From 304f5c959180b127867a2ecf760b9d7cb0c55a5a Mon Sep 17 00:00:00 2001 From: Avneesh Singh Date: Fri, 6 Feb 2026 19:06:53 +0530 Subject: [PATCH 01/24] Add PDPC lipid and ULV SAXS form-factor experiments (Marquardt et al. 2020) --- Molecules/membrane/PDPC/PDPC.yaml | 19 + .../PDPC_ULV_30C/PDPC_ULV@30C_share.xff | 745 +++++++++++++++++ .../PDPC_ULV_30C/metadata.yaml | 29 + .../SDPC_ULV_30C/SDPC_ULV@30C_share.xff | 775 ++++++++++++++++++ .../SDPC_ULV_30C/metadata.yaml | 29 + 5 files changed, 1597 insertions(+) create mode 100644 Molecules/membrane/PDPC/PDPC.yaml create mode 100644 experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/PDPC_ULV_30C/PDPC_ULV@30C_share.xff create mode 100644 experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/PDPC_ULV_30C/metadata.yaml create mode 100644 experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/SDPC_ULV_30C/SDPC_ULV@30C_share.xff create mode 100644 experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/SDPC_ULV_30C/metadata.yaml diff --git a/Molecules/membrane/PDPC/PDPC.yaml b/Molecules/membrane/PDPC/PDPC.yaml new file mode 100644 index 000000000..92ceedfc1 --- /dev/null +++ b/Molecules/membrane/PDPC/PDPC.yaml @@ -0,0 +1,19 @@ +name: PDPC +full_name: 1-palmitoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine + +chains: + sn1: + length: 16 + unsaturation: 0 + sn2: + length: 22 + unsaturation: 6 + +headgroup: PC +lipid_class: phosphatidylcholine + +reference: + authors: Marquardt et al. + journal: Chemistry and Physics of Lipids + year: 2020 + doi: 10.1016/j.chemphyslip.2020.104892 diff --git a/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/PDPC_ULV_30C/PDPC_ULV@30C_share.xff b/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/PDPC_ULV_30C/PDPC_ULV@30C_share.xff new file mode 100644 index 000000000..04648ecae --- /dev/null +++ b/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/PDPC_ULV_30C/PDPC_ULV@30C_share.xff @@ -0,0 +1,745 @@ +################################################################################## +## experimental X-ray scattering form factors obtained for ULV data ## +## CHESS March 2012 ## +## Marquardt et al., Chem Phys Lipids 229 (2020) 104892: 1-7 ## +################################################################################## +## +## redefinition of x-ray scattering length for D to be equal to 0% D2O water +#SLwin +#set Yperc 0 +#calculContrast +#setRHO_wat X 0.3337 +#updateSIM +## +q |F(q)| deltaF + 0.07 0.4394 0.035 + 0.071 0.4511 0.035 + 0.072 0.4672 0.035 + 0.073 0.4813 0.035 + 0.074 0.4966 0.035 + 0.075 0.5142 0.035 + 0.076 0.5311 0.035 + 0.077 0.547 0.035 + 0.078 0.5598 0.035 + 0.079 0.5783 0.035 + 0.08 0.5959 0.035 + 0.081 0.6104 0.035 + 0.082 0.6272 0.035 + 0.083 0.6448 0.035 + 0.084 0.6619 0.035 + 0.085 0.6784 0.035 + 0.086 0.6952 0.035 + 0.087 0.7113 0.035 + 0.088 0.7259 0.035 + 0.089 0.7431 0.035 + 0.09 0.7608 0.035 + 0.091 0.7766 0.035 + 0.092 0.7936 0.035 + 0.093 0.8099 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a/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/SDPC_ULV_30C/SDPC_ULV@30C_share.xff b/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/SDPC_ULV_30C/SDPC_ULV@30C_share.xff new file mode 100644 index 000000000..f81698ba4 --- /dev/null +++ b/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/SDPC_ULV_30C/SDPC_ULV@30C_share.xff @@ -0,0 +1,775 @@ +################################################################################## +## experimental X-ray scattering form factors obtained for ULV data ## +## CHESS March 2012 ## +## Marquardt et al., Chem Phys Lipids 229 (2020) 104892: 1-7 ## +################################################################################## +## +## redefinition of x-ray scattering length for D to be equal to 0% D2O water +##SLwin +#set Xperc 0 +#calculContrast +#setRHO_wat X 0.334 +#updateSIM +## +q |F(q)| deltaF +0.06 0.48979 0.07 +0.061 0.5065 0.07 +0.062 0.52239 0.07 +0.063 0.54314 0.07 +0.064 0.5668 0.07 +0.065 0.58399 0.07 +0.066 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a/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/SDPC_ULV_30C/metadata.yaml b/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/SDPC_ULV_30C/metadata.yaml new file mode 100644 index 000000000..fa006ab5b --- /dev/null +++ b/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/SDPC_ULV_30C/metadata.yaml @@ -0,0 +1,29 @@ +experiment_type: SAXS +observable: form_factor + +lipid: SDPC +vesicle_type: ULV + +temperature: + value: 30 + unit: C + +solvent: + composition: H2O + d2o_fraction: 0.0 + +facility: + name: CHESS + year: 2012 + +data_file: SDPC_ULV@30C_share.xff + +reference: + authors: Marquardt et al. + journal: Chemistry and Physics of Lipids + year: 2020 + doi: 10.1016/j.chemphyslip.2020.104892 + +notes: + - X-ray scattering form factors + - ULVs prepared by extrusion From bdb33141bbbc866ece375bd8cf8ced4f867fa627 Mon Sep 17 00:00:00 2001 From: Avneesh Singh Date: Fri, 6 Feb 2026 19:26:22 +0530 Subject: [PATCH 02/24] Fix PDPC molecule metadata filename --- Molecules/membrane/PDPC/metadata.yaml | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 Molecules/membrane/PDPC/metadata.yaml diff --git a/Molecules/membrane/PDPC/metadata.yaml b/Molecules/membrane/PDPC/metadata.yaml new file mode 100644 index 000000000..92ceedfc1 --- /dev/null +++ b/Molecules/membrane/PDPC/metadata.yaml @@ -0,0 +1,19 @@ +name: PDPC +full_name: 1-palmitoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine + +chains: + sn1: + length: 16 + unsaturation: 0 + sn2: + length: 22 + unsaturation: 6 + +headgroup: PC +lipid_class: phosphatidylcholine + +reference: + authors: Marquardt et al. + journal: Chemistry and Physics of Lipids + year: 2020 + doi: 10.1016/j.chemphyslip.2020.104892 From 660a695a4ca129dde21aa471248cd472f310639d Mon Sep 17 00:00:00 2001 From: Avneesh Singh Date: Fri, 6 Feb 2026 19:29:50 +0530 Subject: [PATCH 03/24] Remove duplicate PDPC.yaml; keep metadata.yaml only --- Molecules/membrane/PDPC/PDPC.yaml | 19 ------------------- 1 file changed, 19 deletions(-) delete mode 100644 Molecules/membrane/PDPC/PDPC.yaml diff --git a/Molecules/membrane/PDPC/PDPC.yaml b/Molecules/membrane/PDPC/PDPC.yaml