[Chimera-users] Write out coordinates for Centre of mass

Elaine Meng meng at cgl.ucsf.edu
Fri Feb 10 13:29:24 PST 2017

Hi Soumya,
Sure, you could do either of the following:

(1) save as a marker file from Volume Tracer (show it with menu: Tools… Volume Data… Volume Tracer), and in that dialog:
 A. make sure that the “Marker set” is the one that you want (it is a pulldown menu if there is more than one)
 B. in the dialog menu choose File… save current marker set as…   to save a marker file with name ending in .cmm.  You can open it later in Chimera with the open command or menu: File… Open.

marker files:
(2) save as PDB.  Although it is hidden from the dialog shown with menu: File… Save PDB, since markers are really fake atoms, you can still save it as PDB from the command line.  Show Command Line from the Favorites menu.  Also show the Model Panel from the Favorites menu so that you can see what model number the marker has.  Then, for example if your original structure were model #0 and the marker of interest were #1, the command would be something like:

write relative #0 #1 ~/Desktop/domain-center.pdb

(or whatever name/location you want the file to be).   Manual page for write command:

 I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Feb 10, 2017, at 12:44 PM, Soumya Govinda Remesh <sgremesh at lbl.gov> wrote:
> Hello,
>  I wanted to know if I can write out the coordinates for the object placed at the 'centre of mass' of selected atoms from a domain. 
> I used the following command to place a marker at the location of interest.  
>  - measure center sel mark true
> Thanks
> Best,
> Soumya Govinda Remesh, Ph.D.
> Postdoctoral Fellow at Advanced Light Source
> Lawrence Berkeley National Laboratory

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