@possumtech/rummy 2.2.0 → 2.3.1

package/audit/sweep/protein-assembly/turns/turn_027.md

@@ -1,143 +0,0 @@
-# turn 027
-
-tokens: prompt=15937 cached=2319 completion=670 reasoning=0 total=16607 cost=0
-created: 2026-05-02 00:04:21
-
-update: status=155 body=pdb_ids.txt distilled; preparing plasmid.gb+antibody.fasta
-
----
-
-## reasoning (think)
-
-```
-# Plan for Distillation Stage
-1. /app/pdb_ids.txt is now accessible via env://turn_26/cat_/app/pdb_ids.txt_1 (tail shown, 20 PDB IDs)
-2. Promote full contents with <get path="env://turn_26/cat_/app/pdb_ids.txt_1"/> (50 tokens, fits budget)
-3. Distill pdb_ids list into known://files/pdb_ids_contents to resolve unknown://files/pdb_ids
-4. Update known://api/fpbase_donor and known://api/fpbase_acceptor with sequence strategy
-5. Continue distillation: next promote /app/plasmid.gb for DHFR, /app/antibody.fasta for binder target
-6. Defer PDB FASTA sequence lookup (unknown://api/pdb_sequences) until after file distillation
-Status 155: discovering and distilling more unknown entries
-```
-
-## assistant emission
-
-```
-<think>
-# Plan for Distillation Stage
-1. /app/pdb_ids.txt is now accessible via env://turn_26/cat_/app/pdb_ids.txt_1 (tail shown, 20 PDB IDs)
-2. Promote full contents with <get path="env://turn_26/cat_/app/pdb_ids.txt_1"/> (50 tokens, fits budget)
-3. Distill pdb_ids list into known://files/pdb_ids_contents to resolve unknown://files/pdb_ids
-4. Update known://api/fpbase_donor and known://api/fpbase_acceptor with sequence strategy
-5. Continue distillation: next promote /app/plasmid.gb for DHFR, /app/antibody.fasta for binder target
-6. Defer PDB FASTA sequence lookup (unknown://api/pdb_sequences) until after file distillation
-Status 155: discovering and distilling more unknown entries
-</think>
-
-<get path="env://turn_26/cat_/app/pdb_ids.txt_1"/>
-
-<set path="known://files/pdb_ids_contents" summary="files,pdb_ids,full_list,20_proteins,donor,acceptor,binder">
-# Related
-[prompt requirements](prompt://1)
-[known summary](known://files/pdb_ids)
-[cat /app/pdb_ids.txt](env://turn_26/cat_/app/pdb_ids.txt_1)
-[unknown resolved](unknown://files/pdb_ids)
-
-# Full /app/pdb_ids.txt (20 PDB IDs)
-3M22 2H5Q 3MGF 5Y01 2VZX 4CQH 1YZW 2CHA 3KZY 1AK4
-5P21 1H6R [and 8 more from tail]
-
-Need PDB FASTA sequences via API for: donor(Ex~505nm), acceptor(Em~610nm), molecule binder(SMILES).
-</set>
-
-<set path="known://api/fpbase_donor/sequence_strategy" summary="api,fpbase,donor,sequence,pdb,505nm" visibility="summarized">
-# Related
-[donor selection](known://api/fpbase_donor)
-[pdb_ids](known://files/pdb_ids_contents)
-[unknown resolved](unknown://api/fpbase_donor)
-
-# Sequence Strategy
-mNeonGreen (Ex=506nm→505nm filter). Find matching sequence in pdb_ids.txt via PDB FASTA API.
-</set>
-
-<set path="known://api/fpbase_acceptor/sequence_strategy" summary="api,fpbase,acceptor,sequence,pdb,610nm" visibility="summarized">
-# Related
-[acceptor selection](known://api/fpbase_acceptor)
-[pdb_ids](known://files/pdb_ids_contents)
-[unknown resolved](unknown://api/fpbase_acceptor)
-
-# Sequence Strategy
-Red FP (Em~610nm filter, e.g. mGarnet/mScarlet). Find matching sequence in pdb_ids.txt via PDB FASTA API.
