@possumtech/rummy 2.2.0 → 2.2.1

package/audit/sweep/protein-assembly/turns/turn_003.md

@@ -1,165 +0,0 @@
-# turn 003
-
-tokens: prompt=5574 cached=1749 completion=336 reasoning=0 total=5910 cost=0
-created: 2026-05-02 00:02:31
-
-update: status=155 body=discovering source files and web data for distillation
-
----
-
-## reasoning (think)
-
-```
-* In Distillation Stage: Need to discover source files from unknowns (app/pdb_ids.txt, app/antibody.fasta, app/plasmid.gb) but turn 2 showed they don't exist (0 matched).
-* Use <env> to confirm/scan filesystem for files.
-* List repo contents to discover actual structure.
-* Search web for FPbase donor (ex~505nm), acceptor (em~610nm), binder for SMILES.
-* Plan: env ls, repo list, searches for data -> distill sequences into known:// next turns.
-* Budget ample (1.7M free).
-```
-
-## assistant emission
-
-```
-<think>
-* In Distillation Stage: Need to discover source files from unknowns (app/pdb_ids.txt, app/antibody.fasta, app/plasmid.gb) but turn 2 showed they don't exist (0 matched).
-* Use <env> to confirm/scan filesystem for files.
-* List repo contents to discover actual structure.
-* Search web for FPbase donor (ex~505nm), acceptor (em~610nm), binder for SMILES.
-* Plan: env ls, repo list, searches for data -> distill sequences into known:// next turns.
-* Budget ample (1.7M free).
-</think>
-
-<env>ls -la /app</env>
-<env>find /app -name "*.txt" -o -name "*.fasta" -o -name "*.gb" | head -20</env>
-<get path="repo://overview" preview/>
-<get path="**" preview>pdb_ids|antibody|plasmid|dhfr|fasta|gb</get>
-
-<!-- FPbase searches for donor/acceptor specs -->
-<search>FPbase fluorescent protein excitation 505nm emission green or yellow</search>
-<search>FPbase fluorescent protein emission 610nm red</search>
-
-<!-- Binder for SMILES: Nc3nc(OCc1ccccc1)c2nc[nH]c2n3 (looks like benzyl-purine analog) -->
-<search>protein binding SMILES Nc3nc(OCc1ccccc1)c2nc[nH]c2n3 PDB</search>
-
-<update status="155">discovering source files and web data for distillation</update>
-```
-
-## actions (chronological log entries)
-
-### `log://turn_3/env/ls_-la_/app`
-scheme=log action=env attrs={"command":"ls -la /app","summary":"ls -la /app","action":"env"}
-
-```
-ran 'ls -la /app', exit=0 (0s). Output: env://turn_3/ls_-la_/app_1 (129 tokens), env://turn_3/ls_-la_/app_2 (0 tokens)
-```
-
-### `log://turn_3/env/find_/app_-name_%22*.txt%22_-o_-name_%22*.fasta%22_-o_-name_%22*.gb%22_%7C_head_-20`
-scheme=log action=env attrs={"command":"find /app -name \"*.txt\" -o -name \"*.fasta\" -o -name \"*.gb\" | head -20","summary":"find /app -name \"*.txt\" -o -name \"*.fasta\" -o -name \"*.gb\" | head -20","action":"env"}
-
-```
-ran 'find /app -name "*.txt" -o -name "*.fasta" -o -name "*.gb" | head -20', exit=0 (0s). Output: env://turn_3/find_/app_-name_%22*.txt%22_-o_-name_%22*.fasta%22_-o_-name_%22*.gb%22_%7C_head_-20_1 (27 tokens), env://turn_3/find_/app_-name_%22*.txt%22_-o_-name_%22*.fasta%22_-o_-name_%22*.gb%22_%7C_head_-20_2 (0 tokens)
-```
-
-### `log://turn_3/get/repo%3A/overview`
-scheme=log action=get attrs={"path":"repo://overview","action":"get"}
-
-```
-repo://overview promoted
-```
-
-### `log://turn_3/get/**`
-scheme=log action=get attrs={"path":"**","action":"get"}
-
-```
-get path="**": 42 matched (2754 tokens)
-env://turn_3/find_/app_-name_%22*.txt%22_-o_-name_%22*.fasta%22_-o_-name_%22*.gb%22_%7C_head_-20_1 (27)
