icosahedral reconstruction volume color
Dear Users,
I've done a symmetric reconstruction utilizing Viper (I1) icosahedral symmetry with XMIPP. Is there a way to color my recon.vol file surface according to symmetry?
Kind regards, Reggie
-- Reginald McNulty, Ph.D. Postdoctoral Research Associate The Scripps Research Institute Johnson Lab Department of Molecular Biology La Jolla, California 92037 Email: rmcnulty@scripps.edu
Dear Reggie, I'm not sure what you mean by coloring according to symmetry... radial coloring perhaps? Our expert in this area is away this week, so I will try to answer, but please bear with me.
You can open and display the vol file in Chimera, assuming it is the SPIDER format: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#volume
You can then adjust the isosurface level in the "Volume Viewer" dialog and apply various kinds of coloring to the isosurface with "Surface Color" (in menu under Tools... Volume Data) or command "scolor". http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolor.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html
These support coloring by (a) map value or gradient norm (b) distance from a point, axis or plane
radial coloring = coloring by distance from a point, where the point is the center of symmetry
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 Sep 20, 2012, at 8:00 AM, Reginald McNulty wrote:
Dear Users, I've done a symmetric reconstruction utilizing Viper (I1) icosahedral symmetry with XMIPP. Is there a way to color my recon.vol file surface according to symmetry? Kind regards, Reggie
Hi Elaine,
I'm wondering if I can color just the five-fold vertices of my icosahedral surface red, without coloring the entire surface red.
Reggie ______________ From: Elaine Meng [meng@cgl.ucsf.edu] Sent: Thursday, September 20, 2012 9:22 AM To: Reginald McNulty Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] icosahedral reconstruction volume color
Dear Reggie, I'm not sure what you mean by coloring according to symmetry... radial coloring perhaps? Our expert in this area is away this week, so I will try to answer, but please bear with me.
You can open and display the vol file in Chimera, assuming it is the SPIDER format: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#volume
You can then adjust the isosurface level in the "Volume Viewer" dialog and apply various kinds of coloring to the isosurface with "Surface Color" (in menu under Tools... Volume Data) or command "scolor". http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolor.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html
These support coloring by (a) map value or gradient norm (b) distance from a point, axis or plane
radial coloring = coloring by distance from a point, where the point is the center of symmetry
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 Sep 20, 2012, at 8:00 AM, Reginald McNulty wrote:
Dear Users, I've done a symmetric reconstruction utilizing Viper (I1) icosahedral symmetry with XMIPP. Is there a way to color my recon.vol file surface according to symmetry? Kind regards, Reggie
Hi Reggie, I can't think of a way to do that directly, but here are some related ideas:
(a) for visualizing the 5-fold and 6-fold vertices, the command "hkcage" can be used to create an icosahedral mesh of hexagons and pentagons - you specify radius, h and k values (where virus T number = h^2 + hk +k^2). It makes a wire model which could be converted to sticks with command "meshmol". The difficulty would probably be in getting the orientation and placement of the cage to match that of your reconstruction. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hkcage.html
(b) "Color Zone" colors surfaces to match nearby atoms or pseudoatomic "markers" -- theoretically you could use "Volume Tracer" to place a red marker at each 5-fold vertex and then use Color Zone to color those regions of the surface red, and then undisplay the atoms or markers. (These tools are in the menu under Tools... Volume Data.) However, the difficulty I see is in placing the markers exactly symmetrically so each vertex would get the same amount of coloring. If you knew coordinates for the vertices (again the hard part) you could just create a PDB file with those fake atoms, color them red, ... http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/colorzone/colorzone.html
(c) there is a "Cage Builder" (menu under Tools... Higher-Order Structure) that lets you interactively construct a cage of hexagons and pentagons. This is an additional method of generating markers. The "Create Mesh...." option would generate single edges and vertices from the initially generated doubled set (you'd have to look at the figure in the docs to understand that part) and in the result, you could color the 5-fold vertices red and proceed as above with Color Zone. The difficulty may be in building/scaling/positioning the cage to coincide correctly with your reconstruction. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/cagebuilder/cagebuilder.html
Sorry I haven't come up with simpler solutions, Elaine
On Sep 20, 2012, at 10:04 AM, Reginald McNulty wrote:
Hi Elaine, I'm wondering if I can color just the five-fold vertices of my icosahedral surface red, without coloring the entire surface red. Reggie ______________ From: Elaine Meng [meng@cgl.ucsf.edu] Sent: Thursday, September 20, 2012 9:22 AM To: Reginald McNulty Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] icosahedral reconstruction volume color
Dear Reggie, I'm not sure what you mean by coloring according to symmetry... radial coloring perhaps? Our expert in this area is away this week, so I will try to answer, but please bear with me.
You can open and display the vol file in Chimera, assuming it is the SPIDER format: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#volume
You can then adjust the isosurface level in the "Volume Viewer" dialog and apply various kinds of coloring to the isosurface with "Surface Color" (in menu under Tools... Volume Data) or command "scolor". http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolor.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html
These support coloring by (a) map value or gradient norm (b) distance from a point, axis or plane
radial coloring = coloring by distance from a point, where the point is the center of symmetry
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 Sep 20, 2012, at 8:00 AM, Reginald McNulty wrote:
Dear Users, I've done a symmetric reconstruction utilizing Viper (I1) icosahedral symmetry with XMIPP. Is there a way to color my recon.vol file surface according to symmetry? Kind regards, Reggie
Hi Reggie,
The following video shows how to place markers on your icosahedral map, replicate them using symmetry, then use the Color Zone tool to color part of the map near chosen markers.
http://www.cgl.ucsf.edu/chimera/videodoc/IcosWedge/index.html
The video is trying to solve a different problem from what you want but the same techniques will do the job.