-</set>
-
-<set path="unknown://files/pdb_ids" visibility="summarized"/>
-
-<update status="155">pdb_ids.txt distilled; preparing plasmid.gb+antibody.fasta</update>
-```
-
-## actions (chronological log entries)
-
-### `log://turn_27/get/env%3A/turn_26/cat_/app/pdb_ids.txt_1`
-scheme=log action=get attrs={"path":"env://turn_26/cat_/app/pdb_ids.txt_1","action":"get"}
-
-```
-env://turn_26/cat_/app/pdb_ids.txt_1 promoted
-```
-
-### `log://turn_27/set/known%3A/files/pdb_ids_contents`
-scheme=log action=set attrs={"path":"known://files/pdb_ids_contents","patch":"===================================================================\n--- known://files/pdb_ids_contents\told\t\n+++ known://files/pdb_ids_contents\tnew\t\n@@ -0,0 +1,11 @@\n+# Related\n+[prompt requirements](prompt://1)\n+[known summary](known://files/pdb_ids)\n+[cat /app/pdb_ids.txt](env://turn_26/cat_/app/pdb_ids.txt_1)\n+[unknown resolved](unknown://files/pdb_ids)\n+\n+# Full /app/pdb_ids.txt (20 PDB IDs)\n+3M22 2H5Q 3MGF 5Y01 2VZX 4CQH 1YZW 2CHA 3KZY 1AK4\n+5P21 1H6R [and 8 more from tail]\n+\n+Need PDB FASTA sequences via API for: donor(Ex~505nm), acceptor(Em~610nm), molecule binder(SMILES).\n\\n","merge":"<<<<<<< SEARCH\n=======\n# Related\n[prompt requirements](prompt://1)\n[known summary](known://files/pdb_ids)\n[cat /app/pdb_ids.txt](env://turn_26/cat_/app/pdb_ids.txt_1)\n[unknown resolved](unknown://files/pdb_ids)\n\n# Full /app/pdb_ids.txt (20 PDB IDs)\n3M22 2H5Q 3MGF 5Y01 2VZX 4CQH 1YZW 2CHA 3KZY 1AK4\n5P21 1H6R [and 8 more from tail]\n\nNeed PDB FASTA sequences via API for: donor(Ex~505nm), acceptor(Em~610nm), molecule binder(SMILES).\n>>>>>>> REPLACE","beforeTokens":0,"afterTokens":205,"summary":"files,pdb_ids,full_list,20_proteins,donor,acceptor,binder","action":"set"}
-
-```
-# Related
-[prompt requirements](prompt://1)
-[known summary](known://files/pdb_ids)
-[cat /app/pdb_ids.txt](env://turn_26/cat_/app/pdb_ids.txt_1)
-[unknown resolved](unknown://files/pdb_ids)
-
-# Full /app/pdb_ids.txt (20 PDB IDs)
-3M22 2H5Q 3MGF 5Y01 2VZX 4CQH 1YZW 2CHA 3KZY 1AK4
-5P21 1H6R [and 8 more from tail]
-
-Need PDB FASTA sequences via API for: donor(Ex~505nm), acceptor(Em~610nm), molecule binder(SMILES).
-```
-
-### `log://turn_27/set/known%3A/api/fpbase_donor/sequence_strategy`
-scheme=log action=set attrs={"path":"known://api/fpbase_donor/sequence_strategy","patch":"===================================================================\n--- known://api/fpbase_donor/sequence_strategy\told\t\n+++ known://api/fpbase_donor/sequence_strategy\tnew\t\n@@ -0,0 +1,7 @@\n+# Related\n+[donor selection](known://api/fpbase_donor)\n+[pdb_ids](known://files/pdb_ids_contents)\n+[unknown resolved](unknown://api/fpbase_donor)\n+\n+# Sequence Strategy\n+mNeonGreen (Ex=506nm→505nm filter). Find matching sequence in pdb_ids.txt via PDB FASTA API.\n\\n","merge":"<<<<<<< SEARCH\n=======\n# Related\n[donor selection](known://api/fpbase_donor)\n[pdb_ids](known://files/pdb_ids_contents)\n[unknown resolved](unknown://api/fpbase_donor)\n\n# Sequence Strategy\nmNeonGreen (Ex=506nm→505nm filter). Find matching sequence in pdb_ids.txt via PDB FASTA API.\n>>>>>>> REPLACE","beforeTokens":0,"afterTokens":128,"summary":"api,fpbase,donor,sequence,pdb,505nm","action":"set"}
-
-```
-# Related
-[donor selection](known://api/fpbase_donor)
-[pdb_ids](known://files/pdb_ids_contents)
-[unknown resolved](unknown://api/fpbase_donor)
-
-# Sequence Strategy
-mNeonGreen (Ex=506nm→505nm filter). Find matching sequence in pdb_ids.txt via PDB FASTA API.
-```
-
-### `log://turn_27/set/known%3A/api/fpbase_acceptor/sequence_strategy`
-scheme=log action=set attrs={"path":"known://api/fpbase_acceptor/sequence_strategy","patch":"===================================================================\n--- known://api/fpbase_acceptor/sequence_strategy\told\t\n+++ known://api/fpbase_acceptor/sequence_strategy\tnew\t\n@@ -0,0 +1,7 @@\n+# Related\n+[acceptor selection](known://api/fpbase_acceptor)\n+[pdb_ids](known://files/pdb_ids_contents)\n+[unknown resolved](unknown://api/fpbase_acceptor)\n+\n+# Sequence Strategy\n+Red FP (Em~610nm filter, e.g. mGarnet/mScarlet). Find matching sequence in pdb_ids.txt via PDB FASTA API.\n\\n","merge":"<<<<<<< SEARCH\n=======\n# Related\n[acceptor selection](known://api/fpbase_acceptor)\n[pdb_ids](known://files/pdb_ids_contents)\n[unknown resolved](unknown://api/fpbase_acceptor)\n\n# Sequence Strategy\nRed FP (Em~610nm filter, e.g. mGarnet/mScarlet). Find matching sequence in pdb_ids.txt via PDB FASTA API.\n>>>>>>> REPLACE","beforeTokens":0,"afterTokens":139,"summary":"api,fpbase,acceptor,sequence,pdb,610nm","action":"set"}
-
-```
-# Related
-[acceptor selection](known://api/fpbase_acceptor)
-[pdb_ids](known://files/pdb_ids_contents)
-[unknown resolved](unknown://api/fpbase_acceptor)
-
-# Sequence Strategy
-Red FP (Em~610nm filter, e.g. mGarnet/mScarlet). Find matching sequence in pdb_ids.txt via PDB FASTA API.
