[Chimera-users] Creating a dummy atom on a defined position

[Subha Kalyaanamoorthy]

Thanks Elaine and Tom for the suggestions.
As Tom had said, it would be nice to have a straight forward command to
place a dummy atom (something like the pseusoatom in pymol).

Best Regards,
Subha

On Tue, Oct 11, 2016 at 3:05 PM, Tom Goddard <goddard at sonic.net> wrote:

> We really should have a command for this.  Here is a somewhat less arduous
> trick to place the marker where you want
>
>         cofr 7.5,12,-5 coord #0 ; ac mc
>
> This sets the center of rotation to x,y,z position 7.5,12,-5 using the
> coordinate system of model #0 (a model you already opened, or leave off the
> coord option and it will use global scene coordinates), then the “ac mc”
> runs the accelerator (ie keyboard shortcut) “mc” which places a marker
> (same as an atom) at the center of rotation.
>
>         Tom
>
>
>
>
> > On Oct 11, 2016, at 1:36 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> >
> > Hi Subha,
> > What’s easiest depends on whatyou want to do.  If it is just for display
> purposes, the easiest is to just use “shape sphere,” but that will not
> allow you to do stufff like measure distances.  The “shape” command creates
> a surface model, not an atom.  Example command:
> >
> > shape sphere center 1.5,2.2,0.0
> >
> > … where the 3 comma-sep numbers are the coordinates.  You can also
> specify which coordinate system they should be interpreted in, if you have
> other models open that have been moved separately from one another.  See
> the “shape” manpage:
> > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html>
> >
> > If you actually wanted to measure distances from that point, however,
> you would need to add a marker or atom at the coordinates.  Unfortunately
> there is no command equivalent to adding an atom with specific coordinates
> like you can do in the Build Structure GUI.  I did come up with a rather
> horrible kludge to add a marker at specific coordinates.  A marker allows
> measuring distances but it is not exactly the same as an atom (it's not
> good for structure-building).  The horrible kludge is to make a fake volume
> model using a specific origin, put values into that volume model, and then
> measure its center (which allows putting a marker at that position).
> What’s even worse is that you have to offset the origin of the fake map
> from the coordinates that you want the marker, because the origin is not
> the same as the center.  For example, here’s a command file to put a marker
> at 1.5,2.2,0.0:
> >
> > # subtract 1.00,1.01,1.00 from desired coordinates to give needed origin
> > #
> > vop new junk origin 0.5,1.19,-1.00 size 3 model #10
> > mask ones #10 model #11
> > measure center #11 mark true model #12
> > close #10,11
> > getcrd #12
> >
> > (the last command just reports the coordinates, as a check… I expected
> the need to subtract 1,1,1 but why the middle value needs to have 1.01
> subtracted is a mystery to me… determined empirically)
> >
> > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#new>
> > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mask.html>
> > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/
> measure.html#center>
> >
> > 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 Oct 11, 2016, at 12:03 PM, Subha Kalyaanamoorthy <
> kalyaana at ualberta.ca> wrote:
> >>
> >> Hi There,
> >> Wondering if there is a way to create a dummy atom on a specified
> position(xyz coords) using a chimera command line?
> >> Thanks,
> >> Subha
> >
> >
> > _______________________________________________
> > Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> > Manage subscription: http://plato.cgl.ucsf.edu/
> mailman/listinfo/chimera-users
> >
>
>


-- 
Dr. Subha Kalyaanamoorthy
Post Doctoral Fellow
Faculty of Pharmacy and Pharmaceutical Sciences
University of Alberta
Edmonton, Canada.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20161011/d884165a/attachment.html>