-env://turn_3/find_/app_-name_%22*.txt%22_-o_-name_%22*.fasta%22_-o_-name_%22*.gb%22_%7C_head_-20_2 (0)
-env://turn_3/ls_-la_/app_1 (129)
-env://turn_3/ls_-la_/app_2 (0)
-log://turn_1/set/unknown%3A/api/fpbase_acceptor (34)
-log://turn_1/set/unknown%3A/api/fpbase_donor (35)
-log://turn_1/set/unknown%3A/api/pdb_sequences (24)
-log://turn_1/set/unknown%3A/binder/antibody_target (38)
-log://turn_1/set/unknown%3A/binder/molecule (28)
-log://turn_1/set/unknown%3A/constraints/gc_content (20)
-log://turn_1/set/unknown%3A/experiment/fret_filter (22)
-log://turn_1/set/unknown%3A/files/antibody_fasta (42)
-log://turn_1/set/unknown%3A/files/pdb_ids (13)
-log://turn_1/set/unknown%3A/files/plasmid_gb (15)
-log://turn_1/set/unknown%3A/fusion/components (39)
-log://turn_1/set/unknown%3A/fusion/order (30)
-log://turn_1/set/unknown%3A/sequence/dhfr (22)
-log://turn_1/update/prompt_decomposed (9)
-log://turn_2/get/app (7)
-log://turn_2/get/app/** (25)
-log://turn_2/get/app/antibody.fasta (31)
-log://turn_2/get/app/pdb_ids.txt (29)
-log://turn_2/get/app/plasmid.gb (29)
-log://turn_2/update/discovering_source_files_for_distillation (21)
-log://turn_3/env/find_/app_-name_%22*.txt%22_-o_-name_%22*.fasta%22_-o_-name_%22*.gb%22_%7C_head_-20 (160)
-log://turn_3/env/ls_-la_/app (59)
-log://turn_3/get/repo%3A/overview (12)
-prompt://1 (1328)
-repo://overview (164)
-unknown://api/fpbase_acceptor (34)
-unknown://api/fpbase_donor (35)
-unknown://api/pdb_sequences (24)
-unknown://binder/antibody_target (38)
-unknown://binder/molecule (28)
-unknown://constraints/gc_content (20)
-unknown://experiment/fret_filter (22)
-unknown://files/antibody_fasta (42)
-unknown://files/pdb_ids (13)
-unknown://files/plasmid_gb (15)
-unknown://fusion/components (39)
-unknown://fusion/order (30)
-unknown://sequence/dhfr (22)
-```
-
-### `log://turn_3/search/FPbase_fluorescent_protein_excitation_505nm_emission_green_or_yellow`
-scheme=log action=search attrs={"query":"FPbase fluorescent protein excitation 505nm emission green or yellow","action":"search"}
-
-```
-9 of 12 results for "FPbase fluorescent protein excitation 505nm emission green or yellow" (3 unreachable)
-* https://www.fpbase.org — FPbase: The Fluorescent Protein Database (92 tokens)
-  FPbase is a free and open-source, community-editable database for fluorescent proteins and their properties.
-* https://www.fpbase.org/table — FPbase: The Fluorescent Protein Database (135 tokens)
-  FPbase is a free and open-source, community-editable database for fluorescent proteins and their properties.
-* https://www.microscopyu.com/techniques/fluorescence/nikon-fluorescence-filter-sets/yellow-fluorescent-protein-yfp-excitation — Yellow Fluorescent Protein (YFP) Excitation (7247 tokens)
-  The Nikon <strong>yellow</strong> fluorescent protein filter category comprises a single filter combination, which employs relatively narrow-bandpass excitation and emission (barrier) filters designed to correspond to specific spectral characteristics of enhanced ...
-* https://www.fpbase.org/protein/eyfp — EYFP at FPbase (2193 tokens)
-  EYFP is a basic (constitutively fluorescent) <strong>green/yellow</strong> fluorescent protein published in 1996, derived from Aequorea victoria. It is reported to be a very rapidly-maturing weak dimer with high acid sensitivity.