-```
-
-### `log://turn_27/set/unknown%3A/files/pdb_ids`
-scheme=log action=set attrs={}
-
-```
-unknown://files/pdb_ids set to summarized
-```
-
-### `log://turn_27/update/pdb_ids.txt_distilled%3B_preparing_plasmid.gb%2Bantibody.fasta`
-scheme=log action=update attrs={"status":155,"action":"update"}
-
-```
-pdb_ids.txt distilled; preparing plasmid.gb+antibody.fasta
-```
-

package/audit/sweep/protein-assembly/turns/turn_028.md

@@ -1,106 +0,0 @@
-# turn 028
-
-tokens: prompt=17455 cached=2336 completion=226 reasoning=0 total=17681 cost=0
-created: 2026-05-02 00:04:27
-
-update: status=155 body=getting full pdb_ids + discovering PDB sequences for FPs
-
----
-
-## reasoning (think)
-
-```
-Distillation stage: pdb_ids.txt distilled into known://files/pdb_ids_contents. Next priorities:
-1. Get full pdb_ids.txt list (currently partial/mixed head/tail)
-2. Search PDB for mNeonGreen-like (Ex~505nm) and mGarnet-like (Em~610nm) sequences matching IDs
-3. Promote /app/plasmid.gb for DHFR sequence
-4. Promote /app/antibody.fasta for target antigen
-Resolve unknown://api/pdb_sequences via web search + PDB API discovery.
-```
-
-## assistant emission
-
-```
-<think>
-Distillation stage: pdb_ids.txt distilled into known://files/pdb_ids_contents. Next priorities:
-1. Get full pdb_ids.txt list (currently partial/mixed head/tail)
-2. Search PDB for mNeonGreen-like (Ex~505nm) and mGarnet-like (Em~610nm) sequences matching IDs
-3. Promote /app/plasmid.gb for DHFR sequence
-4. Promote /app/antibody.fasta for target antigen
-Resolve unknown://api/pdb_sequences via web search + PDB API discovery.
-</think>
-
-<get path="env://turn_26/cat_/app/pdb_ids.txt_1" line="-20"/>
-<env>cat /app/pdb_ids.txt</env>
-<get path="/app/plasmid.gb" preview/>
-<get path="/app/antibody.fasta" preview/>
-<search>PDB protein structures fluorescent proteins mNeonGreen EYFP excitation 505nm OR 513nm site:rcsb.org</search>
-
-<update status="155">getting full pdb_ids + discovering PDB sequences for FPs</update>
-```
-
-## actions (chronological log entries)
-
-### `log://turn_28/get/env%3A/turn_26/cat_/app/pdb_ids.txt_1`
-scheme=log action=get attrs={"path":"env://turn_26/cat_/app/pdb_ids.txt_1","lineStart":2,"lineEnd":21,"totalLines":21,"action":"get"}
-
-```
-env://turn_26/cat_/app/pdb_ids.txt_1
-[lines 2–21 / 21 total]
-4KGE
-4Q7T
-1KFD
-5JZL
-6AA7
-3ADF
-5WJ2
-3M22
-2H5Q
-3MGF
-5Y01
-2VZX
-4CQH
-1YZW
-2CHA
-3KZY
-1AK4
-5P21
-1H6R
-
-```
-
-### `log://turn_28/env/cat_/app/pdb_ids.txt`
-scheme=log action=env attrs={"command":"cat /app/pdb_ids.txt","summary":"cat /app/pdb_ids.txt","action":"env"}
-
-```
-ran 'cat /app/pdb_ids.txt', exit=0 (0s). Output: env://turn_28/cat_/app/pdb_ids.txt_1 (50 tokens), env://turn_28/cat_/app/pdb_ids.txt_2 (0 tokens)
-```
-
-### `log://turn_28/get/app/plasmid.gb`
-scheme=log action=get attrs={"path":"/app/plasmid.gb","action":"get"}
-
-```
-/app/plasmid.gb not found
-```
-
-### `log://turn_28/get/app/antibody.fasta`
-scheme=log action=get attrs={"path":"/app/antibody.fasta","action":"get"}
-
-```
-/app/antibody.fasta not found
-```
-
-### `log://turn_28/search/PDB_protein_structures_fluorescent_proteins_mNeonGreen_EYFP_excitation_505nm_OR_`
-scheme=log action=search attrs={"query":"PDB protein structures fluorescent proteins mNeonGreen EYFP excitation 505nm OR 513nm site:rcsb.org","action":"search"}
-
-```
-0 results for "PDB protein structures fluorescent proteins mNeonGreen EYFP excitation 505nm OR 513nm site:rcsb.org"
-```
-
-### `log://turn_28/update/getting_full_pdb_ids_%2B_discovering_PDB_sequences_for_FPs`
-scheme=log action=update attrs={"status":155,"action":"update"}
-
-```
-getting full pdb_ids + discovering PDB sequences for FPs
-```
-

package/audit/sweep/protein-assembly/turns/turn_029.md

@@ -1,93 +0,0 @@
-# turn 029
-
-tokens: prompt=18208 cached=2485 completion=345 reasoning=0 total=18553 cost=0
-created: 2026-05-02 00:04:30
-
-update: status=155 body=discovering PDB FP matches + antibody/plasmid contents
-
----
-
-## reasoning (think)
-
-```
-Current stage: Distillation. Have pdb_ids.txt contents (20 IDs), donor mNeonGreen (Ex~505nm), acceptor red FP (Em~610nm). Next: search PDB for fluorescent proteins matching these spectra in the 20 IDs, plus get antibody.fasta/plasmid.gb contents. Budget ok for targeted gets/searches.
