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comcon1comcon1
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Merge pull request #436 from comcon1/fix-other-errors-in-exps
Fix accidentally found errors in experiments
2 parents 7a339e8 + 5401703 commit 2768a14

8 files changed

Lines changed: 224 additions & 64 deletions

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‎experiments/OrderParameters/10.1021/ja029029o/1/SDPC_OrderParameters.json‎

Lines changed: 7 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -190,5 +190,11 @@
190190
],
191191
"M_G2C23_M M_G2C23H1_M": [
192192
[-0.008, 0.0017]
193+
],
194+
"M_G2C23_M M_G2C23H2_M": [
195+
[-0.008, 0.0017]
196+
],
197+
"M_G2C23_M M_G2C23H3_M": [
198+
[-0.008, 0.0017]
193199
]
194-
}
200+
}

‎experiments/OrderParameters/10.1021/ja029029o/2/SD5PC_OrderParameters.json‎

Lines changed: 1 addition & 34 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
{
22
"M_G2C3_M M_G2C3H1_M": [
3-
[-0.115, 0.023]
3+
[-0.084, 0.0168]
44
],
55
"M_G2C3_M M_G2C3H2_M": [
66
[-0.084, 0.0168]
@@ -14,15 +14,9 @@
1414
"M_G2C5_M M_G2C5H1_M": [
1515
[-0.057, 0.0114]
1616
],
17-
"M_G2C5_M M_G2C5H2_M": [
18-
[-0.215, 0.02]
19-
],
2017
"M_G2C6_M M_G2C6H1_M": [
2118
[-0.03, 0.0061]
2219
],
23-
"M_G2C6_M M_G2C6H2_M": [
24-
[-0.211, 0.02]
25-
],
2620
"M_G2C7_M M_G2C7H1_M": [
2721
[-0.013, 0.0026]
2822
],
@@ -32,15 +26,9 @@
3226
"M_G2C8_M M_G2C8H1_M": [
3327
[-0.039, 0.0078]
3428
],
35-
"M_G2C8_M M_G2C8H2_M": [
36-
[-0.202, 0.02]
37-
],
3829
"M_G2C9_M M_G2C9H1_M": [
3930
[-0.016, 0.0032]
4031
],
41-
"M_G2C9_M M_G2C9H2_M": [
42-
[-0.194, 0.02]
43-
],
4432
"M_G2C10_M M_G2C10H1_M": [
4533
[-0.013, 0.0027]
4634
],
@@ -50,15 +38,9 @@
5038
"M_G2C11_M M_G2C11H1_M": [
5139
[-0.037, 0.0075]
5240
],
53-
"M_G2C11_M M_G2C11H2_M": [
54-
[-0.176, 0.02]
55-
],
5641
"M_G2C12_M M_G2C12H1_M": [
5742
[-0.037, 0.0075]
5843
],
59-
"M_G2C12_M M_G2C12H2_M": [
60-
[-0.155, 0.02]
61-
],
6244
"M_G2C13_M M_G2C13H1_M": [
6345
[-0.013, 0.0027]
6446
],
@@ -68,15 +50,9 @@
6850
"M_G2C14_M M_G2C14H1_M": [
6951
[-0.032, 0.0063]
7052
],
71-
"M_G2C14_M M_G2C14H2_M": [
72-
[-0.122, 0.02]
73-
],
7453
"M_G2C15_M M_G2C15H1_M": [
7554
[-0.006, 0.0012]
7655
],
77-
"M_G2C15_M M_G2C15H2_M": [
78-
[-0.109, 0.02]
79-
],
8056
"M_G2C16_M M_G2C16H1_M": [
8157
[-0.013, 0.0027]
8258
],
@@ -86,24 +62,15 @@
8662
"M_G2C17_M M_G2C17H1_M": [
8763
[-0.01, 0.0021]
8864
],
89-
"M_G2C17_M M_G2C17H2_M": [
90-
[-0.077, 0.02]
91-
],
9265
"M_G2C18_M M_G2C18H1_M": [
9366
[-0.006, 0.0013]
9467
],
95-
"M_G2C18_M M_G2C18H2_M": [
96-
[-0.058, 0.02]
97-
],
9868
"M_G2C19_M M_G2C19H1_M": [
9969
[-0.028, 0.0056]
10070
],
10171
"M_G2C19_M M_G2C19H2_M": [
10272
[-0.028, 0.0056]
10373
],
104-
"M_G2C19_M M_G2C19H3_M": [
105-
[-0.017, 0.02]
106-
],
10774
"M_G2C20_M M_G2C20H1_M": [
10875
[-0.041, 0.0083]
10976
],