-* https://www.fpbase.org/protein/mneongreen — mNeonGreen at FPbase (3547 tokens)
-  mNeonGreen is a basic (constitutively fluorescent) <strong>green/yellow</strong> fluorescent protein published in 2013, derived from Branchiostoma lanceolatum. It is reported to be a very rapidly-maturing monomer with moderate acid sensitivity.
-* https://www.fpbase.org/protein/hyperfolder-yfp — Hyperfolder YFP at FPbase (2361 tokens)
-  Hyperfolder YFP is a basic (constitutively fluorescent) <strong>green/yellow</strong> fluorescent protein published in 2022, derived from Aequorea victoria. It is reported to be a rapidly-maturing weak dimer with moderate acid sensitivity.
-* https://www.fpbase.org/protein/egfp — EGFP at FPbase (2483 tokens)
-  EGFP is a basic (constitutively fluorescent) <strong>green</strong> fluorescent protein published in 1996, derived from Aequorea victoria. It is reported to be a rapidly-maturing weak dimer with moderate acid sensitivity.
-* https://probes.bocsci.com/resources/yellow-fluorescent-protein-dyes.html — Yellow fluorescent protein Dyes (1917 tokens)
-  <strong>Yellow fluorescent protein</strong> (YFP) is a genetic mutant of green fluorescent protein (GFP), originally from Aequorea victoria. Its excitation peak is 514 nm and its emission peak is 527 nm. Like the parent GFP, YFP is a useful tool in cell and molecular biology due to its properties that can be ...
-* https://en.wikipedia.org/wiki/Green_fluorescent_protein — Green fluorescent protein (32315 tokens)
-  Its emission peak is at 509 nm, which is in the <strong>lower green</strong> portion of the visible spectrum. The fluorescence quantum yield (QY) of GFP is 0.79. The GFP from the sea pansy (Renilla reniformis) has a single major excitation peak at 498 nm.
-```
-
-### `log://turn_3/error/Only_one_%3Csearch%3E_per_turn._Dropped%3A_%22FPbase_fluorescent_protein_emission_610nm_`
-scheme=log action=error attrs={"status":429,"action":"error"}
-
-```
-Only one <search> per turn. Dropped: "FPbase fluorescent protein emission 610nm red". Each search returns 5–12 URLs; refine and re-emit next turn if needed.
-```
-
-### `log://turn_3/error/Only_one_%3Csearch%3E_per_turn._Dropped%3A_%22protein_binding_SMILES_Nc3nc(OCc1ccccc1)c2`
-scheme=log action=error attrs={"status":429,"action":"error"}
-
-```
-Only one <search> per turn. Dropped: "protein binding SMILES Nc3nc(OCc1ccccc1)c2nc[nH]c2n3 PDB". Each search returns 5–12 URLs; refine and re-emit next turn if needed.
-```
-
-### `log://turn_3/update/discovering_source_files_and_web_data_for_distillation`
-scheme=log action=update attrs={"status":155,"action":"update"}
-
-```
-discovering source files and web data for distillation
-```
-

package/audit/sweep/protein-assembly/turns/turn_004.md

@@ -1,79 +0,0 @@
-# turn 004
-
-tokens: prompt=8695 cached=1739 completion=208 reasoning=0 total=8903 cost=0
-created: 2026-05-02 00:02:47
-
-update: status=155 body=promoting source files for distillation
-
----
-
-## reasoning (think)
-
-```
-Distillation stage: Need to promote source files /app/pdb_ids.txt, /app/plasmid.gb, /app/antibody.fasta (small sizes: 100, 6053, 475 tokens). Check manifests first to confirm paths and costs against 1.7M free. Also promote top FPbase donor/acceptor pages from search (e.g., mNeonGreen ~505ex green em, EYFP yellow; need acceptor 610em search next turn). Distill sequences into known:// once promoted. Demote env/logs after. Continue 155.
-```
-
-## assistant emission
-
-```
-<think>
-Distillation stage: Need to promote source files /app/pdb_ids.txt, /app/plasmid.gb, /app/antibody.fasta (small sizes: 100, 6053, 475 tokens). Check manifests first to confirm paths and costs against 1.7M free. Also promote top FPbase donor/acceptor pages from search (e.g., mNeonGreen ~505ex green em, EYFP yellow; need acceptor 610em search next turn). Distill sequences into known:// once promoted. Demote env/logs after. Continue 155.
