Dear all, I seem to read some posts in the chimera email-list that discuss split combined mol2 files contains many compound into single mol2 files for virtual screening, but now I cannot find them. I wish to do some virtual screening with autodock 4. I have split a sdf file contains over a thousand compounds into single mol2 file with the linux shell "csplit" command. However, I find lots of such mol2 files still contain multiple ligands （LIG1, LIG2, LIG3, etc.) whose coordinates mix together and so can not be split by shell command "csplit". Please find three such examples at: https://drive.google.com/drive/folders/1AiW00lbA4tRfLu-l47QfxWVn8PqnQ-5J?usp... I can split the ligands in a mol2 file manually in Chimera GUI: first open the mol2 file, then select the ligands and save them as pdb files respectively to get separate pdb files for these ligands. After then reopen these pdb files respectively and save them as mol2 file. However, to process a large amount of mol2 files manually is impossible, so I need a command or script to do this. I hope chimera can do this. Chimera has a command "split": split [ model_number(s) ] [ chains ] [ ligands ] [ connected ] [ atoms atom-spec ]n However, it doesn't seem to be suitable for my scenario. Does anyone know whether chimera can split such mol2 files and how? I will appreciate any help of you. Best regards. Yeping Sun