How to create a custom amino acid in a scientific library in UNIFI - WKB191444

OBJECTIVE or GOAL

Create custom amino acids in a scientific library in UNIFI.

ENVIRONMENT

• UNIFI
• waters_connect

PROCEDURE

1. Create a new library item, and if necessary a new custom library,  by following the KCS article How to create an item in a custom library in UNIFI - WKB26968.
2. In a web browser go to https://www.chemspider.com/ ,  search for the cutome amino acid you want to add tot he library
3. If the custom amino acid is in the Chemspider database, download the .mol fil from the search results
4. Complete the following steps.

waters_connect

1. In waters_connect Hub open the Administration app and select Manage Libraries
2. In Administration> Scientific Library > Manage Library Items, select Create Library Items
3. In the item name field type the name of your custom amino acid and select the custom library to which you want to add it from the Library drop down
4. If you have the .mol file for the custom amino acid,
   1. in the library item editor click on Tools, and from the drop down menu select Load structure 
   2. Browse to the .mol file that you downloaded at step 1 and select it. The Hill formula, Average molar mass , monoisotopic mass and molecular structure fields will be automatically populated
5. If you no not have a .mol file for the custom amino acid, enter the chemical formula in the relevant field
6. In the item type field click on the Value, and from the resulting dropdown menu select amino acid 
7. In Properties > Synonyms , click on the synonym type box

7. From the resulting menu select Three Letter Code

8. Enter a three letter code for the modified amino acid  in the Synonym field and press return
9. In the second Synonyms row repeat steps 7 and 8, but this time select the One Letter Code option
10. In the Synonym field enter a single character other than one of the letter used for standard amino acids.
    1. You can use any character except G, A, V, L, I, T, S, M, C, P, F, Y, W, H, K, R, D, E, N, or Q,
    2. You can use any ASCII character including numbers and most punctuation marks. I have not tested Chinese characters
    3. In the example I’ve used £ (pound sterling symbol)
11. Enter the item name. You should now have something that looks like this , although you may have selected something other than the ‘Pound Sterling’ symbol as the single amino acid code. Press the save button to save it

UNIFI 1.9.4

1. Select the Amino Acid item typ from the drop down menu
2. Enter the chemical formula of the custom amino acid, or Import the .mol file to automatically populate the structure and chemical formula fields
3. Enter three letter and one letter codes for the custom amino acid in the Synonyms section 

ADDITIONAL INFORMATION

• To add the structure of the amino acid, follow the KCS article How to add the structure for a small molecule in a scientific library in UNIFI - WKB191442.
• The hydrogen atoms can be hidden from the structure by clicking Tools > Remove explicit hydrogens.
• This article is part of a series of articles on UNIFI scientific libraries (How to build and manage a scientific library in UNIFI - WKB190999) and can also be found with the following link: Advanced UNIFI: Scientific Library building and managing (715007127).