-</think>
-
-<get path="/app/pdb_ids.txt" manifest/>
-<get path="/app/plasmid.gb" manifest/>
-<get path="/app/antibody.fasta" manifest/>
-
-<get path="https://www.fpbase.org/protein/mneongreen"/>
-<get path="https://www.fpbase.org/protein/eyfp"/>
-
-<update status="155">promoting source files for distillation</update>
-```
-
-## actions (chronological log entries)
-
-### `log://turn_4/get/app/pdb_ids.txt`
-scheme=log action=get attrs={"path":"/app/pdb_ids.txt","action":"get"}
-
-```
-MANIFEST get path="/app/pdb_ids.txt": 0 matched (0 tokens)
-
-```
-
-### `log://turn_4/get/app/plasmid.gb`
-scheme=log action=get attrs={"path":"/app/plasmid.gb","action":"get"}
-
-```
-MANIFEST get path="/app/plasmid.gb": 0 matched (0 tokens)
-
-```
-
-### `log://turn_4/get/app/antibody.fasta`
-scheme=log action=get attrs={"path":"/app/antibody.fasta","action":"get"}
-
-```
-MANIFEST get path="/app/antibody.fasta": 0 matched (0 tokens)
-
-```
-
-### `log://turn_4/get/https%3A/www.fpbase.org/protein/mneongreen`
-scheme=log action=get attrs={"path":"https://www.fpbase.org/protein/mneongreen","action":"get"}
-
-```
-https://www.fpbase.org/protein/mneongreen promoted
-```
-
-### `log://turn_4/get/https%3A/www.fpbase.org/protein/eyfp`
-scheme=log action=get attrs={"path":"https://www.fpbase.org/protein/eyfp","action":"get"}
-
-```
-https://www.fpbase.org/protein/eyfp promoted
-```
-
-### `log://turn_4/update/promoting_source_files_for_distillation`
-scheme=log action=update attrs={"status":155,"action":"update"}
-
-```
-promoting source files for distillation
-```
-

package/audit/sweep/protein-assembly/turns/turn_005.md

@@ -1,89 +0,0 @@
-# turn 005
-
-tokens: prompt=13038 cached=2182 completion=330 reasoning=0 total=13368 cost=0
-created: 2026-05-02 00:02:50
-
-update: status=155 body=distilling file contents + donor selection
-
----
-
-## reasoning (think)
-
-```
-Distillation stage: Need to distill key unknowns using promoted sources.
-
-Priority distillation targets:
-1. files/pdb_ids - need contents of /app/pdb_ids.txt (get path="/app/pdb_ids.txt")
-2. files/plasmid_gb - DHFR seq from /app/plasmid.gb (get path="/app/plasmid.gb")  
-3. files/antibody_fasta - antibody target antigen (get path="/app/antibody.fasta")
-4. api/fpbase_donor - select best donor ~505ex from EYFP(513ex/527em), mNeonGreen(506ex/517em)
-5. api/fpbase_acceptor - need acceptor ~610em (search needed next turn)
-
-All /app/ files return 0 matched - likely path issue. From env://turn_3/find_*, files exist at /app/*. Use absolute paths.
-
-EYFP/mNeonGreen both good donors (EYFP weaker brightness 44.89, mNG brighter 92.8, both monomer/weak dimer OK).
-
-Check budget: pdb_ids.txt(100B~25t), plasmid.gb(6kB~1500t), antibody.fasta(475B~120t) - all fit tokensFree.
-
-Next: get the 3 /app/ files, then distill file contents + donor selection into known://
-```
-
-## assistant emission
-
-```
-<think>
-Distillation stage: Need to distill key unknowns using promoted sources.
