@possumtech/rummy 2.0.1 → 2.2.0

package/audit/sweep/protein-assembly/turns/turn_032.md

@@ -0,0 +1,187 @@
+# turn 032
+
+tokens: prompt=23657 cached=2534 completion=326 reasoning=0 total=23983 cost=0
+created: 2026-05-02 00:04:49
+
+update: status=155 body=distilling DHFR sequence + discovering antibody target + molecule binder
+
+---
+
+## reasoning (think)
+
+```
+1. Still in Distillation Stage - need to resolve remaining unknowns:
+   - unknown://sequence/dhfr (DHFR from plasmid.gb)
+   - unknown://files/plasmid_gb (full plasmid.gb contents)
+   - unknown://binder/antibody_target (antigen sequence antibody binds)
+   - unknown://binder/molecule (PDB ID/protein binding SMILES)
+   - unknown://api/pdb_sequences (FASTA for donor/acceptor candidates)
+
+2. Promote plasmid.gb full contents (already partially visible, need CDS region) and distill DHFR
+3. Search for antibody target antigen and SMILES binder from pdb_ids list
+4. Budget check: plasmid.gb slice already promoted (1318t), full acceptable since tokensFree=1.7M
+5. Plan: get full plasmid.gb → distill DHFR → search antibody target + molecule binder → get relevant PDB FASTA
+```
+
+## assistant emission
+
+```
+<think>
+1. Still in Distillation Stage - need to resolve remaining unknowns:
+   - unknown://sequence/dhfr (DHFR from plasmid.gb)
+   - unknown://files/plasmid_gb (full plasmid.gb contents)
+   - unknown://binder/antibody_target (antigen sequence antibody binds)
+   - unknown://binder/molecule (PDB ID/protein binding SMILES)
+   - unknown://api/pdb_sequences (FASTA for donor/acceptor candidates)
+
+2. Promote plasmid.gb full contents (already partially visible, need CDS region) and distill DHFR
+3. Search for antibody target antigen and SMILES binder from pdb_ids list
+4. Budget check: plasmid.gb slice already promoted (1318t), full acceptable since tokensFree=1.7M
+5. Plan: get full plasmid.gb → distill DHFR → search antibody target + molecule binder → get relevant PDB FASTA
+</think>
+
+<get path="env://turn_30/cat_/app/plasmid.gb_1" line="-100"/>
+<get path="env://turn_30/cat_/app/plasmid.gb_1" line="1" limit="100"/>
+<env>grep -A 20 "dihydrofolate reductase" /app/plasmid.gb || cat /app/plasmid.gb</env>
+<search>antibody heavy chain QVQLQQSAAELARPGASVKMSCKASGYSFTTYTIHWVK target antigen sequence</search>
+
+<update status="155">distilling DHFR sequence + discovering antibody target + molecule binder</update>
+```
+
+## actions (chronological log entries)
+
+### `log://turn_32/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":100,"totalLines":100,"action":"get"}
+
+```
+env://turn_30/cat_/app/plasmid.gb_1
+[lines 1–100 / 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."
+BASE COUNT      694 a    671 c    694 g    668 t
+ORIGIN
+        1 gctagtggtg ctagccccgc gaaattaata cgactcacta tagggtctag aaataatttt
+       61 gtttaacttt aagaaggaga tatacatatg atcagtctga ttgcggcgtt agcggtagat
+      121 cgcgttatcg gcatggaaaa cgccatgccg tggaacctgc ctgccgatct cgcctggttt
+      181 aaacgcaaca ccttaaataa acccgtgatt atgggccgcc atacctggga atcaatcggt
+      241 cgtccgttgc caggacgcaa aaatattatc ctcagcagtc aaccgggtac ggacgatcgc
+      301 gtaacgtggg tgaagtcggt ggatgaagcc atcgcggcgt gtggtgacgt accagaaatc
+      361 atggtgattg gcggcggtcg cgtttatgaa cagttcttgc caaaagcgca aaaactgtat
+      421 ctgacgcata tcgacgcaga agtggaaggc gacacccatt tcccggatta cgagccggat
+      481 gactgggaat cggtattcag cgaattccac gatgctgatg cgcagaactc tcacagctat
+      541 tgctttgaga ttctggagcg gcggtaatga ggatcccggg aattctcgag taaggttaac
+      601 ctgcaggagg cctttaatta aggtggtgcg gccgcgctag cggtcccggg ggatcgatcc
+      661 ggctgctaac aaagcccgaa aggaagctga gttggctgct gccaccgctg agcaataact
+      721 agcataaccc cttggggcct ctaaacgggt cttgaggggt tttttgctga aaggaggaac
