"</search>
+
+<update status="155">discovering donor/acceptor FASTA sequences + binder candidates from RCSB pages</update>
+```
+
+## actions (chronological log entries)
+
+### `log://turn_46/get/https%3A/www.rcsb.org/structure/6AA7`
+scheme=log action=get attrs={"path":"https://www.rcsb.org/structure/6AA7","action":"get"}
+
+```
+https://www.rcsb.org/structure/6AA7 promoted
+```
+
+### `log://turn_46/get/https%3A/www.rcsb.org/structure/2IB5`
+scheme=log action=get attrs={"path":"https://www.rcsb.org/structure/2IB5","lineStart":1,"lineEnd":50,"totalLines":50,"action":"get"}
+
+```
+https://www.rcsb.org/structure/2IB5
+[lines 1–50 / 50 total]
+# RCSB PDB - 2IB5: Structural characterization of a blue chromoprotein and its yellow mutant from the sea anemone cnidopus japonicus
+
+#### Structural Characterization of a Blue Chromoprotein and Its Yellow Mutant from the Sea Anemone Cnidopus Japonicus
+
+[Chan, M.C.Y.](https://www.rcsb.org/search?q=citation.rcsb_authors:Chan,%20M.C.Y.)
+,
+[Karasawa, S.](https://www.rcsb.org/search?q=citation.rcsb_authors:Karasawa,%20S.)
+, [Mizuno, H.](https://www.rcsb.org/search?q=citation.rcsb_authors:Mizuno,%20H.)
+,
+[Bosanac, I.](https://www.rcsb.org/search?q=citation.rcsb_authors:Bosanac,%20I.)
+, [Ho, D.](https://www.rcsb.org/search?q=citation.rcsb_authors:Ho,%20D.) ,
+[Prive, G.G.](https://www.rcsb.org/search?q=citation.rcsb_authors:Prive,%20G.G.)
+,
+[Miyawaki, A.](https://www.rcsb.org/search?q=citation.rcsb_authors:Miyawaki,%20A.)
+, [Ikura, M.](https://www.rcsb.org/search?q=citation.rcsb_authors:Ikura,%20M.)
+
+(2006) J Biological Chem **281**: 37813-37819
+
+*   **PubMed:** [17028187](https://www.rcsb.org/search?q=rcsb_pubmed_container_identifiers.pubmed_id:17028187) [Search on PubMed](http://www.ncbi.nlm.nih.gov/pubmed/?term=17028187)
+*   **DOI:** [https://doi.org/10.1074/jbc.M606921200](https://doi.org/10.1074/jbc.M606921200)
+  
+*   **PubMed Abstract:** 
+    
+    Green fluorescent protein (GFP) and its relatives (GFP protein family) have been
+    isolated from marine organisms such as jellyfish and corals that belong to the
+    phylum Cnidaria (stinging aquatic invertebrates). They are intrinsically
+    fluorescent proteins. In search of new members of the family of green
+    fluorescent protein family, we identified a non-fluorescent chromoprotein from
+    the Cnidopus japonicus species of sea anemone that possesses 45% sequence
+    identity to dsRed (a red fluorescent protein). This newly identified blue color
+    protein has an absorbance maximum of 610 nm and is hereafter referred to as
+    cjBlue. Determination of the cjBlue 1.8 A crystal structure revealed a
+    chromophore comprised of Gln(63)-Tyr(64)-Gly(65). The ring stacking between
+    Tyr(64) and His(197) stabilized the cjBlue trans chromophore conformation along
+    the Calpha2-Cbeta2 bond of 5-\[(4-hydroxyphenyl)methylene\]-imidazolinone, which
+    closely resembled that of the "Kindling Fluorescent Protein" and Rtms5.
+    Replacement of Tyr(64) with Leu in wild-type cjBlue produced a visible color
+    change from blue to yellow with a new absorbance maximum of 417 nm.
+    Interestingly, the crystal structure of the yellow mutant Y64L revealed two
+    His(197) imidazole ring orientations, suggesting a flip-flop interconversion
+    between the two conformations in solution. We conclude that the dynamics and
+    structure of the chromophore are both essential for the optical appearance of
+    these color proteins.
+    
+
+* * *
+
+**Organizational Affiliation**: 
+
+*   Division of Signaling Biology, Ontario Cancer Institute and Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada.