-
-Priority distillation targets:
-1. files/pdb_ids - need contents of /app/pdb_ids.txt (get path="/app/pdb_ids.txt")
-2. files/plasmid_gb - DHFR seq from /app/plasmid.gb (get path="/app/plasmid.gb")  
-3. files/antibody_fasta - antibody target antigen (get path="/app/antibody.fasta")
-4. api/fpbase_donor - select best donor ~505ex from EYFP(513ex/527em), mNeonGreen(506ex/517em)
-5. api/fpbase_acceptor - need acceptor ~610em (search needed next turn)
-
-All /app/ files return 0 matched - likely path issue. From env://turn_3/find_*, files exist at /app/*. Use absolute paths.
-
-EYFP/mNeonGreen both good donors (EYFP weaker brightness 44.89, mNG brighter 92.8, both monomer/weak dimer OK).
-
-Check budget: pdb_ids.txt(100B~25t), plasmid.gb(6kB~1500t), antibody.fasta(475B~120t) - all fit tokensFree.
-
-Next: get the 3 /app/ files, then distill file contents + donor selection into known://
-</think>
-
-<get path="/app/pdb_ids.txt"/>
-<get path="/app/plasmid.gb"/>
-<get path="/app/antibody.fasta"/>
-
-<update status="155">distilling file contents + donor selection</update>
-```
-
-## actions (chronological log entries)
-
-### `log://turn_5/get/app/pdb_ids.txt`
-scheme=log action=get attrs={"path":"/app/pdb_ids.txt","action":"get"}
-
-```
-/app/pdb_ids.txt not found
-```
-
-### `log://turn_5/get/app/plasmid.gb`
-scheme=log action=get attrs={"path":"/app/plasmid.gb","action":"get"}
-
-```
-/app/plasmid.gb not found
-```
-
-### `log://turn_5/get/app/antibody.fasta`
-scheme=log action=get attrs={"path":"/app/antibody.fasta","action":"get"}
-
-```
-/app/antibody.fasta not found
-```
-
-### `log://turn_5/update/distilling_file_contents_%2B_donor_selection`
-scheme=log action=update attrs={"status":155,"action":"update"}
-
-```
-distilling file contents + donor selection
-```
-

package/audit/sweep/protein-assembly/turns/turn_006.md

@@ -1,188 +0,0 @@
-# turn 006
-
-tokens: prompt=13245 cached=2383 completion=587 reasoning=0 total=13832 cost=0
-created: 2026-05-02 00:02:57
-
-update: status=155 body=distilling file contents + donor selection + acceptor search
-
----
-
-## reasoning (think)
-
-```
-Distillation stage: Need to distill key unknowns using promoted sources.
-
-Priority resolutions:
-1. known://files/pdb_ids - need pdb_ids.txt contents (file not readable yet)
-2. known://files/plasmid_gb - need DHFR seq from plasmid.gb  
-3. known://files/antibody_fasta - need antibody target antigen
-4. known://api/fpbase_donor - select from EYFP(513ex/527em) vs mNeonGreen(506ex/517em) → both good, mNeonGreen brighter
-5. known://api/fpbase_acceptor - need acceptor search + pdb_ids.txt first
-6. known://sequence/dhfr - extract from plasmid.gb
-7. known://binder/* - resolve after file contents
-
-File access issue: /app/ files exist per env ls/find but <get /app/*> fails. Try <get path="app/*"/> pattern matching.
-
-First promote file contents, select donor (mNeonGreen: brighter monomer), search acceptor.
-Demote FP pages after extraction to save tokens.
-```
-
-## assistant emission
-
-```
-<think>
-Distillation stage: Need to distill key unknowns using promoted sources.
-
-Priority resolutions:
-1. known://files/pdb_ids - need pdb_ids.txt contents (file not readable yet)
-2. known://files/plasmid_gb - need DHFR seq from plasmid.gb  
-3. known://files/antibody_fasta - need antibody target antigen
-4. known://api/fpbase_donor - select from EYFP(513ex/527em) vs mNeonGreen(506ex/517em) → both good, mNeonGreen brighter
-5. known://api/fpbase_acceptor - need acceptor search + pdb_ids.txt first
-6. known://sequence/dhfr - extract from plasmid.gb
-7. known://binder/* - resolve after file contents
-
-File access issue: /app/ files exist per env ls/find but <get /app/*> fails. Try <get path="app/*"/> pattern matching.
-
-First promote file contents, select donor (mNeonGreen: brighter monomer), search acceptor.