-```
-
-## assistant emission
-
-```
-<think>
-Current stage: Distillation. Have pdb_ids.txt contents (20 IDs), donor mNeonGreen (Ex~505nm), acceptor red FP (Em~610nm). Next: search PDB for fluorescent proteins matching these spectra in the 20 IDs, plus get antibody.fasta/plasmid.gb contents. Budget ok for targeted gets/searches.
-</think>
-
-<get path="env://turn_3/ls_-la_/app_1" line="-5" limit="5"/> <!-- confirm file sizes -->
-<env>ls -la /app/antibody.fasta /app/plasmid.gb</env>
-<get path="/app/antibody.fasta" line="1" limit="200"/> <!-- peek antibody -->
-<get path="/app/plasmid.gb" line="1" limit="200"/> <!-- peek plasmid for DHFR -->
-
-<!-- Search PDB for donor/acceptor matches in our 20 IDs -->
-<search results="10">PDB fluorescent proteins mNeonGreen OR EYFP OR YFP OR GFP site:rcsb.org/pdb OR rcsb.org "3M22" OR "2H5Q" OR "3MGF" OR "5Y01" OR "2VZX" OR "4CQH" OR "1YZW" OR "2CHA" OR "3KZY" OR "1AK4" OR "5P21" OR "1H6R"</search>
-
-<!-- Get full pdb_ids list for reference -->
-<get path="env://turn_26/cat_/app/pdb_ids.txt_1"/>
-
-<update status="155">discovering PDB FP matches + antibody/plasmid contents</update>
-```
-
-## actions (chronological log entries)
-
-### `log://turn_29/get/env%3A/turn_3/ls_-la_/app_1`
-scheme=log action=get attrs={"path":"env://turn_3/ls_-la_/app_1","lineStart":3,"lineEnd":7,"totalLines":7,"action":"get"}
-
-```
-env://turn_3/ls_-la_/app_1
-[lines 3–7 / 7 total]
-drwxr-xr-x 1 root root 4096 May  2 00:01 ..
--rw-r--r-- 1 root root  475 Oct 24  2025 antibody.fasta
--rw-r--r-- 1 root root  100 Oct 24  2025 pdb_ids.txt
--rw-r--r-- 1 root root 6053 Oct 24  2025 plasmid.gb
-
-```
-
-### `log://turn_29/env/ls_-la_/app/antibody.fasta_/app/plasmid.gb`
-scheme=log action=env attrs={"command":"ls -la /app/antibody.fasta /app/plasmid.gb","summary":"ls -la /app/antibody.fasta /app/plasmid.gb","action":"env"}
-
-```
-ran 'ls -la /app/antibody.fasta /app/plasmid.gb', exit=0 (0s). Output: env://turn_29/ls_-la_/app/antibody.fasta_/app/plasmid.gb_1 (59 tokens), env://turn_29/ls_-la_/app/antibody.fasta_/app/plasmid.gb_2 (0 tokens)
-```
-
-### `log://turn_29/get/app/antibody.fasta`
-scheme=log action=get attrs={"path":"/app/antibody.fasta","action":"get"}
-
-```
-/app/antibody.fasta not found
-```
-
-### `log://turn_29/get/app/plasmid.gb`
-scheme=log action=get attrs={"path":"/app/plasmid.gb","action":"get"}
-
-```
-/app/plasmid.gb not found
-```
-
-### `log://turn_29/search/PDB_fluorescent_proteins_mNeonGreen_OR_EYFP_OR_YFP_OR_GFP_site%3Arcsb.org/pdb_OR_r`
-scheme=log action=search attrs={"query":"PDB fluorescent proteins mNeonGreen OR EYFP OR YFP OR GFP site:rcsb.org/pdb OR rcsb.org \"3M22\" OR \"2H5Q\" OR \"3MGF\" OR \"5Y01\" OR \"2VZX\" OR \"4CQH\" OR \"1YZW\" OR \"2CHA\" OR \"3KZY\" OR \"1AK4\" OR \"5P21\" OR \"1H6R\"","action":"search"}
-
-```
-0 of 10 results for "PDB fluorescent proteins mNeonGreen OR EYFP OR YFP OR GFP site:rcsb.org/pdb OR rcsb.org "3M22" OR "2H5Q" OR "3MGF" OR "5Y01" OR "2VZX" OR "4CQH" OR "1YZW" OR "2CHA" OR "3KZY" OR "1AK4" OR "5P21" OR "1H6R"" (10 unreachable)
-```
-
-### `log://turn_29/get/env%3A/turn_26/cat_/app/pdb_ids.txt_1`
-scheme=log action=get attrs={"path":"env://turn_26/cat_/app/pdb_ids.txt_1","action":"get"}
-
-```
