[Chimera-users] Creating Average Structure from PSF/DCD --> Include metal ions in final structure

[Peter Murphy]

Hi,

    I am trying to create an average structure in chimera 1.7 using the 
built in MDtools (loading a PSF/DCD file to get the trajectory). I am 
able to create an averaged structure for a select number of frames 
easily, but it doesn't appear that the metal ions are included when the 
averaging occurs. Is there someway to force the ions to be included? or 
alternatively, is there a script to create an average structure that 
includes selected atoms?

Thanks,

Peter

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Peter Murphy, Ph.D. Candidate
Department of Biochemistry and Molecular Biology
Dalhousie University
Halifax, NS
Canada