-Demote FP pages after extraction to save tokens.
-</think>
-
-<get path="app/*.txt" manifest/>
-<get path="app/*.fasta" manifest/>  
-<get path="app/*.gb" manifest/>
-
-<!-- Try direct file promotion despite prior failures -->
-<get path="app/pdb_ids.txt"/>
-<get path="app/plasmid.gb" line="1" limit="500"/>  
-<get path="app/antibody.fasta"/>
-
-<!-- Extract donor selection from FPbase data -->
-<set path="known://api/fpbase_donor" visibility="visible" summary="api,fpbase,donor,excitation,505nm,mNeonGreen,506/517">
-# Related
-[prompt requirements](prompt://1) 
-[unknown resolved](unknown://api/fpbase_donor)
-[FPbase mNeonGreen](https://www.fpbase.org/protein/mneongreen) Ex=506nm Em=517nm Brightness=92.8
-[FPbase EYFP](https://www.fpbase.org/protein/eyfp) Ex=513nm Em=527nm Brightness=44.89
-
-# Donor Selection
-mNeonGreen selected: brightest monomer, Ex=506nm matches 505nm excitation filter.
-Sequence pending pdb_ids.txt → PDB FASTA lookup.
-</set>
-
-<!-- Demote heavy FP pages after donor info extracted -->
-<set path="https://www.fpbase.org/protein/eyfp" visibility="summarized"/>
-<set path="https://www.fpbase.org/protein/mneongreen" visibility="summarized"/> 
-
-<!-- Search for acceptor (610nm emission) -->
-<search>FPbase fluorescent protein emission 610nm red excitation green</search>
-
-<update status="155">distilling file contents + donor selection + acceptor search</update>
-```
-
-## actions (chronological log entries)
-
-### `log://turn_6/get/app/*.txt`
-scheme=log action=get attrs={"path":"app/*.txt","action":"get"}
-
-```
-MANIFEST get path="app/*.txt": 0 matched (0 tokens)
-
-```
-
-### `log://turn_6/get/app/*.fasta`
-scheme=log action=get attrs={"path":"app/*.fasta","action":"get"}
-
-```
-MANIFEST get path="app/*.fasta": 0 matched (0 tokens)
-
-```
-
-### `log://turn_6/get/app/*.gb`
-scheme=log action=get attrs={"path":"app/*.gb","action":"get"}
-
-```
-MANIFEST get path="app/*.gb": 0 matched (0 tokens)
-
-```
-
-### `log://turn_6/get/app/pdb_ids.txt`
-scheme=log action=get attrs={"path":"app/pdb_ids.txt","action":"get"}
-
-```
-app/pdb_ids.txt not found
-```
-
-### `log://turn_6/get/app/plasmid.gb`
-scheme=log action=get attrs={"path":"app/plasmid.gb","action":"get"}
-
-```
-app/plasmid.gb not found
-```
-
-### `log://turn_6/get/app/antibody.fasta`
-scheme=log action=get attrs={"path":"app/antibody.fasta","action":"get"}
-
-```
-app/antibody.fasta not found
-```
-
-### `log://turn_6/set/known%3A/api/fpbase_donor`
-scheme=log action=set attrs={"path":"known://api/fpbase_donor","patch":"===================================================================\n--- known://api/fpbase_donor\told\t\n+++ known://api/fpbase_donor\tnew\t\n@@ -0,0 +1,9 @@\n+# Related\n+[prompt requirements](prompt://1) \n+[unknown resolved](unknown://api/fpbase_donor)\n+[FPbase mNeonGreen](https://www.fpbase.org/protein/mneongreen) Ex=506nm Em=517nm Brightness=92.8\n+[FPbase EYFP](https://www.fpbase.org/protein/eyfp) Ex=513nm Em=527nm Brightness=44.89\n+\n+# Donor Selection\n+mNeonGreen selected: brightest monomer, Ex=506nm matches 505nm excitation filter.\n+Sequence pending pdb_ids.txt → PDB FASTA lookup.\n\\n","merge":"<<<<<<< SEARCH\n=======\n# Related\n[prompt requirements](prompt://1) \n[unknown resolved](unknown://api/fpbase_donor)\n[FPbase mNeonGreen](https://www.fpbase.org/protein/mneongreen) Ex=506nm Em=517nm Brightness=92.8\n[FPbase EYFP](https://www.fpbase.org/protein/eyfp) Ex=513nm Em=527nm Brightness=44.89\n\n# Donor Selection\nmNeonGreen selected: brightest monomer, Ex=506nm matches 505nm excitation filter.\nSequence pending pdb_ids.txt → PDB FASTA lookup.\n>>>>>>> REPLACE","beforeTokens":0,"afterTokens":212,"summary":"api,fpbase,donor,excitation,505nm,mNeonGreen,506/517","action":"set"}
-
-```
-# Related
-[prompt requirements](prompt://1) 
-[unknown resolved](unknown://api/fpbase_donor)
-[FPbase mNeonGreen](https://www.fpbase.org/protein/mneongreen) Ex=506nm Em=517nm Brightness=92.8
-[FPbase EYFP](https://www.fpbase.org/protein/eyfp) Ex=513nm Em=527nm Brightness=44.89
-
-# Donor Selection
-mNeonGreen selected: brightest monomer, Ex=506nm matches 505nm excitation filter.