‎experiments/OrderParameters/10.1039/c2cp42738a/1/README.yaml‎

Lines changed: 21 additions & 19 deletions
Original file line numberDiff line numberDiff line change
@@ -1,37 +1,39 @@
11
ARTICLE_DOI: 10.1039/c2cp42738a
2-
TEMPERATURE: 298
2+
TEMPERATURE: 300
33
MEMBRANE_COMPOSITION:
4-
PAPC: 1.0
4+
POPC: 1.0
55
SOLUTION_COMPOSITION:
6-
ADDITIONAL_MOLECULES:
7-
TRIS: "20 mM"
86
TOTAL_HYDRATION: 50
9-
PH: 7.5
10-
PH_METHOD: buffer
11-
REAGENT_SOURCES: |
12-
Phosphatidylcholine lipids with arachidonoyl chains were synthesized and selectively deuterated.
13-
SAMPLE_PROTOCOL: |
14-
Lipids were hydrated in buffer containing 20 mM Tris (pH 7.5)
15-
to approximately 50 wt% hydration, forming bilayer dispersions.
16-
POPC: 1.0
177
ADDITIONAL_MOLECULES:
18-
TOTAL_HYDRATION: UNKNOWN
198
PH: UNKNOWN
209
PH_METHOD: UNKNOWN
2110
REAGENT_SOURCES:
22-
POPC: Avanti Polar Lipids, Birmingham, AL, USA
11+
POPC: d31-POPC and POPC, Avanti Polar Lipids, Alabaster, AL, USA
2312
H2O: UNKNOWN
2413
SAMPLE_PROTOCOL: |
2514
Lipid samples were prepared by dissolving in organic solvent followed by
2615
solvent evaporation and vacuum drying. Samples were hydrated to form
27-
multilamellar vesicles under controlled conditions.
16+
multilamellar vesicles under controlled conditions. Then samples were centrifuged
17+
and supernatants were discarded. Precise total hydration is unknown.
18+
Paper cites for the closest protocol: 10.1529/biophysj.107.112847
2819
NMR:
29-
INSTRUMENT: UNKNOWN
30-
METHOD: 2H:QE
20+
INSTRUMENT: Bruker Avance AVII-500 NMR with 4 mm CP-MAS HX probe
21+
METHOD: PDLF:R18_1^7
3122
SIGN_MEASURED: NONE
32-
T_RF_HEATING: UNKNOWN
23+
T_RF_HEATING: heating was checked using methanol-filled rotor
3324
DETAILS: |
34-
2H NMR order parameters obtained using quadrupolar echo experiments.
25+
The following setup was used: spectral width of 149.5 ppm;
26+
refocused INEPT with t1 and t2 of 1.79 ms and 1.19 ms respectively;
27+
CP contact time equal to 700 ms; radiofrequency pulses set to give the nutation
28+
frequencies: 45.00 kHz (R1871 pulses), 63.45 kHz (13C 90-
29+
and 180-pulses), 63.45 kHz (1H INEPT pulses), 50 kHz
30+
(1H decoupling pulses), 50.76–63.45 kHz (1H CP ramp pulse
31+
during contact time), 53.66 kHz (13C CP pulse during contact
32+
time); t1 with increments equal to 399.6 ms (0% colesterol, 7%
33+
and 15% cholesterol) and 132.2 ms (34% colesterol, 50% and
34+
60% cholesterol); for each t1 value, 256 scans were recorded
35+
during an acquisition time of 100 ms using 5 s recycle
36+
delay. MAS frequency 5kHz was used.
3537
3638
#outdated fields
3739
MOLAR_FRACTIONS:

‎experiments/OrderParameters/10.1039/c2cp42738a/2/README.yaml‎

Lines changed: 39 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,42 @@
1-
DOI: 10.1039/c2cp42738a
2-
TEMPERATURE: 300.0
1+
ARTICLE_DOI: 10.1039/c2cp42738a
2+
TEMPERATURE: 300
3+
MEMBRANE_COMPOSITION:
4+
POPC: 0.93
5+
CHOL: 0.07
6+
SOLUTION_COMPOSITION:
7+
TOTAL_HYDRATION: 50
8+
ADDITIONAL_MOLECULES:
9+
PH: UNKNOWN
10+
PH_METHOD: UNKNOWN
11+
REAGENT_SOURCES:
12+
POPC: d31-POPC and POPC, Avanti Polar Lipids, Alabaster, AL, USA
13+
H2O: UNKNOWN
14+
SAMPLE_PROTOCOL: |
15+
Lipid samples were prepared by dissolving in organic solvent followed by
16+
solvent evaporation and vacuum drying. Samples were hydrated to form
17+
multilamellar vesicles under controlled conditions. Then samples were centrifuged
18+
and supernatants were discarded. Precise total hydration is unknown.
19+
Paper cites for the closest protocol: 10.1529/biophysj.107.112847
20+
NMR:
21+
INSTRUMENT: Bruker Avance AVII-500 NMR with 4 mm CP-MAS HX probe
22+
METHOD: PDLF:R18_1^7
23+
SIGN_MEASURED: NONE
24+
T_RF_HEATING: heating was checked using methanol-filled rotor
25+
DETAILS: |
26+
The following setup was used: spectral width of 149.5 ppm;
27+
refocused INEPT with t1 and t2 of 1.79 ms and 1.19 ms respectively;
28+
CP contact time equal to 700 ms; radiofrequency pulses set to give the nutation
29+
frequencies: 45.00 kHz (R1871 pulses), 63.45 kHz (13C 90-
30+
and 180-pulses), 63.45 kHz (1H INEPT pulses), 50 kHz
31+
(1H decoupling pulses), 50.76–63.45 kHz (1H CP ramp pulse
32+
during contact time), 53.66 kHz (13C CP pulse during contact
33+
time); t1 with increments equal to 399.6 ms (0% colesterol, 7%
34+
and 15% cholesterol) and 132.2 ms (34% colesterol, 50% and
35+
60% cholesterol); for each t1 value, 256 scans were recorded
36+
during an acquisition time of 100 ms using 5 s recycle
37+
delay. MAS frequency 5kHz was used.
38+
39+
# outdated fields
340
MOLAR_FRACTIONS:
441
POPC: 0.93
542
CHOL: 0.07

‎experiments/OrderParameters/10.1039/c2cp42738a/3/README.yaml‎

Lines changed: 39 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,42 @@
1-
DOI: 10.1039/c2cp42738a
2-
TEMPERATURE: 300.0
1+
ARTICLE_DOI: 10.1039/c2cp42738a
2+
TEMPERATURE: 300
3+
MEMBRANE_COMPOSITION:
4+
POPC: 0.85
5+
CHOL: 0.15
6+
SOLUTION_COMPOSITION:
7+
TOTAL_HYDRATION: 50
8+
ADDITIONAL_MOLECULES:
9+
PH: UNKNOWN
10+
PH_METHOD: UNKNOWN
11+
REAGENT_SOURCES:
12+
POPC: d31-POPC and POPC, Avanti Polar Lipids, Alabaster, AL, USA
13+
H2O: UNKNOWN
14+
SAMPLE_PROTOCOL: |
15+
Lipid samples were prepared by dissolving in organic solvent followed by
16+
solvent evaporation and vacuum drying. Samples were hydrated to form
17+
multilamellar vesicles under controlled conditions. Then samples were centrifuged
18+
and supernatants were discarded. Precise total hydration is unknown.
19+
Paper cites for the closest protocol: 10.1529/biophysj.107.112847
20+
NMR:
21+
INSTRUMENT: Bruker Avance AVII-500 NMR with 4 mm CP-MAS HX probe
22+
METHOD: PDLF:R18_1^7
23+
SIGN_MEASURED: NONE
24+
T_RF_HEATING: heating was checked using methanol-filled rotor
25+
DETAILS: |
26+
The following setup was used: spectral width of 149.5 ppm;
27+
refocused INEPT with t1 and t2 of 1.79 ms and 1.19 ms respectively;
28+
CP contact time equal to 700 ms; radiofrequency pulses set to give the nutation
29+
frequencies: 45.00 kHz (R1871 pulses), 63.45 kHz (13C 90-
30+
and 180-pulses), 63.45 kHz (1H INEPT pulses), 50 kHz
31+
(1H decoupling pulses), 50.76–63.45 kHz (1H CP ramp pulse
32+
during contact time), 53.66 kHz (13C CP pulse during contact
33+
time); t1 with increments equal to 399.6 ms (0% colesterol, 7%
34+
and 15% cholesterol) and 132.2 ms (34% colesterol, 50% and
35+
60% cholesterol); for each t1 value, 256 scans were recorded
36+
during an acquisition time of 100 ms using 5 s recycle
37+
delay. MAS frequency 5kHz was used.
38+
39+
# outdated fields
340
MOLAR_FRACTIONS:
441
POPC: 0.85
542
CHOL: 0.15