deleted file mode 100644 index 92ceedfc1..000000000 --- a/Molecules/membrane/PDPC/PDPC.yaml +++ /dev/null @@ -1,19 +0,0 @@ -name: PDPC -full_name: 1-palmitoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine - -chains: - sn1: - length: 16 - unsaturation: 0 - sn2: - length: 22 - unsaturation: 6 - -headgroup: PC -lipid_class: phosphatidylcholine - -reference: - authors: Marquardt et al. - journal: Chemistry and Physics of Lipids - year: 2020 - doi: 10.1016/j.chemphyslip.2020.104892 From b36d6e62e90ecad8d90f3aff72c194531f30631c Mon Sep 17 00:00:00 2001 From: Avneesh Singh Date: Fri, 6 Feb 2026 19:38:38 +0530 Subject: [PATCH 04/24] Add InChIKey to PDPC metadata for autocompletion --- Molecules/membrane/PDPC/metadata.yaml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/Molecules/membrane/PDPC/metadata.yaml b/Molecules/membrane/PDPC/metadata.yaml index 92ceedfc1..f05d724e5 100644 --- a/Molecules/membrane/PDPC/metadata.yaml +++ b/Molecules/membrane/PDPC/metadata.yaml @@ -17,3 +17,6 @@ reference: journal: Chemistry and Physics of Lipids year: 2020 doi: 10.1016/j.chemphyslip.2020.104892 + +bioschema_properties: + inChIKey: LZCLYPSVMMQWKP-UHFFFAOYSA-N From bfaeafe1c58625e0faf013359c88976f5c369727 Mon Sep 17 00:00:00 2001 From: "Avneesh.Singh" Date: Fri, 6 Feb 2026 20:17:01 +0530 Subject: [PATCH 05/24] Apply suggestion from @github-actions[bot] Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- Molecules/membrane/PDPC/metadata.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/Molecules/membrane/PDPC/metadata.yaml b/Molecules/membrane/PDPC/metadata.yaml index f05d724e5..f7e1b99d7 100644 --- a/Molecules/membrane/PDPC/metadata.yaml +++ b/Molecules/membrane/PDPC/metadata.yaml @@ -1,6 +1,5 @@ name: PDPC full_name: 1-palmitoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine - chains: sn1: length: 16 From 25d1987d98adddf15246b907ba29429aea21f710 Mon Sep 17 00:00:00 2001 From: "Avneesh.Singh" Date: Fri, 6 Feb 2026 20:17:32 +0530 Subject: [PATCH 06/24] Apply suggestion from @github-actions[bot] Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- Molecules/membrane/PDPC/metadata.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/Molecules/membrane/PDPC/metadata.yaml b/Molecules/membrane/PDPC/metadata.yaml index f7e1b99d7..847abe38e 100644 --- a/Molecules/membrane/PDPC/metadata.yaml +++ b/Molecules/membrane/PDPC/metadata.yaml @@ -16,6 +16,5 @@ reference: journal: Chemistry and Physics of Lipids year: 2020 doi: 10.1016/j.chemphyslip.2020.104892 - bioschema_properties: inChIKey: LZCLYPSVMMQWKP-UHFFFAOYSA-N From 20c3c4ef0ce59ffa0b2926e9a6dbe0b8e0a2853f Mon Sep 17 00:00:00 2001 From: "Avneesh.Singh" Date: Fri, 6 Feb 2026 20:17:40 +0530 Subject: [PATCH 07/24] Apply suggestion from @github-actions[bot] Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- Molecules/membrane/PDPC/metadata.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/Molecules/membrane/PDPC/metadata.yaml b/Molecules/membrane/PDPC/metadata.yaml index 847abe38e..74eda2b1a 100644 --- a/Molecules/membrane/PDPC/metadata.yaml +++ b/Molecules/membrane/PDPC/metadata.yaml @@ -10,7 +10,6 @@ chains: headgroup: PC lipid_class: phosphatidylcholine - reference: authors: Marquardt et al. journal: Chemistry and Physics of Lipids From 9ab8f7da692ca28fdfdd4b52cc9e52931e9480aa Mon Sep 17 00:00:00 2001 From: "Avneesh.Singh" Date: Fri, 6 Feb 2026 20:17:48 +0530 Subject: [PATCH 08/24] Apply suggestion from @github-actions[bot] Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- Molecules/membrane/PDPC/metadata.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/Molecules/membrane/PDPC/metadata.yaml b/Molecules/membrane/PDPC/metadata.yaml index 74eda2b1a..67725d12e 100644 --- a/Molecules/membrane/PDPC/metadata.yaml +++ b/Molecules/membrane/PDPC/metadata.yaml @@ -7,7 +7,6 @@ chains: sn2: length: 22 unsaturation: 6 - headgroup: PC lipid_class: phosphatidylcholine reference: From 5e229cbe11be13da2a8486ba8b3e1014fa397fb6 Mon Sep 17 00:00:00 2001 From: "Avneesh.Singh" Date: Fri, 6 Feb 2026 20:24:23 +0530 Subject: [PATCH 09/24] Update metadata.yaml --- .../j.chemphyslip.2020.104892/SDPC_ULV_30C/metadata.yaml | 7 ------- 1 file changed, 7 deletions(-) diff --git a/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/SDPC_ULV_30C/metadata.yaml b/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/SDPC_ULV_30C/metadata.yaml index fa006ab5b..f9a375fa1 100644 --- a/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/SDPC_ULV_30C/metadata.yaml +++ b/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/SDPC_ULV_30C/metadata.yaml @@ -1,29 +1,22 @@ experiment_type: SAXS observable: form_factor - lipid: SDPC vesicle_type: ULV - temperature: value: 30 unit: C - solvent: composition: H2O d2o_fraction: 0.0 - facility: name: CHESS year: 2012 - data_file: SDPC_ULV@30C_share.xff - reference: authors: Marquardt et al. journal: Chemistry and Physics of Lipids year: 2020 doi: 10.1016/j.chemphyslip.2020.104892 - notes: - X-ray scattering form factors - ULVs prepared by extrusion From 94a473cec5882f6f3593f8f2afb8e34d77d279b4 Mon Sep 17 00:00:00 2001 From: "Avneesh.Singh" Date: Fri, 6 Feb 2026 20:24:56 +0530 Subject: [PATCH 10/24] Update metadata.yaml --- .../j.chemphyslip.2020.104892/PDPC_ULV_30C/metadata.yaml | 7 ------- 1 file changed, 7 deletions(-) diff --git a/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/PDPC_ULV_30C/metadata.yaml b/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/PDPC_ULV_30C/metadata.yaml index 7b46fffbc..863952d84 100644 --- a/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/PDPC_ULV_30C/metadata.yaml +++ b/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/PDPC_ULV_30C/metadata.yaml @@ -1,29 +1,22 @@ experiment_type: SAXS observable: form_factor - lipid: PDPC vesicle_type: ULV - temperature: value: 30 unit: C - solvent: composition: H2O d2o_fraction: 0.0 - facility: name: CHESS year: 2012 - data_file: PDPC_ULV@30C_share.xff - reference: authors: Marquardt et al. journal: Chemistry and Physics of Lipids year: 2020 doi: 10.1016/j.chemphyslip.2020.104892 - notes: - X-ray scattering form factors - ULVs prepared by extrusion From d51b092e504647abe17ba35bd253c8ec7664884d Mon Sep 17 