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28 changes: 15 additions & 13 deletions docs/smart_usage.md
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## How to process a raw HSQC spectrum to a NMR table with MestreNova (version 12 and newer)
## How to process a raw HSQC spectrum to a NMR table with MestreNova

1. Open your raw HSQC spectrum in MestreNova
- Drag&Drop your HSQC file (for Bruker data you find your spectrum under: pdata/1/2rr)
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Now each peak should be annotated with two numbers separated by comma (1H, 13C chemical shifts)
![HSQC_annotation](https://user-images.githubusercontent.com/57916837/70353559-7939b080-1822-11ea-84ea-87cc07946574.png)
4. Generate NMR table from annotated HSQC spectrum
- click on 'Analysis' tab
- click on 'NMR Peaks Table'
- click on 'Analysis' tab - 'NMR Peaks Table'
(if you are using classic theme or old version of MestreNova, it would be on 'View' - 'Tables' - 'Peaks'
- move the f2 column to the left of the f1 column
- copy all (ctrl+A)
- click on 'copy peaks' and choose 'copy table'
![HSQC_annotation_to_table](https://user-images.githubusercontent.com/57916837/70353982-6a9fc900-1823-11ea-8704-7458b0a7f783.png)
- Click on 'Setup Report' - 'Setup Table'
![SMART1](https://user-images.githubusercontent.com/41205498/75512744-4c231700-59a7-11ea-9262-90987c9f4ace.png)
- In the 'Visible name' row, revise 'f2(ppm)' and 'f1 (ppm)' to '1H' and '13C' respectively.
- Among the 'Visible' row, turn every checkbox off except 'f2 (ppm)' and 'f1 (ppm)'
- In the 'Decimals' row, change the value of 'f1 (ppm)' from 2 to 1.
- Inside the 'Report' box, Click all the checkboxs off
![MNova_setup_for_SMART](https://user-images.githubusercontent.com/41205498/75512990-20ecf780-59a8-11ea-874c-8aa7e1ab83b8.png)
- Click 'OK' button. This setup will be saved as default
- Click on 'copy peaks' and choose 'copy table'

5. Generate .csv file for SMART Analysis
- open Excel or similar program and paste the table (ctrl+V)
![image](https://user-images.githubusercontent.com/57916837/70354067-958a1d00-1823-11ea-93da-9eaf03f11d2f.png)
- align table in such a way that all values of f2 dimension = 1H are in one column and all values of the f1 dimension = 13C are in another column next to it
![image](https://user-images.githubusercontent.com/57916837/70354383-409ad680-1824-11ea-8847-7eaa167779be.png)
- open a new excel document (ctrl+N)
- type in column A1: '1H' and in column B1: '13C'
- copy and paste the table so that all values with 1H data are in column A2-AX and all values with 13C data are in column B2-BXX ![image](https://user-images.githubusercontent.com/57916837/70354216-e3068a00-1823-11ea-9ac9-cb51e5381091.png)
- reduce column B (13C values) from two decimals to one (for example 128.22 --> **128.2**)
- align the table so that all values with 1H data are in column A2-AX and all values with 13C data are in column B2-BXX
![image](https://user-images.githubusercontent.com/57916837/70354216-e3068a00-1823-11ea-9ac9-cb51e5381091.png)
- mark your table + header (1H,13C) and save as comma-separated file (.csv).

**You are ready to use SMART 2.0 Analysis! :)**
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