[Chimera-users] Using mol2 files

Elaine Meng meng at cgl.ucsf.edu
Wed Jul 11 18:33:55 PDT 2007

Hi Pasquale,
Eric just reminded me of a further problem (sorry): the need for  
standard atom names. Chimera relies on the stereotypical atom and  
residue names to recognize standard amino acid and nucleotide  
residues and assign them Amber parameters for minimization, as  
described here:

I believe these stereotypical names originated with the PDB, but are  
also used in mol2 files generated by programs such as SYBYL.

This atom/residue naming issue will affect ribbon display (which  
relies on backbone atom names) and Amber parameter assignment (for  
minimization).  However, Chimera atom type assignment, hydrogen  
addition, H-bond and clash detection, etc. do not require the use of  
standard atom and residue names.

On Jul 11, 2007, at 1:52 PM, Elaine Meng wrote:

> 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.

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