-env://turn_26/cat_/app/pdb_ids.txt_1 promoted
-```
-
-### `log://turn_29/update/discovering_PDB_FP_matches_%2B_antibody/plasmid_contents`
-scheme=log action=update attrs={"status":155,"action":"update"}
-
-```
-discovering PDB FP matches + antibody/plasmid contents
-```
-

package/audit/sweep/protein-assembly/turns/turn_030.md

@@ -1,80 +0,0 @@
-# turn 030
-
-tokens: prompt=19383 cached=157 completion=311 reasoning=0 total=19694 cost=0
-created: 2026-05-02 00:04:39
-
-update: status=155 body=promoting antibody.fasta+plasmid.gb+full pdb_ids for sequence distillation
-
----
-
-## reasoning (think)
-
-```
-# Distillation Stage Plan
-1. Full pdb_ids.txt now visible from env://turn_26/cat_/app/pdb_ids.txt_1 (20 IDs listed)
-2. Need sequences for antibody.fasta (binder target) & plasmid.gb (DHFR) - promote via env cat
-3. Search PDB REST API for FASTA sequences matching pdb_ids.txt IDs (donor/acceptor/binder)
-4. Key unknowns remaining: api/pdb_sequences, binder/antibody_target, binder/molecule, files/antibody_fasta, files/plasmid_gb, sequence/dhfr
-5. Budget ok: promote small env cats first, then search API pattern
-```
-
-## assistant emission
-
-```
-<think>
-# Distillation Stage Plan
-1. Full pdb_ids.txt now visible from env://turn_26/cat_/app/pdb_ids.txt_1 (20 IDs listed)
-2. Need sequences for antibody.fasta (binder target) & plasmid.gb (DHFR) - promote via env cat
-3. Search PDB REST API for FASTA sequences matching pdb_ids.txt IDs (donor/acceptor/binder)
-4. Key unknowns remaining: api/pdb_sequences, binder/antibody_target, binder/molecule, files/antibody_fasta, files/plasmid_gb, sequence/dhfr
-5. Budget ok: promote small env cats first, then search API pattern
-</think>
-
-<env>cat /app/antibody.fasta</env>
-<env>cat /app/plasmid.gb</env>
-<get path="env://turn_26/cat_/app/pdb_ids.txt_1" line="-1" limit="20"/>
-
-<search>PDB REST API FASTA sequence by ID "3M22" OR "2H5Q" OR "3MGF" OR "5Y01" OR "2VZX" OR "4CQH" OR "1YZW" OR "2CHA" OR "3KZY" OR "1AK4" OR "5P21" OR "1H6R" site:rcsb.org</search>
-
-<update status="155">promoting antibody.fasta+plasmid.gb+full pdb_ids for sequence distillation</update>
-```
-
-## actions (chronological log entries)
-
-### `log://turn_30/env/cat_/app/antibody.fasta`
-scheme=log action=env attrs={"command":"cat /app/antibody.fasta","summary":"cat /app/antibody.fasta","action":"env"}
-
-```
-ran 'cat /app/antibody.fasta', exit=0 (0s). Output: env://turn_30/cat_/app/antibody.fasta_1 (238 tokens), env://turn_30/cat_/app/antibody.fasta_2 (0 tokens)
-```
-
-### `log://turn_30/env/cat_/app/plasmid.gb`
-scheme=log action=env attrs={"command":"cat /app/plasmid.gb","summary":"cat /app/plasmid.gb","action":"env"}
-
-```
-ran 'cat /app/plasmid.gb', exit=0 (0s). Output: env://turn_30/cat_/app/plasmid.gb_1 (3027 tokens), env://turn_30/cat_/app/plasmid.gb_2 (0 tokens)
-```
-
-### `log://turn_30/get/env%3A/turn_26/cat_/app/pdb_ids.txt_1`
-scheme=log action=get attrs={"path":"env://turn_26/cat_/app/pdb_ids.txt_1","lineStart":21,"lineEnd":21,"totalLines":21,"action":"get"}
-
-```
-env://turn_26/cat_/app/pdb_ids.txt_1
-[lines 21–21 / 21 total]
-
-```
-
-### `log://turn_30/search/PDB_REST_API_FASTA_sequence_by_ID_%223M22%22_OR_%222H5Q%22_OR_%223MGF%22_OR_%225Y01%22_OR_%222VZX%22`
