@possumtech/rummy 2.2.0 → 2.2.1

package/audit/sweep/protein-assembly/turns/turn_039.md

@@ -1,132 +0,0 @@
-# turn 039
-
-tokens: prompt=42544 cached=5456 completion=727 reasoning=0 total=43271 cost=0
-created: 2026-05-02 00:06:24
-
-update: status=? body=Aborted — preceding <search> failed.
-
----
-
-## reasoning (think)
-
-```
-# Distillation Stage Plan
-1. Confirm donor: 5JZL (muGFP/usGFP) is green FP (Ex~488-505nm) in pdb_ids.txt - promote RCSB page fully if needed
-2. No red FP (Em~610nm) in pdb_ids.txt - need to identify acceptor from list or reject
-3. No molecule binder (SMILES benzotriazole-like) matches - check remaining PDBs
-4. Antibody target unknown - searches failed, likely synthetic, reject or assume DHFR
-5. DHFR already distilled ✓
-6. Need sequences via PDB REST API: https://files.rcsb.org/download/{ID}.fasta 
-7. Bulk check remaining PDBs for acceptor/molecule binder properties
-8. Once sequences obtained, can move to Deployment for fusion construction
-
-Priorities this turn:
-- Get 5JZL FASTA sequence 
-- Manifest check all pdb_ids.txt FASTA URLs token costs
-- Search remaining PDBs for red FP or ligand binding
-- Distill donor confirmation
-```
-
-## assistant emission
-
-```
-<think>
-# Distillation Stage Plan
-1. Confirm donor: 5JZL (muGFP/usGFP) is green FP (Ex~488-505nm) in pdb_ids.txt - promote RCSB page fully if needed
-2. No red FP (Em~610nm) in pdb_ids.txt - need to identify acceptor from list or reject
-3. No molecule binder (SMILES benzotriazole-like) matches - check remaining PDBs
-4. Antibody target unknown - searches failed, likely synthetic, reject or assume DHFR
-5. DHFR already distilled ✓
-6. Need sequences via PDB REST API: https://files.rcsb.org/download/{ID}.fasta 
-7. Bulk check remaining PDBs for acceptor/molecule binder properties
-8. Once sequences obtained, can move to Deployment for fusion construction
-
-Priorities this turn:
-- Get 5JZL FASTA sequence 
-- Manifest check all pdb_ids.txt FASTA URLs token costs
-- Search remaining PDBs for red FP or ligand binding
-- Distill donor confirmation</think>
-
-<get path="https://files.rcsb.org/download/5JZL.fasta"/>
-<get path="known://files/pdb_ids_full_list" visibility="visible"/>
-<get path="https://files.rcsb.org/download/*.fasta" manifest>2IB5 4KGE 4Q7T 1KFD 5JZL 6AA7 3ADF 5WJ2 3M22 2H5Q 3MGF 5Y01 2VZX 4CQH 1YZW 2CHA 3KZY 1AK4 5P21 1H6R</get>
-<search results="10">rcsb pdb "2IB5" OR "4KGE" OR "4Q7T" OR "1KFD" OR "6AA7" OR "3ADF" OR "5WJ2" OR "3M22" OR "2H5Q" OR "3MGF" OR "5Y01" OR "2VZX" OR "4CQH" OR "1YZW" OR "2CHA" OR "3KZY" OR "1AK4" OR "5P21" OR "1H6R" "fluorescent protein" OR GFP OR YFP OR "red fluorescent" OR mcherry OR "far-red" OR ligand OR benzotriazole</search>
-
-<set path="known://sequence/donor_5JZL" summary="sequence,donor,5JZL,muGFP,green,505nm,pdb">
-# Related
-[prompt requirements](prompt://1)
-[donor selection](known://api/fpbase_donor)  
-[pdb_ids list](known://files/pdb_ids_full_list)
-[5JZL structure](https://www.rcsb.org/structure/5JZL)
-[unknown progress](unknown://api/fpbase_donor)
-[unknown progress](unknown://api/pdb_sequences)
-
-# Donor: muGFP (5JZL)
-Monomeric ultra-stable GFP variant. Green FP suitable for 505nm excitation.
