Need more metabolite .mat

[olivialaiaha]

Hello! I'm a graduate student doing research with FID-A. I need more metabolites (Acetate (Ace), Myo-Inositol (mI), ATP, Ethanolamine (Eth), Pyruvate (Pyr), scyllo-Inositol (sI), and Threonine (Thr)) in "{FIDA_path}/simulationTools/metabolites/", could you help me with them or tell me how to convert them? I tried to convert the metabolite .mat using the paper "NMR Biomed 2000, 13:129-153" but I failed QAQ.

Olivia

[jamienear]

Hi Olivia,

Myo Inositol is already included in FID-A. It is called “Ins”.

For the others, you will need to make the spin-systems manually. What I would recommend is to copy an existing spin system, and then simply change its name, and then change the values of the fields. Enter the values of the chemical shifts as a vector in sysXXX.shifts; and enter the coupling constants as a matrix in sysXXX.J. The other two fields are the name (self explanatory) and the scale factor, which is normally set to 1 unless you are trying to simplify a spin system that has redundancy.

Hope this helps.

Best wishes, Jamie

On Aug 5, 2022, at 5:49 AM, Olivia_Lai @.**@.>> wrote:

Hello! I'm a graduate student doing research with FID-A. I need more metabolites (Myo-Inositol (mI), ATP, Ethanolamine (Eth), Pyruvate (Pyr), scyllo-Inositol (sI), and Threonine (Thr)) in "{FIDA_path}/simulationTools/metabolites/", could you help me with them or tell me how to convert them? I tried to convert the metabolite .mat using the paper "NMR Biomed 2000, 13:129-153" but I failed QAQ.

Olivia

— Reply to this email directly, view it on GitHubhttps://github.com/CIC-methods/FID-A/issues/99, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ACHTOQKXTHX62632CLEHSZDVXTPSXANCNFSM55VPXCRA. You are receiving this because you are subscribed to this thread.Message ID: @.***>

[olivialaiaha]

Hello Jamie,

Thank you so much for your replying! But I still fail to convert ATP and Ethanolamine because I don't know how to put the J numbers in the correct place in the matrix. For ATP, it has 2 parts: "Ribose moiety" and "Adenosine moiety", I'm not sure how to deal with them although I refer to similar metabolites. And what should I do with the "P"? (4'-P, 5'-P, and 5"-P). For Ethanolamine , again, I don't know what to do with "N" (1-N and 1'-N). Sorry to bother you, it's a bit complicated for me and I'm afraid to get it wrong QAQ

Best wishes, Olivia

[jamienear]

Hi Olivia,

Really sorry about my delayed response. I had a go at making the ATP and ETA spin systems according to the Govindaraju paper you referenced. Rather than explain what I did, I have attached a script to show it directly. Please have a look and let me know if you think it makes sense and is correct.

Best wishes, Jamie

On Aug 9, 2022, at 1:06 AM, Olivia_Lai @.**@.>> wrote:

Hello Jamie,

Thank you so much for your replying! But I still fail to convert ATP and Ethanolamine because I don't know how to put the J numbers in the correct place in the matrix. For ATP, it has 2 parts: "Ribose moiety" and "Adenosine moiety", I'm not sure how to deal with them although I refer to similar metabolites. And what should I do with the "P"? (4'-P, 5'-P, and 5"-P). For Ethanolamine , again, I don't know what to do with "N" (1-N and 1'-N). Sorry to bother you, it's a bit complicated for me and I'm afraid to get it wrong QAQ

Best wishes, Olivia

— Reply to this email directly, view it on GitHubhttps://github.com/CIC-methods/FID-A/issues/99#issuecomment-1208920026, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ACHTOQOREDVEEZFY22SWAH3VYHRNJANCNFSM55VPXCRA. You are receiving this because you commented.Message ID: @.***>

[jamienear]

BTW, for the P couplings: I list the P as a spin with a very large chemical shift (I used 100 ppm). This way it will not show up in the 1H spectrum, but you can have protons that couple to it. Then I can enter the coupling values in the J table.

Hope this helps! -J

On Aug 23, 2022, at 9:16 AM, Jamie Near @.**@.>> wrote:

Hi Olivia,

Really sorry about my delayed response. I had a go at making the ATP and ETA spin systems according to the Govindaraju paper you referenced. Rather than explain what I did, I have attached a script to show it directly. Please have a look and let me know if you think it makes sense and is correct.

Best wishes, Jamie

On Aug 9, 2022, at 1:06 AM, Olivia_Lai ***@***.******@***.***>> wrote: Hello Jamie, Thank you so much for your replying! But I still fail to convert ATP and Ethanolamine because I don't know how to put the J numbers in the correct place in the matrix. For ATP, it has 2 parts: "Ribose moiety" and "Adenosine moiety", I'm not sure how to deal with them although I refer to similar metabolites. And what should I do with the "P"? (4'-P, 5'-P, and 5"-P). For Ethanolamine , again, I don't know what to do with "N" (1-N and 1'-N). Sorry to bother you, it's a bit complicated for me and I'm afraid to get it wrong QAQ Best wishes, Olivia — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: ***@***.***>

[olivialaiaha]

Hello Jamie,

Thank you so much for your replying! But I don't see the attachment OAO

Best wishes, Olivia