-scheme=log action=search attrs={"query":"PDB REST API FASTA sequence by ID \"3M22\" OR \"2H5Q\" OR \"3MGF\" OR \"5Y01\" OR \"2VZX\" OR \"4CQH\" OR \"1YZW\" OR \"2CHA\" OR \"3KZY\" OR \"1AK4\" OR \"5P21\" OR \"1H6R\" site:rcsb.org","action":"search"}
-
-```
-0 results for "PDB REST API FASTA sequence by ID "3M22" OR "2H5Q" OR "3MGF" OR "5Y01" OR "2VZX" OR "4CQH" OR "1YZW" OR "2CHA" OR "3KZY" OR "1AK4" OR "5P21" OR "1H6R" site:rcsb.org"
-```
-
-### `log://turn_30/update/promoting_antibody.fasta%2Bplasmid.gb%2Bfull_pdb_ids_for_sequence_distillation`
-scheme=log action=update attrs={"status":155,"action":"update"}
-
-```
-promoting antibody.fasta+plasmid.gb+full pdb_ids for sequence distillation
-```
-

package/audit/sweep/protein-assembly/turns/turn_031.md

@@ -1,168 +0,0 @@
-# turn 031
-
-tokens: prompt=20927 cached=2845 completion=815 reasoning=0 total=21742 cost=0
-created: 2026-05-02 00:04:43
-
-update: status=155 body=distilling antibody.fasta+plasmid.gb+pdb_ids full list
-
----
-
-## reasoning (think)
-
-```
-- Still in Distillation Stage: Need to distill antibody.fasta, plasmid.gb, and identify sequences from pdb_ids.txt for donor/acceptor/binder.
-- Promote antibody.fasta (238 tokens) and plasmid.gb tail (3027 tokens too big → use line slices).
-- Full pdb_ids list now available from env://turn_26/cat_/app/pdb_ids.txt_1: 2IB5 4KGE 4Q7T 1KFD 5JZL 6AA7 3ADF 5WJ2 3M22 2H5Q 3MGF 5Y01 2VZX 4CQH 1YZW 2CHA 3KZY 1AK4 5P21 1H6R.
-- Next: Distill these files into known:// entries for sequences, then search PDB API for matching FP sequences.
-- Budget ok: 1.7M free.
-```
-
-## assistant emission
-
-```
-<think>
-- Still in Distillation Stage: Need to distill antibody.fasta, plasmid.gb, and identify sequences from pdb_ids.txt for donor/acceptor/binder.
-- Promote antibody.fasta (238 tokens) and plasmid.gb tail (3027 tokens too big → use line slices).
-- Full pdb_ids list now available from env://turn_26/cat_/app/pdb_ids.txt_1: 2IB5 4KGE 4Q7T 1KFD 5JZL 6AA7 3ADF 5WJ2 3M22 2H5Q 3MGF 5Y01 2VZX 4CQH 1YZW 2CHA 3KZY 1AK4 5P21 1H6R.
-- Next: Distill these files into known:// entries for sequences, then search PDB API for matching FP sequences.
-- Budget ok: 1.7M free.
-</think>
-
-<get path="env://turn_30/cat_/app/antibody.fasta_1" tokens="238"/>
-<get path="env://turn_30/cat_/app/plasmid.gb_1" line="-100" limit="50" tokens="~200"/>
-<get path="env://turn_26/cat_/app/pdb_ids.txt_1"/>
-
-<set path="known://files/antibody_fasta_contents" summary="files,antibody,fasta,heavy_chain,light_chain,binder,target">
-# Related
-[prompt requirements](prompt://1)
-[unknown resolved](unknown://files/antibody_fasta)
-[cat /app/antibody.fasta](env://turn_30/cat_/app/antibody.fasta_1)
-
-# /app/antibody.fasta contents
-Heavy chain: QVQLQQSAAELARPGASVKMSCKASGYSFTTYTIHWVKQRPGQGLEWIGYINPSSGYAAYNQNFKDETTLTADPSSSTAYMELNSLTSEDSAVYYCAREKFYGYDYWGQGATLTVSSASTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSQTVTCNVAHPASSTKVDKKIVPRAAAHHHHHHHH
-Light chain: DVLMTQIPLSLPVSLGDQASISCRSSQSIVHRNGNTYLEWYLLKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPYTFGGGTKLEIRRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNQC
-
-Need target antigen sequence that this antibody binds (most common variant).
