Add PDPC lipid and ULV SAXS form-factor experiments (Marquardt et al.…#283
Add PDPC lipid and ULV SAXS form-factor experiments (Marquardt et al.…#283comcon1 merged 24 commits intoNMRLipids:mainfrom
Conversation
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
There was a problem hiding this comment.
Metadata should be filled by template. We have a documentation piece about it:
https://nmrlipids.github.io/FAIRMD_lipids/stable/contrib/addingMolecule.html
please read it. And please check the template. You can also read metadata files of other lipids.
Note that you may not fill "image" and "alternative names" - they will be filled automatically.
| facility: | ||
| name: CHESS | ||
| year: 2012 | ||
| data_file: PDPC_ULV@30C_share.xff |
There was a problem hiding this comment.
data file should be converted to json. We have small convertors directly in BilayerData/experiments/
There was a problem hiding this comment.
Metadata format is wrong. Please read this documentation piece:
https://nmrlipids.github.io/FAIRMD_lipids/stable/contrib/addingExpData.html
and especially this:
https://nmrlipids.github.io/FAIRMD_lipids/stable/schemas/experiment_metadata.html#readmeexp
AvNeEsH71-iam
force-pushed
the
add-pdpc-ulv-saxs
branch
from
71c57c8 to
71609f5
Compare
comcon1
left a comment
comcon1
left a comment
There was a problem hiding this comment.
Thanks. It's much better. See the rest of small things.
| PDPC: 1 | ||
| SOLUTION_COMPOSITION: | ||
| H2O: 1.0 # SAXS measurements | ||
| D2O: VARIABLE # 100%, 75%, 50% for SANS contrasts |
There was a problem hiding this comment.
This is for SAXS experiment. For SANS experiment the record should be different and we currently don't support SANS.
| SOLUTION_COMPOSITION: | ||
| H2O: 1.0 # SAXS measurements | ||
| D2O: VARIABLE # 100%, 75%, 50% for SANS contrasts | ||
| TOTAL_HYDRATION: "full hydration" |
There was a problem hiding this comment.
TOTAL_HYDRATION is water mass %. If lipid concentration is 12 mg/ml, then it is (1000-12)/1000 which is close to 99%. So there you should put 99.
("full hydration" we use for outdated fields. I will fill them in the end. We will remove outdated fields soon, but they are still with us.)
| REAGENT_SOURCES: | ||
| PDPC: Avanti Polar Lipids | ||
| H2O: High-Q purification system | ||
| D2O: Cambridge Isotopes |
| 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). |
| @@ -0,0 +1,30 @@ | |||
| DOI: 10.1016/j.chemphyslip.2020.104892 | |||
| TEMPERATURE: 303 K # K (30 °C) | |||
There was a problem hiding this comment.
remove 'K'. Should be number. Can keep in the comment.
| @@ -0,0 +1,30 @@ | |||
| DOI: 10.1016/j.chemphyslip.2020.104892 | |||
There was a problem hiding this comment.
this is ARTICLE_DOI. We don't use just DOI anymore. We use ARTICLE_DOI and DATA_DOI if the data is deposited separately.
| @@ -0,0 +1,29 @@ | |||
| DOI: 10.1016/j.chemphyslip.2020.104892 | |||
| TEMPERATURE: 303 K # K (30 °C) | |||
There was a problem hiding this comment.
Please modify the file in the same way as previous one.
AvNeEsH71-iam
force-pushed
the
add-pdpc-ulv-saxs
branch
from
aa81157 to
b0ebbc6
Compare
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
| 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 |
There was a problem hiding this comment.
Why did you remove all the metadata? I asked you to remove only stuff related to SANS (including D2O, because D2O is used only as a contrast in neutron scattering). Everything from SAXS experiment MUST be in.
There was a problem hiding this comment.
I am very sorry sir, it was an accident.
I have added back all of the data and updated both of the files.
|
I have made the above mentioned changes. I am sorry for the mistake. |
Ok. Thanx! It should be fine. The mapping file we will checked after at least one trajectory will be added. Don't worry. It's half a problem of our documentation. I will insert some outdated fields because they are still required. |
Updated sample type from ULV to SUV and added outdated fields for molar fractions and ion concentrations.
Updated sample type from ULV to SUV and added outdated fields for molar fractions and ion concentrations.
2 participants
This pull request adds new PUFA-containing lipid data and corresponding
experimental SAXS form-factor measurements to the NMRlipids/BilayerData
repository.
Added content:
The experimental data are taken from:
Marquardt et al., Chem. Phys. Lipids 229 (2020) 104892
DOI: 10.1016/j.chemphyslip.2020.104892