-Sequence pending FASTA download from https://files.rcsb.org/download/5JZL.fasta
-</set>
-
-<set path="unknown://api/pdb_sequences" visibility="summarized"/>
-<set path="unknown://files/pdb_ids" visibility="summarized"/>
-<update status="155">getting donor FASTA + acceptor/molecule binder from PDB REST API</update>
-```
-
-## actions (chronological log entries)
-
-### `log://turn_39/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_39/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_39/get/https%3A/files.rcsb.org/download/*.fasta`
-scheme=log action=get attrs={"path":"https://files.rcsb.org/download/*.fasta","action":"get"}
-
-```
-MANIFEST get path="https://files.rcsb.org/download/*.fasta": 0 matched (0 tokens)
-
-```
-
-### `log://turn_39/error/Dispatch_crash_in_search%3A_Brave_422%3A_Unprocessable_Entity`
-scheme=log action=error attrs={"status":500,"action":"error"}
-
-```
-Dispatch crash in search: Brave 422: Unprocessable Entity
-```
-
-### `log://turn_39/set/known%3A/sequence/donor_5JZL`
-scheme=log action=set attrs={"error":"Aborted — preceding <search> failed.","action":"set"}
-
-```
-Aborted — preceding <search> failed.
-```
-
-### `log://turn_39/set/unknown%3A/api/pdb_sequences`
-scheme=log action=set attrs={"error":"Aborted — preceding <search> failed.","action":"set"}
-
-```
-Aborted — preceding <search> failed.
-```
-
-### `log://turn_39/set/unknown%3A/files/pdb_ids`
-scheme=log action=set attrs={"error":"Aborted — preceding <search> failed.","action":"set"}
-
-```
-Aborted — preceding <search> failed.
-```
-
-### `log://turn_39/update/_`
-scheme=log action=update attrs={"error":"Aborted — preceding <search> failed.","action":"update"}
-
-```
-Aborted — preceding <search> failed.
-```
-

package/audit/sweep/protein-assembly/turns/turn_040.md

@@ -1,115 +0,0 @@
-# turn 040
-
-tokens: prompt=43095 cached=7306 completion=461 reasoning=0 total=43556 cost=0
-created: 2026-05-02 00:06:34
-
-update: status=? body=Aborted — preceding <search> failed.
-
----
-
-## reasoning (think)
-
-```
-Distillation stage: Need to resolve remaining unknowns for deployment (gBlock design).
-
-Key unresolved:
-1. unknown://api/pdb_sequences - Need donor (5JZL muGFP, Ex~505nm), acceptor (red FP Em~610nm), molecule binder from pdb_ids.txt
-2. unknown://binder/antibody_target - Antigen sequence antibody binds
-3. unknown://binder/molecule - Protein binding SMILES Nc3nc(OCc1ccccc1)c2nc[nH]c2n3 (benzotriazole derivative)
-
-Progress: 5JZL confirmed as donor (muGFP green FP). No red FPs found in pdb_ids.txt. DHFR sequence distilled.
-
-Plan:
-- Search PDB FASTA API for 5JZL sequence (priority)
-- Search remaining pdb_ids for acceptor candidates (Em~610nm red FP)
-- Search antibody target antigen via heavy chain CDR sequence
-- Search molecule binder via SMILES/PDB IDs
-- Distill sequences into known:// entries
-- Budget: 1.7M free, can promote large FASTA files
-```
-
-## assistant emission
-
-```
-<think>
-Distillation stage: Need to resolve remaining unknowns for deployment (gBlock design).
-
-Key unresolved:
-1. unknown://api/pdb_sequences - Need donor (5JZL muGFP, Ex~505nm), acceptor (red FP Em~610nm), molecule binder from pdb_ids.txt
-2. unknown://binder/antibody_target - Antigen sequence antibody binds
-3. unknown://binder/molecule - Protein binding SMILES Nc3nc(OCc1ccccc1)c2nc[nH]c2n3 (benzotriazole derivative)
-
-Progress: 5JZL confirmed as donor (muGFP green FP). No red FPs found in pdb_ids.txt. DHFR sequence distilled.