-</set>
-
-<set path="known://files/pdb_ids_full_list" summary="files,pdb_ids,complete,20_ids,donor,acceptor,binder" visibility="summarized">
-# Related
-[previous pdb_ids](known://files/pdb_ids_contents)
-[cat /app/pdb_ids.txt](env://turn_26/cat_/app/pdb_ids.txt_1)
-
-# Complete /app/pdb_ids.txt (20 PDB IDs)
-2IB5 4KGE 4Q7T 1KFD 5JZL 6AA7 3ADF 5WJ2 3M22 2H5Q 3MGF 5Y01 2VZX 4CQH 1YZW 2CHA 3KZY 1AK4 5P21 1H6R
-</set>
-
-<update status="155">distilling antibody.fasta+plasmid.gb+pdb_ids full list</update>
-```
-
-## actions (chronological log entries)
-
-### `log://turn_31/get/env%3A/turn_30/cat_/app/antibody.fasta_1`
-scheme=log action=get attrs={"path":"env://turn_30/cat_/app/antibody.fasta_1","action":"get"}
-
-```
-env://turn_30/cat_/app/antibody.fasta_1 promoted
-```
-
-### `log://turn_31/get/env%3A/turn_30/cat_/app/plasmid.gb_1`
-scheme=log action=get attrs={"path":"env://turn_30/cat_/app/plasmid.gb_1","lineStart":1,"lineEnd":50,"totalLines":100,"action":"get"}
-
-```
-env://turn_30/cat_/app/plasmid.gb_1
-[lines 1–50 / 100 total]
-LOCUS       DHFR_Control_Template   2727 bp    DNA     circular     30-DEC-2009
-DEFINITION  Control vector DHFR_Control_Template, complete sequence.
-ACCESSION
-VERSION
-KEYWORDS    .
-SOURCE      Control vector DHFR_Control_Template
-  ORGANISM  Control vector DHFR_Control_Template
-            other sequences; artificial sequences; vectors.
-REFERENCE   1  (bases 1 to 2727)
-  AUTHORS   Cantor,E.
-  TITLE     Direct Submission
-  JOURNAL   Submitted (30-DEC-2009) Research Department, New England Biolabs,
-            240 County Road, Ipswich, MA 01938, USA
-FEATURES             Location/Qualifiers
-     source          1..2727
-                     /organism="Control vector DHFR_Control_Template"
-                     /mol_type="other DNA"
-     promoter        26..43
-                     /note="T7 promoter (transcript start 43 clockwise)"
-     gene            88..567
-                     /gene="folA"
-     CDS             88..567
-                     /gene="folA"
-                     /codon_start=1
-                     /product="dihydrofolate reductase (DHFR)"
-                     /translation="MISLIAALAVDRVIGMENAMPWNLPADLAWFKRNTLNKPVIMGR
-                     HTWESIGRPLPGRKNIILSSQPGTDDRVTWVKSVDEAIAACGDVPEIMVIGGGRVYEQ
-                     FLPKAQKLYLTHIDAEVEGDTHFPDYEPDDWESVFSEFHDADAQNSHSYCFEILERR"
-     terminator      663..785
-                     /note="T7 Tphi transcription terminator"
-     rep_origin      complement(984..1572)
-                     /note="pUC19 origin of replication (counter-clockwise)
-                     (RNAII -35 to RNA/DNA switch point)"
-     gene            complement(1744..2604)
-                     /gene="bla"
-     CDS             complement(1744..2604)
-                     /gene="bla"
-                     /note="ampR (confers resistance to ampicillin)"
-                     /codon_start=1
-                     /product="beta-lactamase"
-                     /translation="MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGY
-                     IELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVE
-                     YSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGGPKELTAFLHNMGDHVTRL
-                     DRWEPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGPL
-                     LRSALPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIA
-                     EIGASLIKHW"
-     sig_peptide     complement(2536..2604)
-                     /gene="bla"
-                     /note="Required for secretion to the periplasm; cleaved
-                     off to form the mature beta-lactamase protein."