+      781 tatatccgga agcttggcac tggccgaccg gggtcgagca ctgactcgct gcgctcggtc
+      841 gttcggctgc ggcgagcggt atcagctcac tcaaaggcgg taatacggtt atccacagaa
+      901 tcaggggata acgcaggaaa gaacatgtga gcaaaaggcc agcaaaaggc caggaaccgt
+      961 aaaaaggccg cgttgctggc gtttttccat aggctccgcc cccctgacga gcatcacaaa
+     1021 aatcgacgct caagtcagag gtggcgaaac ccgacaggac tataaagata ccaggcgttt
+     1081 ccccctggaa gctccctcgt gcgctctcct gttccgaccc tgccgcttac cggatacctg
+     1141 tccgcctttc tcccttcggg aagcgtggcg ctttctcata gctcacgctg taggtatctc
+     1201 agttcggtgt aggtcgttcg ctccaagctg ggctgtgtgc acgaaccccc cgttcagccc
+     1261 gaccgctgcg ccttatccgg taactatcgt cttgagtcca acccgctaag acacgactta
+     1321 tcgccactgg cagcagccac tggtaacagg attagcagag cgaggtatgt aggcggtgct
+     1381 acagagttct tgaagtggtg gcctaactac ggctacacta gaagaacagt atttggtatc
+     1441 tgcgctctgc tgaagccagt taccttcgga aaaagagttg gtagctcttg atccggcaaa
+     1501 caaaccaccg ctggtagcgg tggttttttt gtttgcaagc agcagattac gcgcagaaaa
+     1561 aaaggatctc aagaagatcc tttgatcttt tctacggggt ctgacgctca gtggaacgaa
+     1621 aactcacaga tccgggattt tggtcatgag attatcaaaa aggatcttca cctagatcct
+     1681 tttaaattaa aaatgaagtt ttaaatcaat ctaaagtata tatgagtaaa cttggtctga
+     1741 cagttaccaa tgcttaatca gtgaggcacc tatctcagcg atctgtctat ttcgttcatc
+     1801 catagttgcc tgactccccg tcgtgtagat aactacgata cgggagggct taccatctgg
+     1861 ccccagtgct gcaatgatac cgcgggaccc acgctcaccg gctccagatt tatcagcaat
+     1921 aaaccagcca gccggaaggg ccgagcgcag aagtggtcct gcaactttat ccgcctccat
+     1981 ccagtctatt aattgttgcc gggaagctag agtaagtagt tcgccagtta atagtttgcg
+     2041 caacgttgtt gccattgcta caggcatcgt ggtgtcacgc tcgtcgtttg gtatggcttc
+     2101 attcagctcc ggttcccaac gatcaaggcg agttacatga tcccccatgt tgtgcaaaaa
+     2161 agcggttagc tccttcggtc ctccgatcgt tgtcagaagt aagttggccg cagtgttatc
+     2221 actcatggtt atggcagcac tgcataattc tcttactgtc atgccatccg taagatgctt
+     2281 ttctgtgact ggtgagtact caaccaagtc attctgagaa tagtgtatgc ggcgaccgag
+     2341 ttgctcttgc ccggcgtcaa tacgggataa taccgcgcca catagcagaa ctttaaaagt
+     2401 gctcatcatt ggaaaacgtt cttcggggcg aaaactctca aggatcttac cgctgttgag
+     2461 atccagttcg atgtaaccca ctcgtgcacc caactgatct tcagcatctt ttactttcac
+     2521 cagcgtttct gggtgagcaa aaacaggaag gcaaaatgcc gcaaaaaagg gaataagggc
+     2581 gacacggaaa tgttgaatac tcatactctt cctttttcaa tattattgaa gcatttatca
+     2641 gggttattgt ctcatgagcg gatacatatt tgaatgtatt tagaaaaata aacaaatagg
+     2701 ggttccgcgc acatttcccc gaaaagt
+//
+
+```
+
+### `log://turn_32/env/grep_-A_20_%22dihydrofolate_reductase%22_/app/plasmid.gb_%7C%7C_cat_/app/plasmid.gb`
+scheme=log action=env attrs={"command":"grep -A 20 \"dihydrofolate reductase\" /app/plasmid.gb || cat /app/plasmid.gb","summary":"grep -A 20 \"dihydrofolate reductase\" /app/plasmid.gb || cat /app/plasmid.gb","action":"env"}
+
+```
+ran 'grep -A 20 "dihydrofolate reductase" /app/plasmid.gb || cat /app/plasmid.gb', exit=0 (0s). Output: env://turn_32/grep_-A_20_%22dihydrofolate_reductase%22_/app/plasmid.gb_%7C%7C_cat_/app/plasmid.gb_1 (639 tokens), env://turn_32/grep_-A_20_%22dihydrofolate_reductase%22_/app/plasmid.gb_%7C%7C_cat_/app/plasmid.gb_2 (0 tokens)
+```
+
+### `log://turn_32/search/antibody_heavy_chain_QVQLQQSAAELARPGASVKMSCKASGYSFTTYTIHWVK_target_antigen_seque`
+scheme=log action=search attrs={"query":"antibody heavy chain QVQLQQSAAELARPGASVKMSCKASGYSFTTYTIHWVK target antigen sequence","action":"search"}
+
+```
+3 of 12 results for "antibody heavy chain QVQLQQSAAELARPGASVKMSCKASGYSFTTYTIHWVK target antigen sequence" (9 unreachable)
+* https://www.bioatla.com/appendix/antibody-structure — Antibody Structure | BioAtla (3821 tokens)