+```
+
+### `log://turn_46/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_46/get/https%3A/files.rcsb.org/download/6AA7.fasta`
+scheme=log action=get attrs={"path":"https://files.rcsb.org/download/6AA7.fasta","action":"get"}
+
+```
+https://files.rcsb.org/download/6AA7.fasta not found
+```
+
+### `log://turn_46/get/https%3A/data.rcsb.org/rest/v1/core/polymer_entity/5JZL/1`
+scheme=log action=get attrs={"path":"https://data.rcsb.org/rest/v1/core/polymer_entity/5JZL/1","action":"get"}
+
+```
+https://data.rcsb.org/rest/v1/core/polymer_entity/5JZL/1 promoted
+```
+
+### `log://turn_46/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_46/search/PDB_REST_API_FASTA_exact_endpoint_data.rcsb.org_%225JZL%22_OR_%22sequence_fasta%22_OR_%22p`
+scheme=log action=search attrs={"query":"PDB REST API FASTA exact endpoint data.rcsb.org \"5JZL\" OR \"sequence fasta\" OR \"polymer_entity/sequence\"","action":"search"}
+
+```
+8 of 12 results for "PDB REST API FASTA exact endpoint data.rcsb.org "5JZL" OR "sequence fasta" OR "polymer_entity/sequence"" (4 unreachable)
+* https://data.rcsb.org — data-api – RCSB PDB Data API: Understanding and Using (18075 tokens)
+  The relationships between these objects are explicitly implemented through attributes in a dedicated container object: rcsb_[...]_container_identifiers, where [...] should be replaces with the type of the object, e.g. entry, polymer_entity, assembly.
+* https://search.rcsb.org — search-api – RCSB PDB Search API: Understanding and Using (69208 tokens)
+  For each bucket terms faceting counts the documents (entry, polymer_entity, etc.) that contain a given value in a given field. For example, you can run the terms aggregation on the field rcsb_primary_citation.rcsb_journal_abbrev which holds the abbreviated name of a journal associated with an entry.
+* https://www.rcsb.org/docs/programmatic-access/web-apis-overview — Web APIs Overview (4282 tokens)
+  This Search API example shows how to find all PDB structures and CSMs for a given UniProtKB sequence · The ModelServer is a service for accessing subsets of macromolecular model data. It delivers atomic coordinates together with annotations in the primary data files in a compressed BinaryCIF encoding (BCIF). Structure data can be served at different levels of granularity (e.g., assembly, polymer chain, ligand), and ligand data may also be delivered in popular chemical informatics formats (e.g., SDF, MOL, MOL2).
+* https://www.rcsb.org/docs/programmatic-access/file-download-services — File Download Services (10600 tokens)
+  Please note these are to be discontinued when the PDB transitions to extended PDB IDs. Small molecule files, including the ligands/chemical components maintained in the Chemical Component Dictionary and the Biologically Interesting Molecule Reference Dictionary (BIRD) are available in multiple formats. This table includes structure factors, NMR constraints, chemical shifts, electron density maps and map coefficient files. Sequence data in FASTA format (full deposited sequence as in SEQRES records).
+* https://education.molssi.org/python-scripting-biochemistry/chapters/rcsb_api.html — Retrieving Information from the PDB using the Web API — Python Data and Scripting for Biochemists and Molecular Biologists (10555 tokens)
+  You can also use the PDB Data API to retrieve information about interfaces between polymeric entities (protein, or nucleic acids) using one of the API endpoints by changing the URL. ... In the cell below, we get the first interface for assembly 1 (there is only one assembly in this PDB entry). interface = requests.get(&quot;https://data.rcsb.org/rest/v1/core/interface/4hhb/1/1&quot;)
+* https://www.blopig.com/blog/2025/09/exploring-the-protein-data-bank-programmatically — Exploring the Protein Data Bank programmatically (22007 tokens)
+  The Worldwide Protein Data Bank ... and parsing individual entries as mmCIF files (or as legacy PDB files), or by downloading aggregated data, such as the RCSB‘s collection in a single FASTA file of all polymer entity sequences....
+* https://cdn.rcsb.org/rcsb-pdb/general_information/news_publications/newsletters/2020q3/query.html — Data Exploration Services (2687 tokens)
+  Use Advanced Search to find short sequence patterns in PDB structure FASTA sequences using the following syntax options:
+* https://www.rcsb.org/downloads/fasta — RCSB PDB - Downloads - FASTA (344 tokens)
+  As a member of the wwPDB, the RCSB PDB curates and annotates PDB data according to agreed upon standards. The RCSB PDB also provides a variety of tools and resources. Users can perform simple and advanced searches based on annotations relating to sequence, structure and function.
+```
+
+### `log://turn_46/update/discovering_donor/acceptor_FASTA_sequences_%2B_binder_candidates_from_RCSB_pages`
+scheme=log action=update attrs={"status":155,"action":"update"}
+
+```
+discovering donor/acceptor FASTA sequences + binder candidates from RCSB pages
+```
+