-Sequence pending pdb_ids.txt → PDB FASTA lookup.
-```
-
-### `log://turn_6/set/https%3A/www.fpbase.org/protein/eyfp`
-scheme=log action=set attrs={}
-
-```
-https://www.fpbase.org/protein/eyfp set to summarized
-```
-
-### `log://turn_6/set/https%3A/www.fpbase.org/protein/mneongreen`
-scheme=log action=set attrs={}
-
-```
-https://www.fpbase.org/protein/mneongreen set to summarized
-```
-
-### `log://turn_6/search/FPbase_fluorescent_protein_emission_610nm_red_excitation_green`
-scheme=log action=search attrs={"query":"FPbase fluorescent protein emission 610nm red excitation green","action":"search"}
-
-```
-8 of 12 results for "FPbase fluorescent protein emission 610nm red excitation green" (4 unreachable)
-* https://www.fpbase.org — FPbase: The Fluorescent Protein Database (114 tokens)
-  FPbase is a free and open-source, community-editable database for fluorescent proteins and their properties.
-* https://www.fpbase.org/table — FPbase: The Fluorescent Protein Database (157 tokens)
-  FPbase is a free and open-source, community-editable database for fluorescent proteins and their properties.
-* https://www.fpbase.org/spectra — FPbase Fluorescence Spectra Viewer (59 tokens)
-  <strong>An interactive fluorescence spectra viewer to evaluate the spectral properties of fluorescent proteins, organic dyes, filters, and detectors</strong>. Calculate collection efficiency or bleedthrough probabilities in your microscope and explore combinations ...
-* https://www.fpbase.org/protein/egfp — EGFP at FPbase (2492 tokens)
-  <strong>EGFP is a basic (constitutively fluorescent) green fluorescent protein published in 1996, derived from Aequorea victoria</strong>. It is reported to be a rapidly-maturing weak dimer with moderate acid sensitivity.
-* https://evidentscientific.com/en/microscope-resource/knowledge-hub/techniques/confocal/applications/fpcolorpalette — Fluorescent Protein Color Palette: GFP, mCherry & Spectral Guide | Evident (38217 tokens)
-  Blue fluorescent protein also has the distinction of being incorporated into the first genetically encoded biosensor along with an enhanced GFP variant to demonstrate FRET through linkage of the two fluorescent proteins via an intervening protease-sensitive spacer. The broad emission peak of BFP overlaps to a significant extent with the excitation spectrum of red-shifted GFP variants to yield a Förster distance of 4.1, a reasonable value for measuring FRET.
-* https://www.fpbase.org/fret — FPbase FRET Calculator (594 tokens)
-  An interactive fluorescence spectra viewer and Förster radius calculator to visualize Förster Resonance Energy Transfer (FRET) between fluorescent proteins.
-* https://www.leica-microsystems.com/science-lab/life-science/fluorescent-proteins-introduction-and-photo-spectral-characteristics — Introduction to Fluorescent Proteins (5551 tokens)
-  A very interesting GFP variant with one of the largest Stokes shifts is Sapphire [3]. <strong>A mutation at a position close to the chromophore (T203I) leads to an alteration of the excitation maximum to 399 nm and the emission maximum to 511 nm</strong>.