+  The paratope is shaped at the amino terminal end of the antibody monomer by the variable domains from the heavy and light chains. The variable domain is also referred to as the Fv region and is the most important region for binding to antigens. More specifically, variable loops (three each on the light (VL) and heavy (VH) chains) are responsible for binding to the antigen.
+* https://www.creative-diagnostics.com/blog/index.php/antibody-heavy-and-light-chains — Antibody Heavy and Light Chains - Creative Diagnostics (4926 tokens)
+  Recognizing one antigenic determinant requires a set of heavy chain and light chain hypervariable regions to complement it, and another antigenic determinant requires another set. Complementary hypervariable regions. At present, more than 200 kinds of hypervariable regions have been discovered, and their different sets can recognize countless antigenic determinants. The relatively constant region between hypervariable regions is called the framework region. Because the variability of the amino acid sequence outside the hypervariable region is very small, this indicates that the hypervariable region alone forms a highly specialized surface for the binding site.
+* https://www.abcam.com/en-us/technical-resources/guides/antibody-basics/antibody-basics — Antibody basics | Abcam (2500 tokens)
+  VH – heavy chain variable domain, VL- light chain variable domain, CH – heavy chain constant domain, CL – light chain constant domain. The Y-shape of an antibody can be cleaved into three fragments by the proteolytic enzyme pepsin: two F(ab) regions and an Fc region. The F(ab) regions contain the variable domain that binds to cognate (specific) antigens.
+```
+
+### `log://turn_32/update/distilling_DHFR_sequence_%2B_discovering_antibody_target_%2B_molecule_binder`
+scheme=log action=update attrs={"status":155,"action":"update"}
+
+```
+distilling DHFR sequence + discovering antibody target + molecule binder
+```
+

package/audit/sweep/protein-assembly/turns/turn_033.md

@@ -0,0 +1,215 @@
+# turn 033
+
+tokens: prompt=27319 cached=3661 completion=349 reasoning=0 total=27668 cost=0
+created: 2026-05-02 00:05:08
+
+update: status=155 body=distilling DHFR + discovering FP PDB matches + antibody target
+
+---
+
+## reasoning (think)
+
+```
+Distillation stage: Resolve remaining unknowns using promoted sources.
+
+Key resolutions needed:
+1. unknown://sequence/dhfr - Extract from plasmid.gb CDS translation (remove N-Met)
+2. unknown://files/plasmid_gb - Distill DHFR details  
+3. unknown://binder/antibody_target - No exact antigen match found; reject or use placeholder
+4. unknown://api/pdb_sequences - No FP matches in pdb_ids.txt; need to check which PDBs are FPs
+5. unknown://binder/molecule - No SMILES binder identified
+6. unknown://api/fpbase_donor/acceptor sequences - No matching PDB FASTA found
+
+First promote plasmid.gb grep for DHFR, then distill sequences. Search for PDB FP matches and antibody target.
+Check first few PDB IDs for fluorescent proteins via RCSB search.
+```
+
+## assistant emission
+
+```
+<think>
+Distillation stage: Resolve remaining unknowns using promoted sources.
+
+Key resolutions needed:
+1. unknown://sequence/dhfr - Extract from plasmid.gb CDS translation (remove N-Met)
+2. unknown://files/plasmid_gb - Distill DHFR details  
+3. unknown://binder/antibody_target - No exact antigen match found; reject or use placeholder
+4. unknown://api/pdb_sequences - No FP matches in pdb_ids.txt; need to check which PDBs are FPs
+5. unknown://binder/molecule - No SMILES binder identified
+6. unknown://api/fpbase_donor/acceptor sequences - No matching PDB FASTA found
+
+First promote plasmid.gb grep for DHFR, then distill sequences. Search for PDB FP matches and antibody target.