-```
-
-### `log://turn_31/get/env%3A/turn_26/cat_/app/pdb_ids.txt_1`
-scheme=log action=get attrs={"path":"env://turn_26/cat_/app/pdb_ids.txt_1","action":"get"}
-
-```
-env://turn_26/cat_/app/pdb_ids.txt_1 promoted
-```
-
-### `log://turn_31/set/known%3A/files/antibody_fasta_contents`
-scheme=log action=set attrs={"path":"known://files/antibody_fasta_contents","patch":"===================================================================\n--- known://files/antibody_fasta_contents\told\t\n+++ known://files/antibody_fasta_contents\tnew\t\n@@ -0,0 +1,10 @@\n+# Related\n+[prompt requirements](prompt://1)\n+[unknown resolved](unknown://files/antibody_fasta)\n+[cat /app/antibody.fasta](env://turn_30/cat_/app/antibody.fasta_1)\n+\n+# /app/antibody.fasta contents\n+Heavy chain: QVQLQQSAAELARPGASVKMSCKASGYSFTTYTIHWVKQRPGQGLEWIGYINPSSGYAAYNQNFKDETTLTADPSSSTAYMELNSLTSEDSAVYYCAREKFYGYDYWGQGATLTVSSASTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSQTVTCNVAHPASSTKVDKKIVPRAAAHHHHHHHH\n+Light chain: DVLMTQIPLSLPVSLGDQASISCRSSQSIVHRNGNTYLEWYLLKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPYTFGGGTKLEIRRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNQC\n+\n+Need target antigen sequence that this antibody binds (most common variant).\n\\n","merge":"<<<<<<< SEARCH\n=======\n# Related\n[prompt requirements](prompt://1)\n[unknown resolved](unknown://files/antibody_fasta)\n[cat /app/antibody.fasta](env://turn_30/cat_/app/antibody.fasta_1)\n\n# /app/antibody.fasta contents\nHeavy chain: QVQLQQSAAELARPGASVKMSCKASGYSFTTYTIHWVKQRPGQGLEWIGYINPSSGYAAYNQNFKDETTLTADPSSSTAYMELNSLTSEDSAVYYCAREKFYGYDYWGQGATLTVSSASTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSQTVTCNVAHPASSTKVDKKIVPRAAAHHHHHHHH\nLight chain: DVLMTQIPLSLPVSLGDQASISCRSSQSIVHRNGNTYLEWYLLKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPYTFGGGTKLEIRRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNQC\n\nNeed target antigen sequence that this antibody binds (most common variant).\n>>>>>>> REPLACE","beforeTokens":0,"afterTokens":373,"summary":"files,antibody,fasta,heavy_chain,light_chain,binder,target","action":"set"}
-
-```
-# Related
-[prompt requirements](prompt://1)
-[unknown resolved](unknown://files/antibody_fasta)
-[cat /app/antibody.fasta](env://turn_30/cat_/app/antibody.fasta_1)
-
-# /app/antibody.fasta contents
-Heavy chain: QVQLQQSAAELARPGASVKMSCKASGYSFTTYTIHWVKQRPGQGLEWIGYINPSSGYAAYNQNFKDETTLTADPSSSTAYMELNSLTSEDSAVYYCAREKFYGYDYWGQGATLTVSSASTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSQTVTCNVAHPASSTKVDKKIVPRAAAHHHHHHHH
-Light chain: DVLMTQIPLSLPVSLGDQASISCRSSQSIVHRNGNTYLEWYLLKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPYTFGGGTKLEIRRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNQC
-
-Need target antigen sequence that this antibody binds (most common variant).
-```
-
-### `log://turn_31/set/known%3A/files/pdb_ids_full_list`
-scheme=log action=set attrs={"path":"known://files/pdb_ids_full_list","patch":"===================================================================\n--- known://files/pdb_ids_full_list\told\t\n+++ known://files/pdb_ids_full_list\tnew\t\n@@ -0,0 +1,6 @@\n+# Related\n+[previous pdb_ids](known://files/pdb_ids_contents)\n+[cat /app/pdb_ids.txt](env://turn_26/cat_/app/pdb_ids.txt_1)\n+\n+# Complete /app/pdb_ids.txt (20 PDB IDs)\n+2IB5 4KGE 4Q7T 1KFD 5JZL 6AA7 3ADF 5WJ2 3M22 2H5Q 3MGF 5Y01 2VZX 4CQH 1YZW 2CHA 3KZY 1AK4 5P21 1H6R\n\\n","merge":"<<<<<<< SEARCH\n=======\n# Related\n[previous pdb_ids](known://files/pdb_ids_contents)\n[cat /app/pdb_ids.txt](env://turn_26/cat_/app/pdb_ids.txt_1)\n\n# Complete /app/pdb_ids.txt (20 PDB IDs)\n2IB5 4KGE 4Q7T 1KFD 5JZL 6AA7 3ADF 5WJ2 3M22 2H5Q 3MGF 5Y01 2VZX 4CQH 1YZW 2CHA 3KZY 1AK4 5P21 1H6R\n>>>>>>> REPLACE","beforeTokens":0,"afterTokens":132,"summary":"files,pdb_ids,complete,20_ids,donor,acceptor,binder","action":"set"}
-
-```
-# Related
-[previous pdb_ids](known://files/pdb_ids_contents)
-[cat /app/pdb_ids.txt](env://turn_26/cat_/app/pdb_ids.txt_1)
-
-# Complete /app/pdb_ids.txt (20 PDB IDs)
-2IB5 4KGE 4Q7T 1KFD 5JZL 6AA7 3ADF 5WJ2 3M22 2H5Q 3MGF 5Y01 2VZX 4CQH 1YZW 2CHA 3KZY 1AK4 5P21 1H6R
-```
-
-### `log://turn_31/update/distilling_antibody.fasta%2Bplasmid.gb%2Bpdb_ids_full_list`
-scheme=log action=update attrs={"status":155,"action":"update"}
-
-```
-distilling antibody.fasta+plasmid.gb+pdb_ids full list
-```
-