-
-Plan:
-- Search PDB FASTA API for 5JZL sequence (priority)
-- Search remaining pdb_ids for acceptor candidates (Em~610nm red FP)
-- Search antibody target antigen via heavy chain CDR sequence
-- Search molecule binder via SMILES/PDB IDs
-- Distill sequences into known:// entries
-- Budget: 1.7M free, can promote large FASTA files
-</think>
-
-<get path="https://files.rcsb.org/download/5JZL.fasta"/>
-<get path="known://files/pdb_ids_full_list"/>
-<search>PDB FASTA sequence download API "5JZL" OR "files.rcsb.org/download/5JZL.fasta" OR rcsb pdb 5JZL sequence</search>
-<search>rcsb pdb "2IB5" OR "4KGE" OR "4Q7T" OR "1KFD" OR "6AA7" OR "3ADF" OR "5WJ2" OR "3M22" OR "2H5Q" OR "3MGF" OR "5Y01" OR "2VZX" OR "4CQH" OR "1YZW" OR "2CHA" OR "3KZY" OR "1AK4" OR "5P21" OR "1H6R" red fluorescent protein OR mcherry OR mscarlet OR far-red OR emission 610nm</search>
-
-<update status="155">discovering critical donor/acceptor/binder sequences from PDB</update>
-```
-
-## actions (chronological log entries)
-
-### `log://turn_40/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_40/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_40/search/PDB_FASTA_sequence_download_API_%225JZL%22_OR_%22files.rcsb.org/download/5JZL.fasta%22_O`
-scheme=log action=search attrs={"query":"PDB FASTA sequence download API \"5JZL\" OR \"files.rcsb.org/download/5JZL.fasta\" OR rcsb pdb 5JZL sequence","action":"search"}
-
-```
-9 of 12 results for "PDB FASTA sequence download API "5JZL" OR "files.rcsb.org/download/5JZL.fasta" OR rcsb pdb 5JZL sequence" (3 unreachable)
-* https://www.rcsb.org/downloads/fasta — RCSB PDB - Downloads - FASTA (328 tokens)
-  <strong>Download a file containing sequences in FASTA format for all entries in the PDB archive</strong>
-* https://www.rcsb.org/downloads — RCSB PDB Batch Download Service (341 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/structure/5JZL — RCSB PDB - 5JZL: The Structure of Monomeric Ultra Stable Green Fluorescent Protein (1469 tokens)
-  FASTA Sequence · mmCIF Format · mmCIF Format (Header) Legacy PDB Format · Legacy PDB Format (Header) Download Files · FASTA Sequence · PDBx/mmCIF Format · PDBx/mmCIF Format (gz) BinaryCIF Format (gz) Legacy PDB Format ·
-* https://www.rcsb.org/docs/programmatic-access/file-download-services — File Download Services (10587 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://bioinformaticsreview.com/20220614/how-to-download-fasta-sequences-from-pdb-for-multiple-structures — How to download FASTA sequences from PDB for multiple structures? (391 tokens)
-  You can download FASTA sequences as separate files or in a single file for multiple structures in PDB. Follow these steps: <strong>Go to https://www.rcsb.org/downloads/fasta</strong> Select an appropriate option from the […]
-* https://www.rcsb.org — RCSB PDB: Homepage (2012 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/news/5764422199cccf72e74ca3c1 — Download Batches of Data (496 tokens)
-  Selecting the PDB file format option ... in PDB format. <strong>The Download Tool can also be used to download FASTA sequence files and SDF ligand files, with an option to download these data for the entire archive</strong>....
-* https://cdn.rcsb.org/rcsb-pdb/general_information/news_publications/newsletters/2004q2/query.html — RCSB PDB Newsletter (1153 tokens)
-  The RCSB PDB maintains several FASTA formatted sequence files on the FTP archives. The sequences for all currently released experimental structures are contained in pdb_seqres.txt, available in uncompressed form at <strong>ftp://ftp.rcsb.org/pub/pdb/derived_data/pdb_seqres.txt</strong> and in Unix compressed ...
-* https://data.rcsb.org — data-api – RCSB PDB Data API: Understanding and Using (18046 tokens)
-  The rcsb-api package provides a Python interface to the RCSB PDB Search and Data APIs (an overview has been published in Journal for Molecular Biology). Use the rcsbapi.search module to fetch lists of PDB IDs corresponding to advanced query searches, and the rcsbapi.data module to fetch data about a given set of structure IDs.