+Check first few PDB IDs for fluorescent proteins via RCSB search.
+</think>
+
+<get path="env://turn_32/grep_-A_20_%22dihydrofolate_reductase%22_/app/plasmid.gb_%7C%7C_cat_/app/plasmid.gb_1" line="1" limit="50"/>
+<get path="env://turn_30/cat_/app/plasmid.gb_1" line="-100"/>
+<env>grep -A 5 "folA" /app/plasmid.gb</env>
+<search results="10">rcsb pdb "2IB5" OR "4KGE" OR "4Q7T" OR "1KFD" OR "5JZL" fluorescent protein OR GFP OR YFP OR mNeon</search>
+
+<update status="155">distilling DHFR + discovering FP PDB matches + antibody target</update>
+```
+
+## actions (chronological log entries)
+
+### `log://turn_33/get/env%3A/turn_32/grep_-A_20_%2522dihydrofolate_reductase%2522_/app/plasmid.gb_%257C%257C_ca`
+scheme=log action=get attrs={"path":"env://turn_32/grep_-A_20_%22dihydrofolate_reductase%22_/app/plasmid.gb_%7C%7C_cat_/app/plasmid.gb_1","lineStart":1,"lineEnd":22,"totalLines":22,"action":"get"}
+
+```
+env://turn_32/grep_-A_20_%22dihydrofolate_reductase%22_/app/plasmid.gb_%7C%7C_cat_/app/plasmid.gb_1
+[lines 1–22 / 22 total]
+                     /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
+
+```
+
+### `log://turn_33/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":100,"totalLines":100,"action":"get"}
+
+```
+env://turn_30/cat_/app/plasmid.gb_1
+[lines 1–100 / 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."
+BASE COUNT      694 a    671 c    694 g    668 t
+ORIGIN
+        1 gctagtggtg ctagccccgc gaaattaata cgactcacta tagggtctag aaataatttt
+       61 gtttaacttt aagaaggaga tatacatatg atcagtctga ttgcggcgtt agcggtagat
+      121 cgcgttatcg gcatggaaaa cgccatgccg tggaacctgc ctgccgatct cgcctggttt
+      181 aaacgcaaca ccttaaataa acccgtgatt atgggccgcc atacctggga atcaatcggt
+      241 cgtccgttgc caggacgcaa aaatattatc ctcagcagtc aaccgggtac ggacgatcgc
+      301 gtaacgtggg tgaagtcggt ggatgaagcc atcgcggcgt gtggtgacgt accagaaatc
+      361 atggtgattg gcggcggtcg cgtttatgaa cagttcttgc caaaagcgca aaaactgtat
+      421 ctgacgcata tcgacgcaga agtggaaggc gacacccatt tcccggatta cgagccggat
+      481 gactgggaat cggtattcag cgaattccac gatgctgatg cgcagaactc tcacagctat
+      541 tgctttgaga ttctggagcg gcggtaatga ggatcccggg aattctcgag taaggttaac
+      601 ctgcaggagg cctttaatta aggtggtgcg gccgcgctag cggtcccggg ggatcgatcc
+      661 ggctgctaac aaagcccgaa aggaagctga gttggctgct gccaccgctg agcaataact
+      721 agcataaccc cttggggcct ctaaacgggt cttgaggggt tttttgctga aaggaggaac
+      781 tatatccgga agcttggcac tggccgaccg gggtcgagca ctgactcgct gcgctcggtc
+      841 gttcggctgc ggcgagcggt atcagctcac tcaaaggcgg taatacggtt atccacagaa
+      901 tcaggggata acgcaggaaa gaacatgtga gcaaaaggcc agcaaaaggc caggaaccgt
+      961 aaaaaggccg cgttgctggc gtttttccat aggctccgcc cccctgacga gcatcacaaa
+     1021 aatcgacgct caagtcagag gtggcgaaac ccgacaggac tataaagata ccaggcgttt
+     1081 ccccctggaa gctccctcgt gcgctctcct gttccgaccc tgccgcttac cggatacctg
+     1141 tccgcctttc tcccttcggg aagcgtggcg ctttctcata gctcacgctg taggtatctc
+     1201 agttcggtgt aggtcgttcg ctccaagctg ggctgtgtgc acgaaccccc cgttcagccc
+     1261 gaccgctgcg ccttatccgg taactatcgt cttgagtcca acccgctaag acacgactta
+     1321 tcgccactgg cagcagccac tggtaacagg attagcagag cgaggtatgt aggcggtgct
+     1381 acagagttct tgaagtggtg gcctaactac ggctacacta gaagaacagt atttggtatc
+     1441 tgcgctctgc tgaagccagt taccttcgga aaaagagttg gtagctcttg atccggcaaa
+     1501 caaaccaccg ctggtagcgg tggttttttt gtttgcaagc agcagattac gcgcagaaaa
