[Chimera-users] Using mol2 files

[Elaine Meng]

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:

http://www.tripos.com/mol2/mol2_format8.html
   ATOM section - need substructure ID and name (residue number and  
name) for each atom

http://www.tripos.com/mol2/mol2_format33.html#1370
   SUBSTRUCTURE section - more information on those substructures  
(residues)

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
-----
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
                      http://www.cgl.ucsf.edu/home/meng/index.html

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