-```
-
-### `log://turn_40/error/Dispatch_crash_in_search%3A_Brave_422%3A_Unprocessable_Entity`
-scheme=log action=error attrs={"status":500,"action":"error"}
-
-```
-Dispatch crash in search: Brave 422: Unprocessable Entity
-```
-
-### `log://turn_40/update/_`
-scheme=log action=update attrs={"error":"Aborted — preceding <search> failed.","action":"update"}
-
-```
-Aborted — preceding <search> failed.
-```
-

package/audit/sweep/protein-assembly/turns/turn_041.md

@@ -1,147 +0,0 @@
-# turn 041
-
-tokens: prompt=44308 cached=7306 completion=316 reasoning=0 total=44624 cost=0
-created: 2026-05-02 00:06:52
-
-update: status=155 body=getting 5JZL donor FASTA + scanning pdb_ids for acceptor/binder
-
----
-
-## reasoning (think)
-
-```
-* Still in Distillation: Need donor sequence (5JZL muGFP), acceptor (no red FP in pdb_ids.txt), antibody target antigen, molecule binder protein.
-* 5JZL FASTA URL wrong (download/ vs view/); search revealed correct PDB FASTA API at rcsb.org/downloads/fasta & structure pages have FASTA links.
-* No red FPs (Em~610nm) in pdb_ids.txt per prior greps; need to confirm all 20 PDBs or select best donor-only compromise.
-* Antibody target & SMILES binder unresolved - no hits in pdb_ids.txt.
-* Plan: Get 5JZL structure page for FASTA link, search remaining PDBs for acceptor/binder, then distill sequences.
-* Budget ok: target low-token sources first.
-```
-
-## assistant emission
-
-```
-<think>
-* Still in Distillation: Need donor sequence (5JZL muGFP), acceptor (no red FP in pdb_ids.txt), antibody target antigen, molecule binder protein.
-* 5JZL FASTA URL wrong (download/ vs view/); search revealed correct PDB FASTA API at rcsb.org/downloads/fasta & structure pages have FASTA links.
-* No red FPs (Em~610nm) in pdb_ids.txt per prior greps; need to confirm all 20 PDBs or select best donor-only compromise.
-* Antibody target & SMILES binder unresolved - no hits in pdb_ids.txt.
-* Plan: Get 5JZL structure page for FASTA link, search remaining PDBs for acceptor/binder, then distill sequences.
-* Budget ok: target low-token sources first.
-</think>
-
-<get path="https://www.rcsb.org/structure/5JZL" line="-50"/>
-<get path="known://files/pdb_ids_full_list" manifest/>
-<search>PDB FASTA sequence API rcsb "5JZL" OR "2IB5" OR "4KGE" OR "4Q7T" OR "1KFD" OR "6AA7" OR "3ADF" OR "5WJ2" site:rcsb.org</search>
-<get path="https://www.rcsb.org/downloads/fasta" line="1" limit="20"/>
-
-<update status="155">getting 5JZL donor FASTA + scanning pdb_ids for acceptor/binder</update>
-```
-
-## actions (chronological log entries)
-
-### `log://turn_41/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_41/get/known%3A/files/pdb_ids_full_list`
-scheme=log action=get attrs={"path":"known://files/pdb_ids_full_list","action":"get"}
-
-```
-MANIFEST get path="known://files/pdb_ids_full_list": 1 matched (132 tokens)
-known://files/pdb_ids_full_list (132)
-```
-
-### `log://turn_41/search/PDB_FASTA_sequence_API_rcsb_%225JZL%22_OR_%222IB5%22_OR_%224KGE%22_OR_%224Q7T%22_OR_%221KFD%22_OR_%226`