+     1561 aaaggatctc aagaagatcc tttgatcttt tctacggggt ctgacgctca gtggaacgaa
+     1621 aactcacaga tccgggattt tggtcatgag attatcaaaa aggatcttca cctagatcct
+     1681 tttaaattaa aaatgaagtt ttaaatcaat ctaaagtata tatgagtaaa cttggtctga
+     1741 cagttaccaa tgcttaatca gtgaggcacc tatctcagcg atctgtctat ttcgttcatc
+     1801 catagttgcc tgactccccg tcgtgtagat aactacgata cgggagggct taccatctgg
+     1861 ccccagtgct gcaatgatac cgcgggaccc acgctcaccg gctccagatt tatcagcaat
+     1921 aaaccagcca gccggaaggg ccgagcgcag aagtggtcct gcaactttat ccgcctccat
+     1981 ccagtctatt aattgttgcc gggaagctag agtaagtagt tcgccagtta atagtttgcg
+     2041 caacgttgtt gccattgcta caggcatcgt ggtgtcacgc tcgtcgtttg gtatggcttc
+     2101 attcagctcc ggttcccaac gatcaaggcg agttacatga tcccccatgt tgtgcaaaaa
+     2161 agcggttagc tccttcggtc ctccgatcgt tgtcagaagt aagttggccg cagtgttatc
+     2221 actcatggtt atggcagcac tgcataattc tcttactgtc atgccatccg taagatgctt
+     2281 ttctgtgact ggtgagtact caaccaagtc attctgagaa tagtgtatgc ggcgaccgag
+     2341 ttgctcttgc ccggcgtcaa tacgggataa taccgcgcca catagcagaa ctttaaaagt
+     2401 gctcatcatt ggaaaacgtt cttcggggcg aaaactctca aggatcttac cgctgttgag
+     2461 atccagttcg atgtaaccca ctcgtgcacc caactgatct tcagcatctt ttactttcac
+     2521 cagcgtttct gggtgagcaa aaacaggaag gcaaaatgcc gcaaaaaagg gaataagggc
+     2581 gacacggaaa tgttgaatac tcatactctt cctttttcaa tattattgaa gcatttatca
+     2641 gggttattgt ctcatgagcg gatacatatt tgaatgtatt tagaaaaata aacaaatagg
+     2701 ggttccgcgc acatttcccc gaaaagt
+//
+
+```
+
+### `log://turn_33/env/grep_-A_5_%22folA%22_/app/plasmid.gb`
+scheme=log action=env attrs={"command":"grep -A 5 \"folA\" /app/plasmid.gb","summary":"grep -A 5 \"folA\" /app/plasmid.gb","action":"env"}
+
+```
+ran 'grep -A 5 "folA" /app/plasmid.gb', exit=0 (0s). Output: env://turn_33/grep_-A_5_%22folA%22_/app/plasmid.gb_1 (218 tokens), env://turn_33/grep_-A_5_%22folA%22_/app/plasmid.gb_2 (0 tokens)
+```
+
+### `log://turn_33/search/rcsb_pdb_%222IB5%22_OR_%224KGE%22_OR_%224Q7T%22_OR_%221KFD%22_OR_%225JZL%22_fluorescent_protein_OR_G`
+scheme=log action=search attrs={"query":"rcsb pdb \"2IB5\" OR \"4KGE\" OR \"4Q7T\" OR \"1KFD\" OR \"5JZL\" fluorescent protein OR GFP OR YFP OR mNeon","action":"search"}
+
+```
+1 results for "rcsb pdb "2IB5" OR "4KGE" OR "4Q7T" OR "1KFD" OR "5JZL" fluorescent protein OR GFP OR YFP OR mNeon"
+* https://www.rcsb.org/structure/5JZL — RCSB PDB - 5JZL: The Structure of Monomeric Ultra Stable Green Fluorescent Protein (1426 tokens)
+  The Structure of Monomeric Ultra Stable Green Fluorescent Protein
+```
+
+### `log://turn_33/update/distilling_DHFR_%2B_discovering_FP_PDB_matches_%2B_antibody_target`
+scheme=log action=update attrs={"status":155,"action":"update"}
+
+```
+distilling DHFR + discovering FP PDB matches + antibody target
+```
+

package/audit/sweep/protein-assembly/turns/turn_034.md

@@ -0,0 +1,143 @@
+# turn 034
+
+tokens: prompt=31063 cached=4116 completion=763 reasoning=0 total=31826 cost=0
+created: 2026-05-02 00:05:15
+
+update: status=155 body=distilling DHFR; discovering donor 5JZL FASTA + acceptor/molecule binder PDB …
+
+---
+
+## reasoning (think)
+
+```
+# Distillation Stage Plan
+1. **DHFR sequence**: Extract from plasmid.gb (already visible, folA CDS translation MISLIAALAV... → ISLIAALAV... remove N-Met)
+2. **Donor FP**: Found 5JZL = "Monomeric Ultra Stable Green Fluorescent Protein" (Ex~488-510nm range for 505nm filter). Need PDB FASTA sequence.
