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

Eric Pettersen pett at cgl.ucsf.edu
Mon Jul 8 15:04:59 PDT 2013

On Jul 5, 2013, at 11:51 AM, Peter Murphy <pwmurphy at dal.ca> wrote:

> 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?

Hi Peter,
	There is no easy way to do this "honestly" in Chimera, but a colleague suggested a cheat-y workaround:  create a bond between each metal and the nearest atom that does get included in the average (e.g. select both and type "bond sel" in Chimera's command line).  That will force the metal into the set of atoms that gets included in the average.  After the average structure is opened, those fake bonds will probably be shown as metal-coordination pseudobonds, which you can leave as is, or hide/delete using the Pseudobond Panel (in Tools/General Controls).
	Including bound metals in the average structure is clearly desirable, so I will be changing the averaging interface/code to allow that and will drop a note back to the list when it becomes available.


                        Eric Pettersen
                        UCSF Computer Graphics Lab

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