[Chimera-users] How to split multiple ligands in mol2 files

Elaine Meng meng at cgl.ucsf.edu
Thu Apr 9 11:49:00 PDT 2020

Hi Yeping Sun,
I tried opening your first example mol2 file (TMS0418.mol2) and then using command

split #0 connected


and it makes the one model #0 into five models #0.1, 0.2, ... 0.5, as you can see in the Model Panel (show from Favorites menu).  Then you can write mol2 or pdb files for the individual models using the File menu or command "write".  However, four of them are the same molecule.

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Apr 9, 2020, at 8:36 AM, sunyeping <sunyeping at aliyun.com> wrote:
> 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=sharing
> 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

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