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
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
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. Tom 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
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Elaine & Tom Thank you very much for your kind response . May I have an appointment with you , I would like to come to San Fransisco . All the best for you Osama ________________________________________ From: Elaine Meng [meng@cgl.ucsf.edu] Sent: Monday, August 29, 2011 10:42 AM To: Fakron, Osama Mohamed Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] (no subject) 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
Hi Osama, You're always welcome to visit us at UCSF if you come to San Francisco. Here's a video showing Elaine's method of measuring positions in an EM map. http://www.cgl.ucsf.edu/chimera/videodoc/MarkerXYZ/ Tom Fakron, Osama Mohamed wrote:
Hi Elaine& Tom
Thank you very much for your kind response . May I have an appointment with you , I would like to come to San Fransisco .
All the best for you Osama ________________________________________ From: Elaine Meng [meng@cgl.ucsf.edu] Sent: Monday, August 29, 2011 10:42 AM To: Fakron, Osama Mohamed Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] (no subject)
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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participants (3)
-
Elaine Meng -
Fakron, Osama Mohamed -
Tom Goddard