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: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/ minimize.html#parameters 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. Elaine 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.