-scheme=log action=search attrs={"query":"PDB FASTA sequence API rcsb \"5JZL\" OR \"2IB5\" OR \"4KGE\" OR \"4Q7T\" OR \"1KFD\" OR \"6AA7\" OR \"3ADF\" OR \"5WJ2\" site:rcsb.org","action":"search"}
-
-```
-2 results for "PDB FASTA sequence API rcsb "5JZL" OR "2IB5" OR "4KGE" OR "4Q7T" OR "1KFD" OR "6AA7" OR "3ADF" OR "5WJ2" site:rcsb.org"
-* https://www.rcsb.org/structure/5JZL — RCSB PDB - 5JZL: The Structure of Monomeric Ultra Stable Green Fluorescent Protein (1469 tokens)
-  The Structure of Monomeric Ultra Stable Green Fluorescent Protein
-* https://www.rcsb.org/structure/5WJ2 — RCSB PDB - 5WJ2: Crystal structure of the green fluorescent protein Clover (583 tokens)
-  Crystal structure of the green fluorescent protein Clover
-```
-
-### `log://turn_41/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_41/update/getting_5JZL_donor_FASTA_%2B_scanning_pdb_ids_for_acceptor/binder`
-scheme=log action=update attrs={"status":155,"action":"update"}
-
-```
-getting 5JZL donor FASTA + scanning pdb_ids for acceptor/binder
-```
-

package/audit/sweep/protein-assembly/turns/turn_042.md

@@ -1,126 +0,0 @@
-# turn 042
-
-tokens: prompt=45970 cached=7480 completion=388 reasoning=0 total=46358 cost=0
-created: 2026-05-02 00:06:59
-
-update: status=155 body=getting 5JZL donor FASTA + antibody target + scanning binders
-
----
-
-## reasoning (think)
-
-```
-# Distillation Stage Plan
-1. **Donor (5JZL/muGFP)**: Confirmed green FP (Ex~488-509nm matches 505nm filter). Need FASTA sequence from RCSB (https://files.rcsb.org/download/5JZL.fasta failed; try API endpoint from search://turn_40).
-2. **Acceptor**: No red FP (Em~610nm) in pdb_ids.txt. Reject or use closest match.
-3. **Antibody binder**: Need target antigen sequence for antibody heavy chain QVQLQQSAAELARPGASVKMSCKASGYSFTTYTIHWVK.
-4. **Molecule binder**: No PDB match for SMILES Nc3nc(OCc1ccccc1)c2nc[nH]c2n3 (benzotriazole derivative).
-5. **DHFR**: Already distilled (known://sequence/dhfr).
-6. Promote 5JZL FASTA + search antibody target + check remaining pdb_ids for binders.
-
-Actions:
-- Get 5JZL FASTA via correct RCSB path
-- Search antibody target antigen
-- Manifest remaining pdb_ids for acceptor/binder candidates
-- Distill donor sequence + resolve/reject others
-```
-
-## assistant emission
-
-```
-<think>
-# Distillation Stage Plan
-1. **Donor (5JZL/muGFP)**: Confirmed green FP (Ex~488-509nm matches 505nm filter). Need FASTA sequence from RCSB (https://files.rcsb.org/download/5JZL.fasta failed; try API endpoint from search://turn_40).
-2. **Acceptor**: No red FP (Em~610nm) in pdb_ids.txt. Reject or use closest match.
-3. **Antibody binder**: Need target antigen sequence for antibody heavy chain QVQLQQSAAELARPGASVKMSCKASGYSFTTYTIHWVK.
-4. **Molecule binder**: No PDB match for SMILES Nc3nc(OCc1ccccc1)c2nc[nH]c2n3 (benzotriazole derivative).
-5. **DHFR**: Already distilled (known://sequence/dhfr).
-6. Promote 5JZL FASTA + search antibody target + check remaining pdb_ids for binders.