00:00:00 2001 From: Avneesh Singh Date: Sun, 8 Feb 2026 02:00:01 +0530 Subject: [PATCH 11/24] Fix XRAY experiment metadata to follow README schema --- .../PDPC_ULV_30C/README.yaml | 21 ++++++++++++++++++ .../PDPC_ULV_30C/metadata.yaml | 22 ------------------- .../SDPC_ULV_30C/README.yaml | 21 ++++++++++++++++++ .../SDPC_ULV_30C/metadata.yaml | 22 ------------------- 4 files changed, 42 insertions(+), 44 deletions(-) create mode 100644 experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/PDPC_ULV_30C/README.yaml delete mode 100644 experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/PDPC_ULV_30C/metadata.yaml create mode 100644 experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/SDPC_ULV_30C/README.yaml delete mode 100644 experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/SDPC_ULV_30C/metadata.yaml diff --git a/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/PDPC_ULV_30C/README.yaml b/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/PDPC_ULV_30C/README.yaml new file mode 100644 index 000000000..7dba22f3e --- /dev/null +++ b/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/PDPC_ULV_30C/README.yaml @@ -0,0 +1,21 @@ +ARTICLE_DOI: 10.1016/j.chemphyslip.2020.104892 + +TEMPERATURE: 303 + +MEMBRANE_COMPOSITION: + PDPC: 1.0 + +SAMPLE_PROTOCOL: > + Unilamellar vesicles prepared as described in + Marquardt et al., Chem. Phys. Lipids 229 (2020) 104892. + +XRAY: + SOURCE: CHESS synchrotron + LAMBDA: 1.0 Å + QRANGE: 0.01-0.5 Å^-1 + DETECTOR: UNKNOWN + DISTANCE: UNKNOWN + DATATYPE: batch + EXPOSURE: UNKNOWN + FRAMES: UNKNOWN + SAMPLE_TYPE: ULV diff --git a/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/PDPC_ULV_30C/metadata.yaml b/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/PDPC_ULV_30C/metadata.yaml deleted file mode 100644 index 863952d84..000000000 --- a/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/PDPC_ULV_30C/metadata.yaml +++ /dev/null @@ -1,22 +0,0 @@ -experiment_type: SAXS -observable: form_factor -lipid: PDPC -vesicle_type: ULV -temperature: - value: 30 - unit: C -solvent: - composition: H2O - d2o_fraction: 0.0 -facility: - name: CHESS - year: 2012 -data_file: PDPC_ULV@30C_share.xff -reference: - authors: Marquardt et al. - journal: Chemistry and Physics of Lipids - year: 2020 - doi: 10.1016/j.chemphyslip.2020.104892 -notes: - - X-ray scattering form factors - - ULVs prepared by extrusion diff --git a/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/SDPC_ULV_30C/README.yaml b/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/SDPC_ULV_30C/README.yaml new file mode 100644 index 000000000..e4854655f --- /dev/null +++ b/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/SDPC_ULV_30C/README.yaml @@ -0,0 +1,21 @@ +ARTICLE_DOI: 10.1016/j.chemphyslip.2020.104892 + +TEMPERATURE: 303 + +MEMBRANE_COMPOSITION: + SDPC: 1.0 + +SAMPLE_PROTOCOL: > + Unilamellar vesicles prepared as described in + Marquardt et al., Chem. Phys. Lipids 229 (2020) 104892. + +XRAY: + SOURCE: CHESS synchrotron + LAMBDA: 1.0 Å + QRANGE: 0.01-0.5 Å^-1 + DETECTOR: UNKNOWN + DISTANCE: UNKNOWN + DATATYPE: batch + EXPOSURE: UNKNOWN + FRAMES: UNKNOWN + SAMPLE_TYPE: ULV diff --git a/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/SDPC_ULV_30C/metadata.yaml b/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/SDPC_ULV_30C/metadata.yaml deleted file mode 100644 index f9a375fa1..000000000 --- a/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/SDPC_ULV_30C/metadata.yaml +++ /dev/null @@ -1,22 +0,0 @@ -experiment_type: SAXS -observable: form_factor -lipid: SDPC -vesicle_type: ULV -temperature: - value: 30 - unit: C -solvent: - composition: H2O - d2o_fraction: 0.0 -facility: - name: CHESS - year: 2012 -data_file: SDPC_ULV@30C_share.xff -reference: - authors: Marquardt et al. - journal: Chemistry and Physics of Lipids - year: 2020 - doi: 10.1016/j.chemphyslip.2020.104892 -notes: - - X-ray scattering form factors - - ULVs prepared by extrusion From 41e300547c5ed29a71449058841ba38423a8104f Mon Sep 17 00:00:00 2001 From: Avneesh Singh Date: Sun, 8 Feb 2026 10:18:52 +0530 Subject: [PATCH 12/24] Add PDPC and SDPC SAXS form factors, PDPC molecule metadata, and CHARMM mapping --- .../membrane/PDPC/mappingPDPCcharmm.yaml | 188 ++++++++++++++++++ Molecules/membrane/PDPC/metadata.yaml | 20 +- .../membrane/SDPC/mappingSDPCcharmm.yaml | 2 +- .../PDPC_ULV@30C_share.xff | 0 .../1/PDPC_ULV_30C_FormFactor.json | 1 + .../j.chemphyslip.2020.104892/1/README.yaml | 30 +++ .../j.chemphyslip.2020.104892/2/README.yaml | 29 +++ .../SDPC_ULV@30C_share.xff | 0 .../2/SDPC_ULV_30C_FormFactor.json | 1 + .../PDPC_ULV_30C/README.yaml | 21 -- .../SDPC_ULV_30C/README.yaml | 21 -- 11 files changed, 269 insertions(+), 44 deletions(-) create mode 100644 Molecules/membrane/PDPC/mappingPDPCcharmm.yaml rename experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/{PDPC_ULV_30C => 1}/PDPC_ULV@30C_share.xff (100%) create mode 100644 experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/1/PDPC_ULV_30C_FormFactor.json create mode 100644 experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/1/README.yaml create mode 100644 experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/2/README.yaml rename experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/{SDPC_ULV_30C => 2}/SDPC_ULV@30C_share.xff (100%) create mode 100644 experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/2/SDPC_ULV_30C_FormFactor.json delete mode 100644 experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/PDPC_ULV_30C/README.yaml delete mode 100644 experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/SDPC_ULV_30C/README.yaml diff --git a/Molecules/membrane/PDPC/mappingPDPCcharmm.yaml b/Molecules/membrane/PDPC/mappingPDPCcharmm.yaml new file mode 100644 index 000000000..6d1ebd612 --- /dev/null +++ b/Molecules/membrane/PDPC/mappingPDPCcharmm.yaml @@ -0,0 +1,188 @@ +M_G1_M: + ATOMNAME: C3 + FRAGMENT: glycerol backbone +M_G1H1_M: + ATOMNAME: HX + FRAGMENT: glycerol backbone +M_G1H2_M: + ATOMNAME: HY + FRAGMENT: glycerol backbone +M_G1O1_M: + ATOMNAME: O31 + FRAGMENT: glycerol backbone +# sn-1 +M_G1C2_M: + ATOMNAME: C31 + FRAGMENT: sn-1 +M_G1C2O1_M: + ATOMNAME: O32 + FRAGMENT: sn-1 +M_G1C3_M: + ATOMNAME: C32 + FRAGMENT: sn-1 +M_G1C3H1_M: + ATOMNAME: H2X + FRAGMENT: sn-1 +M_G1C3H2_M: + ATOMNAME: H2Y + FRAGMENT: sn-1 +M_G1C4_M: + ATOMNAME: C33 + FRAGMENT: sn-1 +M_G1C4H1_M: + ATOMNAME: H3X + FRAGMENT: sn-1 +M_G1C4H2_M: + ATOMNAME: H3Y + FRAGMENT: sn-1 +M_G1C5_M: + ATOMNAME: C34 + FRAGMENT: sn-1 +M_G1C5H1_M: + ATOMNAME: H4X + FRAGMENT: sn-1 +M_G1C5H2_M: + ATOMNAME: H4Y + FRAGMENT: sn-1 +M_G1C6_M: + ATOMNAME: C35 + FRAGMENT: sn-1 +M_G1C6H1_M: + ATOMNAME: H5X + FRAGMENT: sn-1 +M_G1C6H2_M: + ATOMNAME: H5Y + FRAGMENT: sn-1 +M_G1C7_M: + ATOMNAME: C36 + FRAGMENT: sn-1 +M_G1C7H1_M: + ATOMNAME: H6X + FRAGMENT: sn-1 +M_G1C7H2_M: + ATOMNAME: H6Y + FRAGMENT: sn-1 +M_G1C8_M: + ATOMNAME: C37 + FRAGMENT: sn-1 +M_G1C8H1_M: + ATOMNAME: H7X + FRAGMENT: sn-1 +M_G1C8H2_M: + ATOMNAME: H7Y + FRAGMENT: sn-1 +M_G1C9_M: + ATOMNAME: C38 + FRAGMENT: sn-1 +M_G1C9H1_M: + ATOMNAME: H8X + FRAGMENT: sn-1 +M_G1C9H2_M: + ATOMNAME: H8Y + FRAGMENT: sn-1 +M_G1C10_M: + ATOMNAME: C39 + FRAGMENT: sn-1 +M_G1C10H1_M: + ATOMNAME: H9X + FRAGMENT: sn-1 +M_G1C10H2_M: + ATOMNAME: H9Y + FRAGMENT: sn-1 +M_G1C11_M: + ATOMNAME: C310 + FRAGMENT: sn-1 +M_G1C11H1_M: + ATOMNAME: H10X + FRAGMENT: sn-1 +M_G1C11H2_M: + ATOMNAME: H10Y + FRAGMENT: sn-1 +M_G1C12_M: + ATOMNAME: C311 + FRAGMENT: sn-1 +M_G1C12H1_M: + ATOMNAME: H11X + FRAGMENT: sn-1 +M_G1C12H2_M: + ATOMNAME: H11Y + FRAGMENT: sn-1 +M_G1C13_M: + ATOMNAME: C312 + FRAGMENT: sn-1 +M_G1C13H1_M: + ATOMNAME: H12X + FRAGMENT: sn-1 +M_G1C13H2_M: + ATOMNAME: H12Y + FRAGMENT: sn-1 +M_G1C14_M: + ATOMNAME: C313 + FRAGMENT: sn-1 +M_G1C14H1_M: + ATOMNAME: H13X + FRAGMENT: sn-1 +M_G1C14H2_M: + ATOMNAME: H13Y + FRAGMENT: sn-1 +M_G1C15_M: + ATOMNAME: C314 + FRAGMENT: sn-1 +M_G1C15H1_M: + ATOMNAME: H14X + FRAGMENT: sn-1 +M_G1C15H2_M: + ATOMNAME: H14Y + FRAGMENT: sn-1 +M_G1C16_M: + ATOMNAME: C315 + FRAGMENT: sn-1 +M_G1C16H1_M: + ATOMNAME: H15X + FRAGMENT: sn-1 +M_G1C16H2_M: + ATOMNAME: H15Y + FRAGMENT: sn-1 +M_G1C17_M: + ATOMNAME: C316 + FRAGMENT: sn-1 +M_G1C17H1_M: + ATOMNAME: H16X + FRAGMENT: sn-1 +M_G1C17H2_M: + ATOMNAME: H16Y + FRAGMENT: sn-1 +# sn-2 +M_G3P2_M: + ATOMNAME: P + FRAGMENT: headgroup +M_G3P2O1_M: + ATOMNAME: O14 + FRAGMENT: headgroup +M_G3P2O2_M: + ATOMNAME: O13 + FRAGMENT: headgroup +M_G3O3_M: + ATOMNAME: O12 + FRAGMENT: headgroup +M_G3C4_M: + ATOMNAME: C11 + FRAGMENT: headgroup +M_G3C4H1_M: + ATOMNAME: H11A + FRAGMENT: headgroup +M_G3C4H2_M: + ATOMNAME: H11B + FRAGMENT: headgroup +M_G3C5_M: + ATOMNAME: C12 + FRAGMENT: headgroup +M_G3C5H1_M: + ATOMNAME: H12A + FRAGMENT: headgroup +M_G3C5H2_M: + ATOMNAME: H12B + FRAGMENT: headgroup +M_G3N6_M: + ATOMNAME: N + FRAGMENT: headgroup diff --git a/Molecules/membrane/PDPC/metadata.yaml b/Molecules/membrane/PDPC/metadata.yaml index 67725d12e..462808ad8 100644 --- a/Molecules/membrane/PDPC/metadata.yaml +++ b/Molecules/membrane/PDPC/metadata.yaml @@ -14,5 +14,23 @@ reference: journal: Chemistry and Physics of Lipids year: 2020 doi: 10.1016/j.chemphyslip.2020.104892 +NMRlipids: + id: PDPC + name: 1-palmitoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine + charge: 0 +sameAs: + ChEBI: CHEBI:84928 + pubchem.compound: 10134146 + lipidmaps: LMGP01010535 bioschema_properties: - inChIKey: LZCLYPSVMMQWKP-UHFFFAOYSA-N + iupacName: "[(2R)-2-[(4Z,7Z,10Z,13Z,16Z,19Z)-docosa-4,7,10,13,16,19-hexaenoyl]oxy-3-hexadecanoyloxypropyl] 2-(trimethylazaniumyl)ethyl phosphate" + smiles: 'CCCCCCCCCCCCCCCC(=O)O[C@H](CO[P@](=O)([O-])OCC[N+](C)(C)C)COC(=O)CCCC/C=C\\C=C/C=C\\C=C/C=C\\C=C/CC' + inChI: InChI=1S/C48H84NO8P/c1-6-8-10-12-14-16-18-20-22-24-26-28-30-32-34-36-38-40-42-44-46-48(50)56-43-41-58-59(53,54)57-39-37-35-33-31-29-27-25-23-21-19-17-15-13-11-9-7-2/h8,10,12,14,16,18,20,22,24,26,28,30,32,34,36,38H,6-7,9,11,13,15,17,19,21,23,25,27,29,31,33,35,37,39-44H2,1-5H3,(H,53,54) + inChIKey: XMUJYVYVJAGKIS-UHFFFAOYSA-N + molecularFormula: C48H84NO8P + molecularWeight: 806.1 + name: 1-palmitoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine + image: https://pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?cid=10134146&t=l + alternateName: + - PC(16:0/22:6) + - PDPC diff --git a/Molecules/membrane/SDPC/mappingSDPCcharmm.yaml b/Molecules/membrane/SDPC/mappingSDPCcharmm.yaml index 89460d62e..22c64f3e0 100644 --- a/Molecules/membrane/SDPC/mappingSDPCcharmm.yaml +++ b/Molecules/membrane/SDPC/mappingSDPCcharmm.yaml @@ -444,4 +444,4 @@ M_G3N6C3H2_M: FRAGMENT: headgroup M_G3N6C3H3_M: ATOMNAME: H15C - FRAGMENT: headgroup \ No newline at end of file + FRAGMENT: headgroup diff --git a/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/PDPC_ULV_30C/PDPC_ULV@30C_share.xff b/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/1/PDPC_ULV@30C_share.xff similarity index 100% rename from experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/PDPC_ULV_30C/PDPC_ULV@30C_share.xff rename to experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/1/PDPC_ULV@30C_share.xff diff --git a/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/1/PDPC_ULV_30C_FormFactor.json b/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/1/PDPC_ULV_30C_FormFactor.json new file mode 100644 index 000000000..2d527787d --- /dev/null +++ b/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/1/PDPC_ULV_30C_FormFactor.json @@ -0,0 +1 @@ +[[0.07, 0.4394, 0.035], [0.071, 0.4511, 0.035], [0.072, 0.4672, 0.035], [0.073, 0.4813, 0.035], [0.074, 0.4966, 0.035], [0.075, 0.5142, 0.035], [0.076, 0.5311, 0.035], [0.077, 0.547, 0.035], [0.078, 0.5598, 0.035], [0.079, 0.5783, 0.035], [0.08, 0.5959, 0.035], [0.081, 0.6104, 0.035], [0.082, 0.6272, 0.035], [0.083, 0.6448, 0.035], [0.084, 0.6619, 0.035], [0.085, 0.6784, 0.035], [0.086, 0.6952, 0.035], [0.087, 0.7113, 0.035], [0.088, 0.7259, 0.035], [0.089, 0.7431, 0.035], [0.09, 0.7608, 0.035], [0.091, 0.7766, 0.035], [0.092, 0.7936, 0.035], [0.093, 0.8099, 0.035], [0.094, 0.8261, 0.035], [0.095, 0.8452, 0.035], [0.096, 0.8616, 0.035], [0.097, 0.8777, 0.035], [0.098, 0.894, 0.035], [0.099, 0.9111, 0.035], [0.1, 0.9283, 0.035], [0.101, 0.9451, 0.035], [0.102, 0.9607, 0.035], [0.103, 0.9779, 0.035], [0.104, 0.9934, 0.035], [0.105, 1.007, 0.035], [0.106, 1.023, 0.035], [0.107, 1.039, 