+3. **Antibody target**: No direct hit; reject or search better.
+4. **Acceptor FP & molecule binder**: Still need PDB matches for Em~610nm and SMILES binder from remaining pdb_ids.
+5. **Next actions**: 
+   - Promote 5JZL PDB page + get FASTA via REST API
+   - Search acceptor candidates from pdb_ids (e.g. "rcsb pdb 6AA7 OR 3ADF red fluorescent protein")
+   - Distill DHFR known://sequence/dhfr
+   - Continue distillation
+```
+
+## assistant emission
+
+```
+<think>
+# Distillation Stage Plan
+1. **DHFR sequence**: Extract from plasmid.gb (already visible, folA CDS translation MISLIAALAV... → ISLIAALAV... remove N-Met)
+2. **Donor FP**: Found 5JZL = "Monomeric Ultra Stable Green Fluorescent Protein" (Ex~488-510nm range for 505nm filter). Need PDB FASTA sequence.
+3. **Antibody target**: No direct hit; reject or search better.
+4. **Acceptor FP & molecule binder**: Still need PDB matches for Em~610nm and SMILES binder from remaining pdb_ids.
+5. **Next actions**: 
+   - Promote 5JZL PDB page + get FASTA via REST API
+   - Search acceptor candidates from pdb_ids (e.g. "rcsb pdb 6AA7 OR 3ADF red fluorescent protein")
+   - Distill DHFR known://sequence/dhfr
+   - Continue distillation
+</think>
+
+<get path="https://www.rcsb.org/structure/5JZL"/>
+<get path="https://files.rcsb.org/download/5JZL.fasta" line="1" limit="500"/>
+<env>grep -i "fluorescent\|gfp\|yfp\|mneon" /app/pdb_ids.txt || echo "no FPs in list"</env>
+<search results="10">rcsb pdb "6AA7" OR "3ADF" OR "5WJ2" OR "4KGE" OR "4Q7T" OR "1KFD" red OR far-red OR mcherry OR mgarnet OR mscarlet fluorescent protein</search>
+
+<set path="known://sequence/dhfr" summary="sequence,dhfr,plasmid,folA,remove_met" visibility="visible">
+# Related
+[prompt requirements](prompt://1)
+[plasmid.gb full](env://turn_30/cat_/app/plasmid.gb_1)
+[folA grep](env://turn_33/grep_-A_5_%22folA%22_/app/plasmid.gb_1)
+[unknown resolved](unknown://sequence/dhfr)
+[unknown resolved](unknown://files/plasmid_gb)
+
+# DHFR protein sequence (remove N-terminal Met)
+From plasmid.gb CDS 88..567 /gene="folA" /product="dihydrofolate reductase (DHFR)"
+/translation="MISLIAALAVDRVIGMENAMPWNLPADLAWFKRNTLNKPVIMGRHTWESIGRPLPGRKNIILSSQPGTDDRVTWVKSVDEAIAACGDVPEIMVIGGGRVYEQFLPKAQKLYLTHIDAEVEGDTHFPDYEPDDWESVFSEFHDADAQNSHSYCFEILERR"
+
+**Mature DHFR (no N-Met)**: ISLIAALAVDRVIGMENAMPWNLPADLAWFKRNTLNKPVIMGRHTWESIGRPLPGRKNIILSSQPGTDDRVTWVKSVDEAIAACGDVPEIMVIGGGRVYEQFLPKAQKLYLTHIDAEVEGDTHFPDYEPDDWESVFSEFHDADAQNSHSYCFEILERR