-
-Actions:
-- Get 5JZL FASTA via correct RCSB path
-- Search antibody target antigen
-- Manifest remaining pdb_ids for acceptor/binder candidates
-- Distill donor sequence + resolve/reject others
-</think>
-
-<get path="https://files.rcsb.org/download/5JZL.fasta"/>
-<get path="known://files/pdb_ids_full_list" manifest/>
-<search>PDB REST API FASTA "5JZL" "files.rcsb.org/download/5JZL.fasta" OR rcsb sequence download</search>
-<search>antibody heavy chain QVQLQQSAAELARPGASVKMSCKASGYSFTTYTIHWVK antigen target sequence OR binds protein</search>
-
-<update status="155">getting 5JZL donor FASTA + antibody target + scanning binders</update>
-```
-
-## actions (chronological log entries)
-
-### `log://turn_42/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_42/get/known%3A/files/pdb_ids_full_list`
-scheme=log action=get attrs={"path":"known://files/pdb_ids_full_list","action":"get"}
-
-```
-MANIFEST get path="known://files/pdb_ids_full_list": 1 matched (132 tokens)
-known://files/pdb_ids_full_list (132)
-```
-
-### `log://turn_42/search/PDB_REST_API_FASTA_%225JZL%22_%22files.rcsb.org/download/5JZL.fasta%22_OR_rcsb_sequence_`
-scheme=log action=search attrs={"query":"PDB REST API FASTA \"5JZL\" \"files.rcsb.org/download/5JZL.fasta\" OR rcsb sequence download","action":"search"}
-
-```
-8 of 12 results for "PDB REST API FASTA "5JZL" "files.rcsb.org/download/5JZL.fasta" OR rcsb sequence download" (4 unreachable)
-* 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://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://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://bioinformaticsreview.com/20220614/how-to-download-fasta-sequences-from-pdb-for-multiple-structures — How to download FASTA sequences from PDB for multiple structures? (426 tokens)
-  You can download FASTA sequences as separate files or in a single file for multiple structures in PDB. Follow these steps: <strong>Go to https://www.rcsb.org/downloads/fasta</strong> Select an appropriate option from the […]
-* 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://www.rcsb.org/news/5764422199cccf72e74ca3c1 — Download Batches of Data (510 tokens)
-  Selecting the PDB file format option ... in PDB format. <strong>The Download Tool can also be used to download FASTA sequence files and SDF ligand files, with an option to download these data for the entire archive</strong>....
-* https://www.biotite-python.org/latest/tutorial/database/rcsb.html — Fetching structure files from the RCSB PDB — Biotite (4727 tokens)
-  Downloading structure files from the RCSB PDB is quite easy: We simply <strong>specify the PDB ID, the file format and the target directory for the fetch() function</strong>. The function returns the path to the downloaded file, so you can simply load the file via the biotite.structure.io subpackage (more on ...
-```
-
-### `log://turn_42/search/antibody_heavy_chain_QVQLQQSAAELARPGASVKMSCKASGYSFTTYTIHWVK_antigen_target_seque`
-scheme=log action=search attrs={"query":"antibody heavy chain QVQLQQSAAELARPGASVKMSCKASGYSFTTYTIHWVK antigen target sequence OR binds protein","action":"search"}
-
-```
-9 of 12 results for "antibody heavy chain QVQLQQSAAELARPGASVKMSCKASGYSFTTYTIHWVK antigen target sequence OR binds protein" (3 unreachable)
-* https://www.ncbi.nlm.nih.gov/books/NBK27144 — The structure of a typical antibody molecule (12818 tokens)
-  The amino-terminal variable or V domains of the heavy and light chains (VH and VL, respectively) together make up the V region of the antibody and confer on it the ability to bind specific antigen, while the constant domains (C domains) of the heavy and light chains (CH and CL, respectively) make up the C region (see Fig. 3.1b, c). The multiple heavy-chain C domains are numbered from the amino-terminal end to the carboxy terminus, for example CH1, CH2, and so on. The protein domains described above associate to form larger globular domains.
-* https://www.creative-proteomics.com/proteinseq/resource/antibody-heavy-light-chains-structure-function.htm — Antibody Heavy and Light Chains: Structure and Function (7243 tokens)
-  Fab Fragments: Each Fab fragment consists of one variable domain from a heavy chain (VH) and one variable domain from a light chain (VL), forming the antigen-binding site. The specificity of antibody-antigen interactions is primarily determined by the unique combination of VH and VL domains. Fc Fragment: The Fc fragment is composed of constant domains from the heavy chains (CH2 and CH3). It determines the antibody&#x27;s class (e.g., IgG, IgA, IgM) and mediates interactions with other components of the immune system, such as complement proteins and Fc receptors on immune cells.
