06.4 Saving your Refined Dataset as a Single sdf File
6.4 Saving your Refined Dataset as a Single sdf File
Once you have filtered down your dataset and removed any undesirable compounds you need to save the new dataset as a single sdf file. To do this click file, save special, SD-file…
After choosing where to save your sdf (and naming the file), this will bring up a small dialog box detailing how exactly you are saving the sdf, it is very important that you pay attention to these details as this will define the way the compounds information is saved. For molecular docking experiments you will need to have the 3D conformations of your compounds and sdf files should be saved based on these 3D conformations. To do this click on the drop-down menu next to “Atom coordinates:” and select “3D if available”.
It is also very important that you know which compound is which when looking at your docking results! If your compounds were not named in the original dataset (this is common if you have designed your own compounds in ChemDraw, see sections 7&8), then they will not have any assigned numbers such as the “structure number” column in this dataset. An easy way to get around this is to save the sdf file based on the row number, this will name each compound as the row number it was listed as before you clicked save. It is useful to always order your compounds in the same way in table 1 before you save, you can do this by clicking on the heading of the column you wish to order results by (for example LogP) and DataWarrior will order your compounds in ascending/descending value for this property. To save the compounds name based on row number click on the drop-down menu next to “Compound name column:” in the dialog box, and then select “use row number”.
Once you have saved your refined dataset as a single sdf file based on the 3D atom coordinates of your compounds you now have a sdf file suitable for use in docking experiments. If you open up your saved sdf file you can see a new “molecule name” column in table 1 has appeared. All of the properties you calculated using DataWarrior when examining the original dataset have also remained and been saved in the sdf file.
