[Chimera-users] Using mol2 files
meng at cgl.ucsf.edu
Wed Jul 11 18:33:55 PDT 2007
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
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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