[Chimera-users] Report coordinates in EM map

Tom Goddard goddard at sonic.net
Mon Aug 29 11:56:32 PDT 2011

Hi Osama,

   I think Elaine's procedure for finding coordinates is the way to 
go.   But it is pretty tedious.  It would be nice if you could just show 
a plane of data and have it report the position on the plane as you move 
the mouse to any desired position.  Also would be nice if placing a 
marker in the way Elaine said would report the coordinates without 
having to use the separate getcrd command.  I'll submit feature requests 
for these improvements.


Elaine Meng wrote:
> Hi Osama,
> You could try using the "Volume Tracer" tool (under Tools... Volume Data) to place marker spheres at the location of interest.
> <http://plato.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/framevolpath.html>
> Use the Mouse menu on that tool to control how the markers are placed.
> Then if you select a marker sphere with Ctrl-click and use command "getcrd sel" it will report the coordinates.  The coordinates should be in the same system as the volume, as long as you don't move the markers separately from the volume.
> <http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/getcrd.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 Aug 27, 2011, at 1:48 AM, Fakron, Osama Mohamed wrote:
>> Hello
>> My name is Osama M.Fakron , I am  PhD student  in Mechanical&Material School at Washington State  University , I am working on reconstruct  3D image  from SEM 2D images  by EM3D software ,I am  using  Chimera for  viewing my reconstructed images , I need some help  in  getting 3D position for  any point in  my  reconstructed  image , and also your supporting is appreciated.
>> All the best for you
>> Osama
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