+
+Length: 159 aa (480 nt encoded)
+</set>
+
+<set path="unknown://api/pdb_sequences" visibility="summarized"/>
+<set path="unknown://files/plasmid_gb" visibility="summarized"/>
+
+<update status="155">distilling DHFR; discovering donor 5JZL FASTA + acceptor/molecule binder PDB matches</update>
+```
+
+## actions (chronological log entries)
+
+### `log://turn_34/get/https%3A/www.rcsb.org/structure/5JZL`
+scheme=log action=get attrs={"path":"https://www.rcsb.org/structure/5JZL","action":"get"}
+
+```
+https://www.rcsb.org/structure/5JZL promoted
+```
+
+### `log://turn_34/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_34/env/grep_-i_%22fluorescent%5C%7Cgfp%5C%7Cyfp%5C%7Cmneon%22_/app/pdb_ids.txt_%7C%7C_echo_%22no_FPs_in_list%22`
+scheme=log action=env attrs={"command":"grep -i \"fluorescent\\|gfp\\|yfp\\|mneon\" /app/pdb_ids.txt || echo \"no FPs in list\"","summary":"grep -i \"fluorescent\\|gfp\\|yfp\\|mneon\" /app/pdb_ids.txt || echo \"no FPs in list\"","action":"env"}
+
+```
+ran 'grep -i "fluorescent\|gfp\|yfp\|mneon" /app/pdb_ids.txt || echo "no FPs in list"', exit=0 (0s). Output: env://turn_34/grep_-i_%22fluorescent%5C%7Cgfp%5C%7Cyfp%5C%7Cmneon%22_/app/pdb_ids.txt_%7C%7C_echo_%22no_FPs_in_list%22_1 (8 tokens), env://turn_34/grep_-i_%22fluorescent%5C%7Cgfp%5C%7Cyfp%5C%7Cmneon%22_/app/pdb_ids.txt_%7C%7C_echo_%22no_FPs_in_list%22_2 (0 tokens)
+```
+
+### `log://turn_34/search/rcsb_pdb_%226AA7%22_OR_%223ADF%22_OR_%225WJ2%22_OR_%224KGE%22_OR_%224Q7T%22_OR_%221KFD%22_red_OR_far-red`
+scheme=log action=search attrs={"query":"rcsb pdb \"6AA7\" OR \"3ADF\" OR \"5WJ2\" OR \"4KGE\" OR \"4Q7T\" OR \"1KFD\" red OR far-red OR mcherry OR mgarnet OR mscarlet fluorescent protein","action":"search"}
+
+```
+2 of 10 results for "rcsb pdb "6AA7" OR "3ADF" OR "5WJ2" OR "4KGE" OR "4Q7T" OR "1KFD" red OR far-red OR mcherry OR mgarnet OR mscarlet fluorescent protein" (8 unreachable)
+* https://www.fpbase.org/protein/mscarlet — mScarlet at FPbase (2356 tokens)
+  mScarlet is a <strong>basic (constitutively fluorescent) red fluorescent protein published in 2016, derived from synthetic construct</strong>. It has moderate acid sensitivity.
+* https://www.fpbase.org/protein/mcherry — mCherry at FPbase (4438 tokens)
+  mCherry is <strong>a basic (constitutively fluorescent) red fluorescent protein published in 2004, derived from Discosoma sp</strong>.. It is reported to be a very rapidly-maturing monomer with low acid sensitivity.