‎experiments/OrderParameters/10.1039/c2cp42738a/4/README.yaml‎

Lines changed: 39 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,42 @@
1-
DOI: 10.1039/c2cp42738a
2-
TEMPERATURE: 300.0
1+
ARTICLE_DOI: 10.1039/c2cp42738a
2+
TEMPERATURE: 300
3+
MEMBRANE_COMPOSITION:
4+
POPC: 0.66
5+
CHOL: 0.34
6+
SOLUTION_COMPOSITION:
7+
TOTAL_HYDRATION: 50
8+
ADDITIONAL_MOLECULES:
9+
PH: UNKNOWN
10+
PH_METHOD: UNKNOWN
11+
REAGENT_SOURCES:
12+
POPC: d31-POPC and POPC, Avanti Polar Lipids, Alabaster, AL, USA
13+
H2O: UNKNOWN
14+
SAMPLE_PROTOCOL: |
15+
Lipid samples were prepared by dissolving in organic solvent followed by
16+
solvent evaporation and vacuum drying. Samples were hydrated to form
17+
multilamellar vesicles under controlled conditions. Then samples were centrifuged
18+
and supernatants were discarded. Precise total hydration is unknown.
19+
Paper cites for the closest protocol: 10.1529/biophysj.107.112847
20+
NMR:
21+
INSTRUMENT: Bruker Avance AVII-500 NMR with 4 mm CP-MAS HX probe
22+
METHOD: PDLF:R18_1^7
23+
SIGN_MEASURED: NONE
24+
T_RF_HEATING: heating was checked using methanol-filled rotor
25+
DETAILS: |
26+
The following setup was used: spectral width of 149.5 ppm;
27+
refocused INEPT with t1 and t2 of 1.79 ms and 1.19 ms respectively;
28+
CP contact time equal to 700 ms; radiofrequency pulses set to give the nutation
29+
frequencies: 45.00 kHz (R1871 pulses), 63.45 kHz (13C 90-
30+
and 180-pulses), 63.45 kHz (1H INEPT pulses), 50 kHz
31+
(1H decoupling pulses), 50.76–63.45 kHz (1H CP ramp pulse
32+
during contact time), 53.66 kHz (13C CP pulse during contact
33+
time); t1 with increments equal to 399.6 ms (0% colesterol, 7%
34+
and 15% cholesterol) and 132.2 ms (34% colesterol, 50% and
35+
60% cholesterol); for each t1 value, 256 scans were recorded
36+
during an acquisition time of 100 ms using 5 s recycle
37+
delay. MAS frequency 5kHz was used.
38+
39+
# outdated fields
340
MOLAR_FRACTIONS:
441
POPC: 0.66
542
CHOL: 0.34