-* https://en.wikipedia.org/wiki/Antibody — Antibody (61472 tokens)
-  Two different scFv fragments can be connected together, via a hinge region, to the constant domain of the heavy chain or the constant domain of the light chain. This gives the antibody bispecificity, allowing for the binding specificities of two different antigens. The &quot;knobs-into-holes&quot; format enhances heterodimer formation but does not suppress homodimer formation. To further improve the function of heterodimeric antibodies, many scientists are looking towards artificial constructs. Artificial antibodies are largely diverse protein motifs that use the functional strategy of the antibody molecule, but are not limited by the loop and framework structural constraints of the natural antibody.
-* https://www.ncbi.nlm.nih.gov/books/NBK27160 — The interaction of the antibody molecule with specific antigen (9793 tokens)
-  <strong>Antibodies raised against intact proteins usually bind to the surface of the protein and make contact with residues that are discontinuous in the primary structure of the molecule</strong>; they may, however, occasionally bind peptide fragments of the protein, and antibodies raised against peptides ...
-* https://en.wikipedia.org/wiki/Immunoglobulin_heavy_chain — Immunoglobulin heavy chain (7093 tokens)
-  Cows, specifically Bos taurus, show a variation on the general mammalian theme in which the heavy chain CDR H3 region has adapted to produce a divergent repertoire of antibodies which present a &quot;stalk and knob&quot; antigen interaction surface instead of the more familiar bivalent tip surface. The bovine CDR is unusually long and contains unique sequence attributes which support the production of paired cysteine residues during somatic hypermutation. Thus, where in humans the somatic hypermutation step targets the V(D)J recombination process, the target in cows is on the creation of diverse disulfide bonds and the generation of unique sets of loops which interact with antigen.
-* https://www.abcam.com/en-us/technical-resources/guides/antibody-basics/antibody-basics — Antibody basics | Abcam (2500 tokens)
-  The basic principle of any immunoassay is that a specific antibody binds with its specific antigen, forming an exclusive antibody-antigen complex. This chapter defines what an antigen is and how to choose one to make an antibody. An antigen is any foreign substance that can elicit an immune response in the body (eg, antibody production) and is bound by the specific antibodies produced against it by the immune system. Antigens generally have high molecular weight and are commonly proteins or polysaccharides.
-* https://www.nature.com/articles/s41586-022-05371-z — Functional antibodies exhibit light chain coherence (58789 tokens)
-  Indeed, our findings suggest that all antibodies are recurrent, but at varying rates depending on their junction complexity and the prevalence of their cognate antigen. Our findings also suggest that aside from frequency, more complex antibodies do not behave differently with respect to light chain coherence. This work supports the following model, generalizing observed constraints on gene usage by some antibodies2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24. In nature, many heavy chain configurations yield effective binding of a given antibody target.
-* https://en.vectorbuilder.com/resources/vector-system/pRP_mAb_Heavy_Light_IL2.html — Mammalian Antibody Heavy and Light Chain Coexpression Vector (3471 tokens)
-  The antigen-binding site consists of <strong>VH+VL dimers where VH and VL represent variable fragment heavy chains and light chains, respectively</strong>. Within these fragments, most sequence variation is located in complementarity determining regions (CDRs), which influences antigen-binding specificity.
-* https://www.creative-proteomics.com/proteinseq/antibody-light-and-heavy-chain-sequencing.htm — Antibody Light and Heavy Chain Sequencing (1938 tokens)
-  1. Center: Structure of a typical immunoglobulin (antibody) protein. (Bandeira N, et al,. 2009) Creative Proteomics has established a new monoclonal antibody sequencing workflow based on a de novo sequencing approach without the need for database searches on the basis of the mass spectrometry platform. Our experienced scientists use de novo sequencing engineering to ensure that target antibody sequences are extracted from tens of thousands of MS/MS spectral data to complete antibody sequencing, helping researchers obtain antibodies with 100% coverage and accurate antibody light and heavy chain amino acids sequence information.
-```
-
-### `log://turn_42/update/getting_5JZL_donor_FASTA_%2B_antibody_target_%2B_scanning_binders`
-scheme=log action=update attrs={"status":155,"action":"update"}
-
-```
-getting 5JZL donor FASTA + antibody target + scanning binders
-```
-