I am facing issues fitting proton CEST data using ChemEx version 2022.3.4. The fitting works fine for
15 N CEST (HN) when I tweak the headers, but both amide proton (HN) and Hα CEST show problems, particularly with the interpretation of DW_AB and chemical shift inputs (CS_A), and the inability to fix R1_A for CA nuclei.
Problems observed:
Parsing of chemical shifts fails when the header contains B0, e.g.:
["CS_A, T->30.0C, B0->599.9MHZ"] # ❌ ChemEx fails to read shifts
If I remove the B0->, the chemical shifts are correctly read:
["CS_A, T->30.0C"] # ✅ Works
A similar issue is observed for:
["DW_AB, T->30.0C, B0->599.9MHZ"]
— Removing B0 fixes the issue.
DW_AB block is not detected during Hα CEST fitting, even when chemical shifts are correctly read.
Example from my parameters.toml:
["DW_AB, T->30.0C"]
Q17HA = -0.35
R18HA = 0.10
These values are ignored during fitting.
Relevant snippets from experiment file for the HA CEST:
[experiment]
name = "cest_ch3_1h_ip_ap"
d1 = 2.0
time_t1 = 0.350
carrier = 4.1
b1_frq = 25.034
b1_inh_res = 5
b1_inh_scale = 0.1
[conditions]
h_larmor_frq = 599.875
label = ["13C"]
temperature = 30.0
And the parameter is as followed:
"KEX_AB, T->30.0C" = 2.10350e+02 # (error not calculated)
"PB, T->30.0C" = 8.08365e-03 # (error not calculated)
ETAXY_A = 0
#"ETAZ_A, T->30.0C" = -1
ETAZ_A = -0.2
R2_A = 20
R1_A = 5
["CS_A, T->30.0C"]
Q17HA = 4.4
R18HA = 4.2
["DW_AB, T->30.0C"]
Q17HA= -0.35
R18HA = 0.1
Fixing R1_A for CA nuclei fails, even though it works for N nuclei.
FIX = ["ETAXY_A", "R1_A, NUC->N"] # ✅ Works for amide CEST
FIX = ["ETAXY_A", "R1_A, NUC->CA"] # ❌ Ignored for Hα CEST
R1_A appears to be treated as a free parameter and is getting fit to an extremely small value instead of being fixed.
I am not sure I am putting an incorrect format of the nuclei type somewhere, or if there is a bug. I am using chemex 2022.3.4. Any suggestions would be of great help.
Kindly let me know if any more information is required.
Thank you.
Bodhisatwa Nandi
I am facing issues fitting proton CEST data using ChemEx version 2022.3.4. The fitting works fine for
15 N CEST (HN) when I tweak the headers, but both amide proton (HN) and Hα CEST show problems, particularly with the interpretation of DW_AB and chemical shift inputs (CS_A), and the inability to fix R1_A for CA nuclei.
Problems observed:
Parsing of chemical shifts fails when the header contains B0, e.g.:
["CS_A, T->30.0C, B0->599.9MHZ"] # ❌ ChemEx fails to read shifts
If I remove the B0->, the chemical shifts are correctly read:
["CS_A, T->30.0C"] # ✅ Works
A similar issue is observed for:
["DW_AB, T->30.0C, B0->599.9MHZ"]
— Removing B0 fixes the issue.
DW_AB block is not detected during Hα CEST fitting, even when chemical shifts are correctly read.
Example from my parameters.toml:
["DW_AB, T->30.0C"]
Q17HA = -0.35
R18HA = 0.10
These values are ignored during fitting.
Relevant snippets from experiment file for the HA CEST:
[experiment]
name = "cest_ch3_1h_ip_ap"
d1 = 2.0
time_t1 = 0.350
carrier = 4.1
b1_frq = 25.034
b1_inh_res = 5
b1_inh_scale = 0.1
[conditions]
h_larmor_frq = 599.875
label = ["13C"]
temperature = 30.0
And the parameter is as followed:
"KEX_AB, T->30.0C" = 2.10350e+02 # (error not calculated)
"PB, T->30.0C" = 8.08365e-03 # (error not calculated)
ETAXY_A = 0
#"ETAZ_A, T->30.0C" = -1
ETAZ_A = -0.2
R2_A = 20
R1_A = 5
["CS_A, T->30.0C"]
Q17HA = 4.4
R18HA = 4.2
["DW_AB, T->30.0C"]
Q17HA= -0.35
R18HA = 0.1
Fixing R1_A for CA nuclei fails, even though it works for N nuclei.
FIX = ["ETAXY_A", "R1_A, NUC->N"] # ✅ Works for amide CEST
FIX = ["ETAXY_A", "R1_A, NUC->CA"] # ❌ Ignored for Hα CEST
R1_A appears to be treated as a free parameter and is getting fit to an extremely small value instead of being fixed.
I am not sure I am putting an incorrect format of the nuclei type somewhere, or if there is a bug. I am using chemex 2022.3.4. Any suggestions would be of great help.
Kindly let me know if any more information is required.
Thank you.
Bodhisatwa Nandi