0.035], [0.108, 1.057, 0.035], [0.109, 1.075, 0.035], [0.11, 1.09, 0.035], [0.111, 1.104, 0.035], [0.112, 1.118, 0.035], [0.113, 1.134, 0.035], [0.114, 1.148, 0.035], [0.115, 1.164, 0.035], [0.116, 1.177, 0.035], [0.117, 1.193, 0.035], [0.118, 1.21, 0.035], [0.119, 1.225, 0.035], [0.12, 1.238, 0.035], [0.121, 1.25, 0.035], [0.122, 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+MEMBRANE_COMPOSITION: + PDPC: 1 +SOLUTION_COMPOSITION: + H2O: 1.0 # SAXS measurements + D2O: VARIABLE # 100%, 75%, 50% for SANS contrasts +TOTAL_HYDRATION: "full hydration" +REAGENT_SOURCES: + PDPC: Avanti Polar Lipids + H2O: High-Q purification system + D2O: Cambridge Isotopes +SAMPLE_PROTOCOL: > + PDPC films were prepared from chloroform stock solutions, dried under Ar gas + with gentle heating and further dried in vacuo for at least 4 h. + Samples were hydrated using 7 freeze–thaw–vortex cycles with ultrapure H2O + (for SAXS) or 100% D2O (for SANS). + Vesicles were extruded through 50 nm polycarbonate filters to produce ULVs. + Lipid concentration was approximately 12 mg/ml. + All preparations were performed under an Ar atmosphere (O2 < 2%) to minimize oxidation. +XRAY: + SOURCE: CHESS G-1 station + LAMBDA: 1.18 # Å + BEAMSIZE: 0.24 x 0.24 mm + DETECTOR: FLICAM CCD camera + PIXEL_SIZE: 71 x 71 µm + DISTANCE: 0.4236 # m + SAMPLE_CONTAINER: 1 mm quartz capillary + DATATYPE: ULV + SAMPLE_TYPE: ULV diff --git a/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/2/README.yaml b/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/2/README.yaml new file mode 100644 index 000000000..fd6000e69 --- /dev/null +++ b/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/2/README.yaml @@ -0,0 +1,29 @@ +DOI: 10.1016/j.chemphyslip.2020.104892 +TEMPERATURE: 303 K # K (30 °C) +MEMBRANE_COMPOSITION: + SDPC: 1 +SOLUTION_COMPOSITION: + H2O: 1.0 + D2O: VARIABLE # for neutron contrast variation +TOTAL_HYDRATION: "full hydration" +REAGENT_SOURCES: + SDPC: Avanti Polar Lipids + H2O: High-Q purification system + D2O: Cambridge Isotopes +SAMPLE_PROTOCOL: > + SDPC lipid films were prepared from chloroform stock solutions and dried + under Ar gas with gentle heating, followed by vacuum drying for at least 4 h. + Samples were hydrated with ultrapure H2O or D2O using repeated freeze–thaw cycles. + Vesicles were extruded through 50 nm polycarbonate membranes to form ULVs. + Final lipid concentration was approximately 12 mg/ml. + All handling was performed under an Ar atmosphere to limit lipid oxidation. +XRAY: + SOURCE: CHESS G-1 station + LAMBDA: 1.18 # Å + BEAMSIZE: 0.24 x 0.24 mm + DETECTOR: FLICAM CCD camera + PIXEL_SIZE: 71 x 71 µm + DISTANCE: 0.4236 # m + SAMPLE_CONTAINER: 1 mm quartz capillary + DATATYPE: ULV + SAMPLE_TYPE: ULV diff --git a/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/SDPC_ULV_30C/SDPC_ULV@30C_share.xff b/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/2/SDPC_ULV@30C_share.xff similarity index 100% rename from experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/SDPC_ULV_30C/SDPC_ULV@30C_share.xff rename to experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/2/SDPC_ULV@30C_share.xff diff --git a/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/2/SDPC_ULV_30C_FormFactor.json b/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/2/SDPC_ULV_30C_FormFactor.json new file mode 100644 index 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[0.808, -0.32646, 0.25], [0.809, -0.36671, 0.25], [0.81, -0.41256, 0.25], [0.811, -0.42668, 0.25], [0.812, -0.32586, 0.25], [0.813, -0.41041, 0.25], [0.814, -0.39403, 0.25], [0.815, -0.439, 0.25], [0.816, -0.16106, 0.25], [0.817, -0.43529, 0.25], [0.818, -0.40713, 0.25], [0.819, -0.63064, 0.25], [0.82, -0.39601, 0.25]] \ No newline at end of file diff --git a/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/PDPC_ULV_30C/README.yaml b/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/PDPC_ULV_30C/README.yaml deleted file mode 100644 index 7dba22f3e..000000000 --- a/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/PDPC_ULV_30C/README.yaml +++ /dev/null @@ -1,21 +0,0 @@ -ARTICLE_DOI: 10.1016/j.chemphyslip.2020.104892 - -TEMPERATURE: 303 - -MEMBRANE_COMPOSITION: - PDPC: 1.0 - -SAMPLE_PROTOCOL: > - Unilamellar vesicles prepared as described in - Marquardt et al., Chem. Phys. Lipids 229 (2020) 104892. - -XRAY: - SOURCE: CHESS synchrotron - LAMBDA: 1.0 Å - QRANGE: 0.01-0.5 Å^-1 - DETECTOR: UNKNOWN - DISTANCE: UNKNOWN - DATATYPE: batch - EXPOSURE: UNKNOWN - FRAMES: UNKNOWN - SAMPLE_TYPE: ULV diff --git a/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/SDPC_ULV_30C/README.yaml b/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/SDPC_ULV_30C/README.yaml deleted file mode 100644 index e4854655f..000000000 --- a/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/SDPC_ULV_30C/README.yaml +++ /dev/null @@ -1,21 +0,0 @@ -ARTICLE_DOI: 10.1016/j.chemphyslip.2020.104892 - -TEMPERATURE: 303 - -MEMBRANE_COMPOSITION: - SDPC: 1.0 - -SAMPLE_PROTOCOL: > - Unilamellar vesicles prepared as described in - Marquardt et al., Chem. Phys. Lipids 229 (2020) 104892. - -XRAY: - SOURCE: CHESS synchrotron - LAMBDA: 1.0 Å - QRANGE: 0.01-0.5 Å^-1 - DETECTOR: UNKNOWN - DISTANCE: UNKNOWN - DATATYPE: batch - EXPOSURE: UNKNOWN - FRAMES: UNKNOWN - SAMPLE_TYPE: ULV From b26248b699d8fec710638536aa6783cb3226a36e Mon Sep 17 00:00:00 2001 From: Avneesh Singh Date: Sun, 8 Feb 2026 10:39:18 +0530 Subject: [PATCH 13/24] Revert SDPC molecule files to upstream version --- Molecules/membrane/SDPC/mappingSDPCcharmm.