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

[Soumya Govinda Remesh]

Great. Thanks a lot Elaine for your prompt and detailed response.
Best,
Soumya

On Fri, Feb 10, 2017 at 1:29 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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:
> <http://plato.cgl.ucsf.edu/chimera/docs/ContributedSoftware/
> volumepathtracer/volumepathtracer.html#markerfiles>
>
> (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:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/write.html>
>
>  I hope this helps,
> Elaine
> -----
> 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
>
>


-- 
Soumya Govinda Remesh, Ph.D.
Postdoctoral Fellow at Advanced Light Source
Lawrence Berkeley National Laboratory

1 Cyclotron Road   MS 6R2100
Berkeley, CA 94720
(phone) 510-495-8179
(cell) 804-402-8730

sgremesh at lbl.gov
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