[Chimera-users] Using mol2 files

Elaine Meng meng at cgl.ucsf.edu
Wed Jul 11 13:52:54 PDT 2007

Hi Pasquale,
As Eric figured out, your mol2 file does not contain substructure  
information.  For the structure to be read by Chimera as a series of  
residues, there would need to be residue information in each line in  
the @<TRIPOS>ATOM section and then a corresponding  
@<TRIPOS>SUBSTRUCTURE section at the bottom.  You would have to edit  
that information into your file.  Otherwise, the structure appears as  
one big residue.

Mol2 format description:

   ATOM section - need substructure ID and name (residue number and  
name) for each atom

   SUBSTRUCTURE section - more information on those substructures  

To get an example mol2 file, open a PDB file of a protein in Chimera,  
add hydrogens if you want those in your example, and then write it  
out as Mol2 (File... Save Mol2...)
I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jul 6, 2007, at 10:57 AM, Eric Pettersen wrote:

> Hi Pasquale,
> 	If your structure all got put into a single residue named UNK,  
> that typically means that your file was missing the @SUBSTRUCTURE  
> section (http://www.tripos.com/mol2/mol2_format33.html#1370).   
> There is an entry in our bug database (#3518) for better handling  
> of files with missing @SUBSTRUCTURE sections.  I will add your name  
> to that report so you'll know when it gets fixed.  For now, you  
> will have to edit your file and add an @SUBSTRUCTURE section "by  
> hand".
> --Eric
>> On Jul 6, 2007, at 8:54 AM, Pasquale Iacono wrote:
>>> Hey Elaine,
>>>      My structure is currently being labeled as one big residue  
>>> (UNK) and when I minimize it it says it does not recognize the  
>>> residue, so it seems like the calculation program is using  
>>> residue parameters and not those for specific atoms. Also, my  
>>> structure contains a Zn(II) metal center and I was wondering if  
>>> the parm files would detect it as such if it actually used the  
>>> atom types. I attached my mol2 file so you can check it out. Thanks
>>>          -Pasquale Iacono

More information about the Chimera-users mailing list