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Molecules/membrane/SDPC/mappingSDPCcharmm.yaml b/Molecules/membrane/SDPC/mappingSDPCcharmm.yaml index 22c64f3e0..89460d62e 100644 --- a/Molecules/membrane/SDPC/mappingSDPCcharmm.yaml +++ b/Molecules/membrane/SDPC/mappingSDPCcharmm.yaml @@ -444,4 +444,4 @@ M_G3N6C3H2_M: FRAGMENT: headgroup M_G3N6C3H3_M: ATOMNAME: H15C - FRAGMENT: headgroup + FRAGMENT: headgroup \ No newline at end of file From 71609f5fb4ab090b4de203907f5de12a7160d2bf Mon Sep 17 00:00:00 2001 From: Avneesh Singh Date: Sun, 8 Feb 2026 11:09:01 +0530 Subject: [PATCH 14/24] Fix PDPC molecule metadata (iupac, smiles, weight) --- Molecules/membrane/PDPC/metadata.yaml | 33 +++++++++++---------------- 1 file changed, 13 insertions(+), 20 deletions(-) diff --git a/Molecules/membrane/PDPC/metadata.yaml b/Molecules/membrane/PDPC/metadata.yaml index 462808ad8..af6311724 100644 --- a/Molecules/membrane/PDPC/metadata.yaml +++ b/Molecules/membrane/PDPC/metadata.yaml @@ -1,19 +1,3 @@ -name: PDPC -full_name: 1-palmitoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine -chains: - sn1: - length: 16 - unsaturation: 0 - sn2: - length: 22 - unsaturation: 6 -headgroup: PC -lipid_class: phosphatidylcholine -reference: - authors: Marquardt et al. - journal: Chemistry and Physics of Lipids - year: 2020 - doi: 10.1016/j.chemphyslip.2020.104892 NMRlipids: id: PDPC name: 1-palmitoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine @@ -23,12 +7,21 @@ sameAs: pubchem.compound: 10134146 lipidmaps: LMGP01010535 bioschema_properties: - iupacName: "[(2R)-2-[(4Z,7Z,10Z,13Z,16Z,19Z)-docosa-4,7,10,13,16,19-hexaenoyl]oxy-3-hexadecanoyloxypropyl] 2-(trimethylazaniumyl)ethyl phosphate" - smiles: 'CCCCCCCCCCCCCCCC(=O)O[C@H](CO[P@](=O)([O-])OCC[N+](C)(C)C)COC(=O)CCCC/C=C\\C=C/C=C\\C=C/C=C\\C=C/CC' - inChI: InChI=1S/C48H84NO8P/c1-6-8-10-12-14-16-18-20-22-24-26-28-30-32-34-36-38-40-42-44-46-48(50)56-43-41-58-59(53,54)57-39-37-35-33-31-29-27-25-23-21-19-17-15-13-11-9-7-2/h8,10,12,14,16,18,20,22,24,26,28,30,32,34,36,38H,6-7,9,11,13,15,17,19,21,23,25,27,29,31,33,35,37,39-44H2,1-5H3,(H,53,54) + iupacName: > + [(2R)-2-[(4Z,7Z,10Z,13Z,16Z,19Z)-docosa-4,7,10,13,16,19-hexaenoyl]oxy-3- + hexadecanoyloxypropyl] 2-(trimethylazaniumyl)ethyl phosphate + smiles: > + CCCCCCCCCCCCCCCC(=O)O[C@H](CO[P@](=O)([O-])OCC[N+](C)(C)C) + COC(=O)CCC/C=C\C/C=C\C/C=C\C/C=C\C/C=C\C/C=C\CC + inChI: > + InChI=1S/C48H84NO8P/c1-6-8-10-12-14-16-18-20-22-24-26-28-30-32-34-36-38- + 40-42-48(51)57-46(45-56-58(52,53)55-43-41-49(3,4)5)44-54-47(50)39-37- + 35-33-31-29-27-25-23-21-19-17-15-13-11-9-7-2/h8,10,12,14,16,18,20,22, + 24,26,28,30,32,34,36,46H,6-7,9,11,13,15,17,19,21,23,25,27,29,31,33,35, + 37-45H2,1-5H3/b10-8-,14-12-,18-16-,22-20-,26-24-,30-28-/t46-/m1/s1 inChIKey: XMUJYVYVJAGKIS-UHFFFAOYSA-N molecularFormula: C48H84NO8P - molecularWeight: 806.1 + molecularWeight: 834.2 name: 1-palmitoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine image: https://pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?cid=10134146&t=l alternateName: From b43ad90700a9b8ff6393548a53da542decf06eb9 Mon Sep 17 00:00:00 2001 From: Avneesh Singh Date: Sun, 8 Feb 2026 17:42:36 +0530 Subject: [PATCH 15/24] Fix SAXS README metadata and PDPC molecule metadata --- .../j.chemphyslip.2020.104892/1/README.yaml | 31 +++---------------- .../j.chemphyslip.2020.104892/2/README.yaml | 28 ++--------------- 2 files changed, 7 insertions(+), 52 deletions(-) diff --git a/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/1/README.yaml b/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/1/README.yaml index 04721899c..6b36eaa8d 100644 --- a/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/1/README.yaml +++ b/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/1/README.yaml @@ -1,30 +1,7 @@ -DOI: 10.1016/j.chemphyslip.2020.104892 -TEMPERATURE: 303 K # K (30 °C) +ARTICLE_DOI: 10.1016/j.chemphyslip.2020.104892 +TEMPERATURE: 303 # K (30 °C) MEMBRANE_COMPOSITION: PDPC: 1 SOLUTION_COMPOSITION: - H2O: 1.0 # SAXS measurements - D2O: VARIABLE # 100%, 75%, 50% for SANS contrasts -TOTAL_HYDRATION: "full hydration" -REAGENT_SOURCES: - PDPC: Avanti Polar Lipids - H2O: High-Q purification system - D2O: Cambridge Isotopes -SAMPLE_PROTOCOL: > - PDPC films were prepared from chloroform stock solutions, dried under Ar gas - with gentle heating and further dried in vacuo for at least 4 h. - Samples were hydrated using 7 freeze–thaw–vortex cycles with ultrapure H2O - (for SAXS) or 100% D2O (for SANS). - Vesicles were extruded through 50 nm polycarbonate filters to produce ULVs. - Lipid concentration was approximately 12 mg/ml. - All preparations were performed under an Ar atmosphere (O2 < 2%) to minimize oxidation. -XRAY: - SOURCE: CHESS G-1 station - LAMBDA: 1.18 # Å - BEAMSIZE: 0.24 x 0.24 mm - DETECTOR: FLICAM CCD camera - PIXEL_SIZE: 71 x 71 µm - DISTANCE: 0.4236 # m - SAMPLE_CONTAINER: 1 mm quartz capillary - DATATYPE: ULV - SAMPLE_TYPE: ULV + H2O: 1.0 +TOTAL_HYDRATION: 99 diff --git a/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/2/README.yaml b/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/2/README.yaml index fd6000e69..78e0e53b8 100644 --- a/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/2/README.yaml +++ b/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/2/README.yaml @@ -1,29 +1,7 @@ -DOI: 10.1016/j.chemphyslip.2020.104892 -TEMPERATURE: 303 K # K (30 °C) +ARTICLE_DOI: 10.1016/j.chemphyslip.2020.104892 +TEMPERATURE: 303 # K (30 °C) MEMBRANE_COMPOSITION: SDPC: 1 SOLUTION_COMPOSITION: H2O: 1.0 - D2O: VARIABLE # for neutron contrast variation -TOTAL_HYDRATION: "full hydration" -REAGENT_SOURCES: - SDPC: Avanti Polar Lipids - H2O: High-Q purification system - D2O: Cambridge Isotopes -SAMPLE_PROTOCOL: > - SDPC lipid films were prepared from chloroform stock solutions and dried - under Ar gas with gentle heating, followed by vacuum drying for at least 4 h. - Samples were hydrated with ultrapure H2O or D2O using repeated freeze–thaw cycles. - Vesicles were extruded through 50 nm polycarbonate membranes to form ULVs. - Final lipid concentration was approximately 12 mg/ml. - All handling was performed under an Ar atmosphere to limit lipid oxidation. -XRAY: - SOURCE: CHESS G-1 station - LAMBDA: 1.18 # Å - BEAMSIZE: 0.24 x 0.24 mm - DETECTOR: FLICAM CCD camera - PIXEL_SIZE: 71 x 71 µm - DISTANCE: 0.4236 # m - SAMPLE_CONTAINER: 1 mm quartz capillary - DATATYPE: ULV - SAMPLE_TYPE: ULV +TOTAL_HYDRATION: 99 From b0ebbc677c82eb2c4797fa9644919fea5e3c48de Mon Sep 17 00:00:00 2001 From: Avneesh Singh Date: Sun, 8 Feb 2026 17:45:58 +0530 Subject: [PATCH 16/24] Fix SAXS README metadata and PDPC molecule metadata --- Molecules/membrane/PDPC/metadata.yaml | 17 ++++------------- 1 file changed, 4 insertions(+), 13 deletions(-) diff --git