+```
+
+### `log://turn_34/set/known%3A/sequence/dhfr`
+scheme=log action=set attrs={"path":"known://sequence/dhfr","patch":"===================================================================\n--- known://sequence/dhfr\told\t\n+++ known://sequence/dhfr\tnew\t\n@@ -0,0 +1,14 @@\n+# Related\n+[prompt requirements](prompt://1)\n+[plasmid.gb full](env://turn_30/cat_/app/plasmid.gb_1)\n+[folA grep](env://turn_33/grep_-A_5_%22folA%22_/app/plasmid.gb_1)\n+[unknown resolved](unknown://sequence/dhfr)\n+[unknown resolved](unknown://files/plasmid_gb)\n+\n+# DHFR protein sequence (remove N-terminal Met)\n+From plasmid.gb CDS 88..567 /gene=\"folA\" /product=\"dihydrofolate reductase (DHFR)\"\n+/translation=\"MISLIAALAVDRVIGMENAMPWNLPADLAWFKRNTLNKPVIMGRHTWESIGRPLPGRKNIILSSQPGTDDRVTWVKSVDEAIAACGDVPEIMVIGGGRVYEQFLPKAQKLYLTHIDAEVEGDTHFPDYEPDDWESVFSEFHDADAQNSHSYCFEILERR\"\n+\n+**Mature DHFR (no N-Met)**: ISLIAALAVDRVIGMENAMPWNLPADLAWFKRNTLNKPVIMGRHTWESIGRPLPGRKNIILSSQPGTDDRVTWVKSVDEAIAACGDVPEIMVIGGGRVYEQFLPKAQKLYLTHIDAEVEGDTHFPDYEPDDWESVFSEFHDADAQNSHSYCFEILERR\n+\n+Length: 159 aa (480 nt encoded)\n\\n","merge":"<<<<<<< SEARCH\n=======\n# Related\n[prompt requirements](prompt://1)\n[plasmid.gb full](env://turn_30/cat_/app/plasmid.gb_1)\n[folA grep](env://turn_33/grep_-A_5_%22folA%22_/app/plasmid.gb_1)\n[unknown resolved](unknown://sequence/dhfr)\n[unknown resolved](unknown://files/plasmid_gb)\n\n# DHFR protein sequence (remove N-terminal Met)\nFrom plasmid.gb CDS 88..567 /gene=\"folA\" /product=\"dihydrofolate reductase (DHFR)\"\n/translation=\"MISLIAALAVDRVIGMENAMPWNLPADLAWFKRNTLNKPVIMGRHTWESIGRPLPGRKNIILSSQPGTDDRVTWVKSVDEAIAACGDVPEIMVIGGGRVYEQFLPKAQKLYLTHIDAEVEGDTHFPDYEPDDWESVFSEFHDADAQNSHSYCFEILERR\"\n\n**Mature DHFR (no N-Met)**: ISLIAALAVDRVIGMENAMPWNLPADLAWFKRNTLNKPVIMGRHTWESIGRPLPGRKNIILSSQPGTDDRVTWVKSVDEAIAACGDVPEIMVIGGGRVYEQFLPKAQKLYLTHIDAEVEGDTHFPDYEPDDWESVFSEFHDADAQNSHSYCFEILERR\n\nLength: 159 aa (480 nt encoded)\n>>>>>>> REPLACE","beforeTokens":0,"afterTokens":392,"summary":"sequence,dhfr,plasmid,folA,remove_met","action":"set"}
+
+```
+# Related
+[prompt requirements](prompt://1)
+[plasmid.gb full](env://turn_30/cat_/app/plasmid.gb_1)
+[folA grep](env://turn_33/grep_-A_5_%22folA%22_/app/plasmid.gb_1)
+[unknown resolved](unknown://sequence/dhfr)
+[unknown resolved](unknown://files/plasmid_gb)
+
+# DHFR protein sequence (remove N-terminal Met)
+From plasmid.gb CDS 88..567 /gene="folA" /product="dihydrofolate reductase (DHFR)"
+/translation="MISLIAALAVDRVIGMENAMPWNLPADLAWFKRNTLNKPVIMGRHTWESIGRPLPGRKNIILSSQPGTDDRVTWVKSVDEAIAACGDVPEIMVIGGGRVYEQFLPKAQKLYLTHIDAEVEGDTHFPDYEPDDWESVFSEFHDADAQNSHSYCFEILERR"
+
+**Mature DHFR (no N-Met)**: ISLIAALAVDRVIGMENAMPWNLPADLAWFKRNTLNKPVIMGRHTWESIGRPLPGRKNIILSSQPGTDDRVTWVKSVDEAIAACGDVPEIMVIGGGRVYEQFLPKAQKLYLTHIDAEVEGDTHFPDYEPDDWESVFSEFHDADAQNSHSYCFEILERR
+
+Length: 159 aa (480 nt encoded)
+```
+
+### `log://turn_34/set/unknown%3A/api/pdb_sequences`
+scheme=log action=set attrs={}
+
+```
+unknown://api/pdb_sequences set to summarized
+```
+
+### `log://turn_34/set/unknown%3A/files/plasmid_gb`
+scheme=log action=set attrs={}
+
+```
+unknown://files/plasmid_gb set to summarized
+```
+
+### `log://turn_34/update/distilling_DHFR%3B_discovering_donor_5JZL_FASTA_%2B_acceptor/molecule_binder_PDB_mat`
+scheme=log action=update attrs={"status":155,"action":"update"}
+
+```
+distilling DHFR; discovering donor 5JZL FASTA + acceptor/molecule binder PDB matches
+```
+