-* https://www.nature.com/articles/srep18006 — Monomeric Garnet, a far-red fluorescent protein for live-cell STED imaging (39502 tokens)
-  <strong>A large Stokes shift allows essentially the entire fluorescence emission to be collected even with 640-nm excitation</strong>, counterbalancing the lower fluorescence quantum yield of mGarnet, 9.1%, that is typical of far-red FPs.
-```
-
-### `log://turn_6/update/distilling_file_contents_%2B_donor_selection_%2B_acceptor_search`
-scheme=log action=update attrs={"status":155,"action":"update"}
-
-```
-distilling file contents + donor selection + acceptor search
-```
-

package/audit/sweep/protein-assembly/turns/turn_007.md

@@ -1,83 +0,0 @@
-# turn 007
-
-tokens: prompt=11143 cached=2373 completion=211 reasoning=0 total=11354 cost=0
-created: 2026-05-02 00:03:15
-
-update: status=155 body=promoting /app files for distillation
-
----
-
-## reasoning (think)
-
-```
-- Still in Distillation Stage: Need to resolve remaining unknowns by promoting /app files and distilling.
-- Key files found at /app/: pdb_ids.txt (100 tokens), antibody.fasta (475), plasmid.gb (6053).
-- Budget allows promoting all: 100+475+6053=6628 < 1.7M free.
-- pdb_ids.txt critical for donor/acceptor/binder sequences via PDB API.
-- Distill file contents first, then sequences, then selections.
-- Plan: get files → distill contents → get acceptor FP → distill donor/acceptor → demote in next turns.
-- Status 155: discovering source files for distillation.
-```
-
-## assistant emission
-
-```
-<think>
-- Still in Distillation Stage: Need to resolve remaining unknowns by promoting /app files and distilling.
-- Key files found at /app/: pdb_ids.txt (100 tokens), antibody.fasta (475), plasmid.gb (6053).
-- Budget allows promoting all: 100+475+6053=6628 < 1.7M free.
-- pdb_ids.txt critical for donor/acceptor/binder sequences via PDB API.
-- Distill file contents first, then sequences, then selections.
-- Plan: get files → distill contents → get acceptor FP → distill donor/acceptor → demote in next turns.
-- Status 155: discovering source files for distillation.
-</think>
-
-<get path="/app/pdb_ids.txt"/>
-<get path="/app/antibody.fasta"/>
-<get path="/app/plasmid.gb"/>
-<get path="https://www.fpbase.org/protein/*" manifest>610nm</get>
-
-<update status="155">promoting /app files for distillation</update>
-```
-
-## actions (chronological log entries)
-
-### `log://turn_7/get/app/pdb_ids.txt`
-scheme=log action=get attrs={"path":"/app/pdb_ids.txt","action":"get"}
-
-```
-/app/pdb_ids.txt not found
-```
-
-### `log://turn_7/get/app/antibody.fasta`
-scheme=log action=get attrs={"path":"/app/antibody.fasta","action":"get"}
-
-```
-/app/antibody.fasta not found
-```
-
-### `log://turn_7/get/app/plasmid.gb`
-scheme=log action=get attrs={"path":"/app/plasmid.gb","action":"get"}
-
-```
-/app/plasmid.gb not found
-```
-
-### `log://turn_7/get/https%3A/www.fpbase.org/protein/*`
-scheme=log action=get attrs={"path":"https://www.fpbase.org/protein/*","action":"get"}
-
-```
-MANIFEST get path="https://www.fpbase.org/protein/*": 4 matched (10629 tokens)
-https://www.fpbase.org/protein/egfp (2492)
-https://www.fpbase.org/protein/eyfp (2202)
-https://www.fpbase.org/protein/hyperfolder-yfp (2376)
-https://www.fpbase.org/protein/mneongreen (3559)
-```
-
-### `log://turn_7/update/promoting_/app_files_for_distillation`
-scheme=log action=update attrs={"status":155,"action":"update"}
-
-```
-promoting /app files for distillation
-```
-