‎experiments/OrderParameters/10.1039/c2cp42738a/5/README.yaml‎

Lines changed: 39 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,42 @@
1-
DOI: 10.1039/c2cp42738a
2-
TEMPERATURE: 300.0
1+
ARTICLE_DOI: 10.1039/c2cp42738a
2+
TEMPERATURE: 300
3+
MEMBRANE_COMPOSITION:
4+
POPC: 0.5
5+
CHOL: 0.5
6+
SOLUTION_COMPOSITION:
7+
TOTAL_HYDRATION: 50
8+
ADDITIONAL_MOLECULES:
9+
PH: UNKNOWN
10+
PH_METHOD: UNKNOWN
11+
REAGENT_SOURCES:
12+
POPC: d31-POPC and POPC, Avanti Polar Lipids, Alabaster, AL, USA
13+
H2O: UNKNOWN
14+
SAMPLE_PROTOCOL: |
15+
Lipid samples were prepared by dissolving in organic solvent followed by
16+
solvent evaporation and vacuum drying. Samples were hydrated to form
17+
multilamellar vesicles under controlled conditions. Then samples were centrifuged
18+
and supernatants were discarded. Precise total hydration is unknown.
19+
Paper cites for the closest protocol: 10.1529/biophysj.107.112847
20+
NMR:
21+
INSTRUMENT: Bruker Avance AVII-500 NMR with 4 mm CP-MAS HX probe
22+
METHOD: PDLF:R18_1^7
23+
SIGN_MEASURED: NONE
24+
T_RF_HEATING: heating was checked using methanol-filled rotor
25+
DETAILS: |
26+
The following setup was used: spectral width of 149.5 ppm;
27+
refocused INEPT with t1 and t2 of 1.79 ms and 1.19 ms respectively;
28+
CP contact time equal to 700 ms; radiofrequency pulses set to give the nutation
29+
frequencies: 45.00 kHz (R1871 pulses), 63.45 kHz (13C 90-
30+
and 180-pulses), 63.45 kHz (1H INEPT pulses), 50 kHz
31+
(1H decoupling pulses), 50.76–63.45 kHz (1H CP ramp pulse
32+
during contact time), 53.66 kHz (13C CP pulse during contact
33+
time); t1 with increments equal to 399.6 ms (0% colesterol, 7%
34+
and 15% cholesterol) and 132.2 ms (34% colesterol, 50% and
35+
60% cholesterol); for each t1 value, 256 scans were recorded
36+
during an acquisition time of 100 ms using 5 s recycle
37+
delay. MAS frequency 5kHz was used.
38+
39+
# outdated fields
340
MOLAR_FRACTIONS:
441
POPC: 0.5
542
CHOL: 0.5

‎experiments/OrderParameters/10.1039/c2cp42738a/6/README.yaml‎

Lines changed: 39 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,42 @@
1-
DOI: 10.1039/c2cp42738a
2-
TEMPERATURE: 300.0
1+
ARTICLE_DOI: 10.1039/c2cp42738a
2+
TEMPERATURE: 300
3+
MEMBRANE_COMPOSITION:
4+
POPC: 0.4
5+
CHOL: 0.6
6+
SOLUTION_COMPOSITION:
7+
TOTAL_HYDRATION: 50
8+
ADDITIONAL_MOLECULES:
9+
PH: UNKNOWN
10+
PH_METHOD: UNKNOWN
11+
REAGENT_SOURCES:
12+
POPC: d31-POPC and POPC, Avanti Polar Lipids, Alabaster, AL, USA
13+
H2O: UNKNOWN
14+
SAMPLE_PROTOCOL: |
15+
Lipid samples were prepared by dissolving in organic solvent followed by
16+
solvent evaporation and vacuum drying. Samples were hydrated to form
17+
multilamellar vesicles under controlled conditions. Then samples were centrifuged
18+
and supernatants were discarded. Precise total hydration is unknown.
19+
Paper cites for the closest protocol: 10.1529/biophysj.107.112847
20+
NMR:
21+
INSTRUMENT: Bruker Avance AVII-500 NMR with 4 mm CP-MAS HX probe
22+
METHOD: PDLF:R18_1^7
23+
SIGN_MEASURED: NONE
24+
T_RF_HEATING: heating was checked using methanol-filled rotor
25+
DETAILS: |
26+
The following setup was used: spectral width of 149.5 ppm;
27+
refocused INEPT with t1 and t2 of 1.79 ms and 1.19 ms respectively;
28+
CP contact time equal to 700 ms; radiofrequency pulses set to give the nutation
29+
frequencies: 45.00 kHz (R1871 pulses), 63.45 kHz (13C 90-
30+
and 180-pulses), 63.45 kHz (1H INEPT pulses), 50 kHz
31+
(1H decoupling pulses), 50.76–63.45 kHz (1H CP ramp pulse
32+
during contact time), 53.66 kHz (13C CP pulse during contact
33+
time); t1 with increments equal to 399.6 ms (0% colesterol, 7%
34+
and 15% cholesterol) and 132.2 ms (34% colesterol, 50% and
35+
60% cholesterol); for each t1 value, 256 scans were recorded
36+
during an acquisition time of 100 ms using 5 s recycle
37+
delay. MAS frequency 5kHz was used.
38+
39+
# outdated fields
340
MOLAR_FRACTIONS:
441
POPC: 0.4
542
CHOL: 0.6

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