a/Molecules/membrane/PDPC/metadata.yaml b/Molecules/membrane/PDPC/metadata.yaml index af6311724..d97c582df 100644 --- a/Molecules/membrane/PDPC/metadata.yaml +++ b/Molecules/membrane/PDPC/metadata.yaml @@ -7,21 +7,12 @@ sameAs: pubchem.compound: 10134146 lipidmaps: LMGP01010535 bioschema_properties: - iupacName: > - [(2R)-2-[(4Z,7Z,10Z,13Z,16Z,19Z)-docosa-4,7,10,13,16,19-hexaenoyl]oxy-3- - hexadecanoyloxypropyl] 2-(trimethylazaniumyl)ethyl phosphate - smiles: > - CCCCCCCCCCCCCCCC(=O)O[C@H](CO[P@](=O)([O-])OCC[N+](C)(C)C) - COC(=O)CCC/C=C\C/C=C\C/C=C\C/C=C\C/C=C\C/C=C\CC - inChI: > - InChI=1S/C48H84NO8P/c1-6-8-10-12-14-16-18-20-22-24-26-28-30-32-34-36-38- - 40-42-48(51)57-46(45-56-58(52,53)55-43-41-49(3,4)5)44-54-47(50)39-37- - 35-33-31-29-27-25-23-21-19-17-15-13-11-9-7-2/h8,10,12,14,16,18,20,22, - 24,26,28,30,32,34,36,46H,6-7,9,11,13,15,17,19,21,23,25,27,29,31,33,35, - 37-45H2,1-5H3/b10-8-,14-12-,18-16-,22-20-,26-24-,30-28-/t46-/m1/s1 + iupacName: "[(2R)-2-[(4Z,7Z,10Z,13Z,16Z,19Z)-docosa-4,7,10,13,16,19-hexaenoyl]oxy-3-hexadecanoyloxypropyl] 2-(trimethylazaniumyl)ethyl phosphate" + smiles: 'CCCCCCCCCCCCCCCC(=O)O[C@H](CO[P@](=O)([O-])OCC[N+](C)(C)C)COC(=O)CCCC/C=C\\C=C/C=C\\C=C/C=C\\C=C/CC' + inChI: InChI=1S/C48H84NO8P/c1-6-8-10-12-14-16-18-20-22-24-26-28-30-32-34-36-38-40-42-44-46-48(50)56-43-41-58-59(53,54)57-39-37-35-33-31-29-27-25-23-21-19-17-15-13-11-9-7-2/h8,10,12,14,16,18,20,22,24,26,28,30,32,34,36,38H,6-7,9,11,13,15,17,19,21,23,25,27,29,31,33,35,37,39-44H2,1-5H3,(H,53,54) inChIKey: XMUJYVYVJAGKIS-UHFFFAOYSA-N molecularFormula: C48H84NO8P - molecularWeight: 834.2 + molecularWeight: 806.1 name: 1-palmitoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine image: https://pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?cid=10134146&t=l alternateName: From bd1eaf047f7b63c8b1863d756f3aef76977e05b4 Mon Sep 17 00:00:00 2001 From: "Avneesh.Singh" Date: Sun, 8 Feb 2026 18:00:01 +0530 Subject: [PATCH 17/24] Apply suggestion from @github-actions[bot] Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- Molecules/membrane/PDPC/metadata.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Molecules/membrane/PDPC/metadata.yaml b/Molecules/membrane/PDPC/metadata.yaml index d97c582df..42d97ad62 100644 --- a/Molecules/membrane/PDPC/metadata.yaml +++ b/Molecules/membrane/PDPC/metadata.yaml @@ -16,5 +16,5 @@ bioschema_properties: name: 1-palmitoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine image: https://pubchem.ncbi.nlm.nih.gov/image/imgsrv.fcgi?cid=10134146&t=l alternateName: - - PC(16:0/22:6) - - PDPC + - PC(16:0/22:6) + - PDPC From 0a90861e7978df5789236c018c76847ebaf1bb1b Mon Sep 17 00:00:00 2001 From: "Avneesh.Singh" Date: Sun, 8 Feb 2026 18:00:12 +0530 Subject: [PATCH 18/24] Apply suggestion from @github-actions[bot] Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- Molecules/membrane/PDPC/metadata.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/Molecules/membrane/PDPC/metadata.yaml b/Molecules/membrane/PDPC/metadata.yaml index 42d97ad62..6d8b6edcb 100644 --- a/Molecules/membrane/PDPC/metadata.yaml +++ b/Molecules/membrane/PDPC/metadata.yaml @@ -7,8 +7,9 @@ sameAs: pubchem.compound: 10134146 lipidmaps: LMGP01010535 bioschema_properties: - iupacName: "[(2R)-2-[(4Z,7Z,10Z,13Z,16Z,19Z)-docosa-4,7,10,13,16,19-hexaenoyl]oxy-3-hexadecanoyloxypropyl] 2-(trimethylazaniumyl)ethyl phosphate" - smiles: 'CCCCCCCCCCCCCCCC(=O)O[C@H](CO[P@](=O)([O-])OCC[N+](C)(C)C)COC(=O)CCCC/C=C\\C=C/C=C\\C=C/C=C\\C=C/CC' + iupacName: '[(2R)-2-[(4Z,7Z,10Z,13Z,16Z,19Z)-docosa-4,7,10,13,16,19-hexaenoyl]oxy-3-hexadecanoyloxypropyl] + 2-(trimethylazaniumyl)ethyl phosphate' + smiles: CCCCCCCCCCCCCCCC(=O)O[C@H](CO[P@](=O)([O-])OCC[N+](C)(C)C)COC(=O)CCCC/C=C\\C=C/C=C\\C=C/C=C\\C=C/CC inChI: InChI=1S/C48H84NO8P/c1-6-8-10-12-14-16-18-20-22-24-26-28-30-32-34-36-38-40-42-44-46-48(50)56-43-41-58-59(53,54)57-39-37-35-33-31-29-27-25-23-21-19-17-15-13-11-9-7-2/h8,10,12,14,16,18,20,22,24,26,28,30,32,34,36,38H,6-7,9,11,13,15,17,19,21,23,25,27,29,31,33,35,37,39-44H2,1-5H3,(H,53,54) inChIKey: XMUJYVYVJAGKIS-UHFFFAOYSA-N molecularFormula: C48H84NO8P From cf734a34cd3e8e44ccbd326eac8d5903adc99f88 Mon Sep 17 00:00:00 2001 From: Avneesh Singh Date: Sun, 8 Feb 2026 21:31:03 +0530 Subject: [PATCH 19/24] Updated README.yaml files for PDPC ULV SAXS experiment --- .../j.chemphyslip.2020.104892/1/README.yaml | 18 ++++++++++++++++- .../j.chemphyslip.2020.104892/2/README.yaml | 20 +++++++++++++++++-- 2 files changed, 35 insertions(+), 3 deletions(-) diff --git a/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/1/README.yaml b/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/1/README.yaml index 6b36eaa8d..c46b99096 100644 --- a/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/1/README.yaml +++ b/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/1/README.yaml @@ -3,5 +3,21 @@ TEMPERATURE: 303 # K (30 °C) MEMBRANE_COMPOSITION: PDPC: 1 SOLUTION_COMPOSITION: - H2O: 1.0 + H2O: 1.0 # SAXS TOTAL_HYDRATION: 99 +SAMPLE_PROTOCOL: > + PDPC films were prepared from chloroform stock solutions, dried under Ar gas + with gentle heating and further dried in vacuo for at least 4 h. + Samples were hydrated using freeze–thaw–vortex cycles with ultrapure H2O. + Vesicles were extruded through 50 nm polycarbonate filters to produce ULVs. + Lipid concentration was approximately 12 mg/ml. + All preparations were performed under an Ar atmosphere (O2 < 2%) to minimize oxidation. +XRAY: + SOURCE: CHESS G-1 station + LAMBDA: 1.18 # Å + BEAMSIZE: 0.24 x 0.24 mm + DETECTOR: FLICAM CCD camera + PIXEL_SIZE: 71 x 71 µm + DISTANCE: 0.4236 # m + DATATYPE: ULV + SAMPLE_TYPE: ULV diff --git a/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/2/README.yaml b/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/2/README.yaml index 78e0e53b8..2bbd59ece 100644 --- a/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/2/README.yaml +++ b/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/2/README.yaml @@ -1,7 +1,23 @@ ARTICLE_DOI: 10.1016/j.chemphyslip.2020.104892 -TEMPERATURE: 303 # K (30 °C) +TEMPERATURE: 303 # K MEMBRANE_COMPOSITION: SDPC: 1 SOLUTION_COMPOSITION: - H2O: 1.0 + H2O: 1.0 # SAXS TOTAL_HYDRATION: 99 +SAMPLE_PROTOCOL: > + SDPC lipid films were prepared from chloroform stock solutions and dried + under Ar gas with gentle heating, followed by vacuum drying for at least 4 h. + Samples were hydrated with ultrapure H2O or D2O using repeated freeze–thaw cycles. + Vesicles were extruded through 50 nm polycarbonate membranes to form ULVs. + Final lipid concentration was approximately 12 mg/ml. + All handling was performed under an Ar atmosphere to limit lipid oxidation. +XRAY: + SOURCE: CHESS G-1 station + LAMBDA: 1.18 # Å + BEAMSIZE: 0.24 x 0.24 mm + DETECTOR: FLICAM CCD camera + PIXEL_SIZE: 71 x 71 µm + DISTANCE: 0.4236 # m + DATATYPE: ULV + SAMPLE_TYPE: ULV From 815962a4fab56dabb364146033a3542718169faf Mon Sep 17 00:00:00 2001 From: Avneesh Singh Date: Sun, 8 Feb 2026 21:40:38 +0530 Subject: [PATCH 20/24] Updated README.yaml files for PDPC ULV SAXS experiment --- .../10.1016/j.chemphyslip.2020.104892/1/README.yaml | 3 +++ .../10.1016/j.chemphyslip.2020.104892/2/README.yaml | 3 +++ 2 files changed, 6 insertions(+) diff --git a/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/1/README.yaml b/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/1/README.yaml index c46b99096..8a46ade97 100644 --- a/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/1/README.yaml +++ b/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/1/README.yaml @@ -5,6 +5,9 @@ MEMBRANE_COMPOSITION: SOLUTION_COMPOSITION: H2O: 1.0 # SAXS TOTAL_HYDRATION: 99 +REAGENT_SOURCES: + PDPC: Avanti Polar Lipids + H2O: High-Q purification system SAMPLE_PROTOCOL: > PDPC films were prepared from chloroform stock solutions, dried under Ar gas with gentle heating and further dried in vacuo for at least 4 h. diff --git a/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/2/README.yaml b/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/2/README.yaml index 2bbd59ece..56cd7028d 100644 --- a/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/2/README.yaml +++ b/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/2/README.yaml @@ -5,6 +5,9 @@ MEMBRANE_COMPOSITION: SOLUTION_COMPOSITION: H2O: 1.0 # SAXS TOTAL_HYDRATION: 99 +REAGENT_SOURCES: + SDPC: Avanti Polar Lipids + H2O: High-Q purification system SAMPLE_PROTOCOL: > SDPC lipid films were prepared from chloroform stock solutions and dried under Ar gas with gentle heating, followed by vacuum drying for at least 4 h. From a6cedd52bb89e4e3c865f7b925a36f9191a209ce Mon Sep 17 00:00:00 2001 From: "Avneesh.Singh" Date: Sun, 8 Feb 2026 22:02:44 +0530 Subject: [PATCH 21/24] Update README.yaml --- .../FormFactors/10.1016/j.chemphyslip.2020.104892/1/README.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/1/README.yaml b/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/1/README.yaml index 8a46ade97..710a52451 100644 --- a/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/1/README.yaml +++ b/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/1/README.yaml @@ -22,5 +22,6 @@ XRAY: DETECTOR: FLICAM CCD camera PIXEL_SIZE: 71 x 71 µm DISTANCE: 0.4236 # m + SAMPLE_CONTAINER: 1 mm quartz capillary DATATYPE: ULV SAMPLE_TYPE: ULV From daf22055d21af2a831af47bedbdd3a58d2d118b1 Mon Sep 17 00:00:00 2001 From: "Avneesh.Singh" Date: Sun, 8 Feb 2026 22:03:59 +0530 Subject: [PATCH 22/24] Update README.yaml --- .../FormFactors/10.1016/j.chemphyslip.2020.104892/2/README.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/2/README.yaml b/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/2/README.yaml index 56cd7028d..31d73443a 100644 --- a/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/2/README.yaml +++ b/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/2/README.yaml @@ -22,5 +22,6 @@ XRAY: DETECTOR: FLICAM CCD camera PIXEL_SIZE: 71 x 71 µm DISTANCE: 0.4236 # m + SAMPLE_CONTAINER: 1 mm quartz capillary DATATYPE: ULV SAMPLE_TYPE: ULV From 690ac724751a3a1e1926c50e74e4e6e0d163840d Mon Sep 17 00:00:00 2001 From: Alexey Nesterenko Date: Sun, 8 Feb 2026 21:13:24 +0100 Subject: [PATCH 23/24] Change sample type to SUV and add outdated fields Updated sample type from ULV to SUV and added outdated fields for molar fractions and ion concentrations. --- .../10.1016/j.chemphyslip.2020.104892/1/README.yaml | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/1/README.yaml b/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/1/README.yaml index 710a52451..39221ae00 100644 --- a/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/1/README.yaml +++ b/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/1/README.yaml @@ -3,7 +3,6 @@ TEMPERATURE: 303 # K (30 °C) MEMBRANE_COMPOSITION: PDPC: 1 SOLUTION_COMPOSITION: - H2O: 1.0 # SAXS TOTAL_HYDRATION: 99 REAGENT_SOURCES: PDPC: Avanti Polar Lipids @@ -23,5 +22,13 @@ XRAY: PIXEL_SIZE: 71 x 71 µm DISTANCE: 0.4236 # m SAMPLE_CONTAINER: 1 mm quartz capillary - DATATYPE: ULV - SAMPLE_TYPE: ULV + SAMPLE_TYPE: SUV +# Outdated fields +MOLAR_FRACTIONS: + PDPC: 1 +ION_CONCENTRATIONS: + POT: 0 + SOD: 0 + CLA: 0 + CAL: 0 +TOTAL_LIPID_CONCENTRATION: "full hydration" From b3d8124213736a6dad7e470e85a4e1fbef332edc Mon Sep 17 00:00:00 2001 From: Alexey Nesterenko Date: Sun, 8 Feb 2026 21:14:20 +0100 Subject: [PATCH 24/24] Change sample type to SUV and add outdated fields Updated sample type from ULV to SUV and added outdated fields for molar fractions and ion concentrations. --- .../10.1016/j.chemphyslip.2020.104892/2/README.yaml | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/2/README.yaml b/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/2/README.yaml index 31d73443a..f01aed973 100644 --- a/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/2/README.yaml +++ b/experiments/FormFactors/10.1016/j.chemphyslip.2020.104892/2/README.yaml @@ -3,7 +3,6 @@ TEMPERATURE: 303 # K MEMBRANE_COMPOSITION: SDPC: 1 SOLUTION_COMPOSITION: - H2O: 1.0 # SAXS TOTAL_HYDRATION: 99 REAGENT_SOURCES: SDPC: Avanti Polar Lipids @@ -23,5 +22,13 @@ XRAY: PIXEL_SIZE: 71 x 71 µm DISTANCE: 0.4236 # m SAMPLE_CONTAINER: 1 mm quartz capillary - DATATYPE: ULV - SAMPLE_TYPE: ULV + SAMPLE_TYPE: SUV +# Outdated fields +MOLAR_FRACTIONS: + SDPC: 1 +ION_CONCENTRATIONS: + POT: 0 + SOD: 0 + CLA: 0 + CAL: 0 +TOTAL_LIPID_CONCENTRATION: "full hydration"