Tom
-------- Original Message -------- Subject: Re: [Chimera-users] icosahedral reconstruction volume color From: Elaine Meng To: Reginald McNulty Date: 9/20/12 10:37 AM
Hi Reggie, I can't think of a way to do that directly, but here are some related ideas:
(a) for visualizing the 5-fold and 6-fold vertices, the command "hkcage" can be used to create an icosahedral mesh of hexagons and pentagons - you specify radius, h and k values (where virus T number = h^2 + hk +k^2). It makes a wire model which could be converted to sticks with command "meshmol". The difficulty would probably be in getting the orientation and placement of the cage to match that of your reconstruction. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hkcage.html
(b) "Color Zone" colors surfaces to match nearby atoms or pseudoatomic "markers" -- theoretically you could use "Volume Tracer" to place a red marker at each 5-fold vertex and then use Color Zone to color those regions of the surface red, and then undisplay the atoms or markers. (These tools are in the menu under Tools... Volume Data.) However, the difficulty I see is in placing the markers exactly symmetrically so each vertex would get the same amount of coloring. If you knew coordinates for the vertices (again the hard part) you could just create a PDB file with those fake atoms, color them red, ... http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/colorzone/colorzone.html
(c) there is a "Cage Builder" (menu under Tools... Higher-Order Structure) that lets you interactively construct a cage of hexagons and pentagons. This is an additional method of generating markers. The "Create Mesh...." option would generate single edges and vertices from the initially generated doubled set (you'd have to look at the figure in the docs to understand that part) and in the result, you could color the 5-fold vertices red and proceed as above with Color Zone. The difficulty may be in building/scaling/positioning the cage to coincide correctly with your reconstruction. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/cagebuilder/cagebuilder.html
Sorry I haven't come up with simpler solutions, Elaine
On Sep 20, 2012, at 10:04 AM, Reginald McNulty wrote:
Hi Elaine, I'm wondering if I can color just the five-fold vertices of my icosahedral surface red, without coloring the entire surface red. Reggie ______________ From: Elaine Meng [meng@cgl.ucsf.edu] Sent: Thursday, September 20, 2012 9:22 AM To: Reginald McNulty Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] icosahedral reconstruction volume color
Dear Reggie, I'm not sure what you mean by coloring according to symmetry... radial coloring perhaps? Our expert in this area is away this week, so I will try to answer, but please bear with me.
You can open and display the vol file in Chimera, assuming it is the SPIDER format: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#volume
You can then adjust the isosurface level in the "Volume Viewer" dialog and apply various kinds of coloring to the isosurface with "Surface Color" (in menu under Tools... Volume Data) or command "scolor". http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolor.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/scolor.html
These support coloring by (a) map value or gradient norm (b) distance from a point, axis or plane
radial coloring = coloring by distance from a point, where the point is the center of symmetry
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 Sep 20, 2012, at 8:00 AM, Reginald McNulty wrote:
Dear Users, I've done a symmetric reconstruction utilizing Viper (I1) icosahedral symmetry with XMIPP. Is there a way to color my recon.vol file surface according to symmetry? Kind regards, Reggie
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi, is it possible to change the line thickness in Tools > HighOrderStructure>Icosahedron Surface? Thanks, Dieter
------------------------------------------------------------------------ Dieter Blaas, Max F. Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Fax: 0043 1 4277 9616, e-mail: dieter.blaas@meduniwien.ac.at ------------------------------------------------------------------------
Hi Dieter, You can select the icosahedron (Ctrl-click on a line), click the green magnifying glass icon near the bottom right corner of the Chimera window, and then in the resulting Selection Inspector dialog, change the "line thickness" value (while inspecting "Surface piece"). http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/inspection.html
Alternatively you can specify linewidth directly in the "shape icosahedron" command (instead of using the Icosahedron Surface GUI).... "linewidth" is one of the general options: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html#icosahedron
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 Nov 7, 2012, at 2:57 AM, Dieter Blaas wrote:
Hi, is it possible to change the line thickness in Tools > HighOrderStructure>Icosahedron Surface? Thanks, Dieter
Hi Elaine, sorry for the wrong subject, but now I stick to it for consistency :-). Thanks a lot for the hint, but unfortunately, neither of them works in my hands (vers. 1.6.2 UBUNTU 10.04):
I cannot find any option for line-width in the Icosahedron Surface dialogue and clicking the line does not select anything (the magnifying glass tells me that nothing is selected). Am I doing anything wrong? best, Dieter
Am 07.11.2012 17:53, schrieb Elaine Meng:
Hi Dieter, You can select the icosahedron (Ctrl-click on a line), click the green magnifying glass icon near the bottom right corner of the Chimera window, and then in the resulting Selection Inspector dialog, change the "line thickness" value (while inspecting "Surface piece"). http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/inspection.html
Alternatively you can specify linewidth directly in the "shape icosahedron" command (instead of using the Icosahedron Surface GUI).... "linewidth" is one of the general options: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html#icosahedron
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 Nov 7, 2012, at 2:57 AM, Dieter Blaas wrote:
Hi, is it possible to change the line thickness in Tools > HighOrderStructure>Icosahedron Surface? Thanks, Dieter
Hi Dieter, Selection is with Ctrl-click, same as if you were selecting an atom or bond. Sounds like your mistake might be clicking instead of Ctrl-clicking. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/selection.html#pickselect
The linewidth setting is in the Selection Inspector dialog opened by clicking the magnifying glass (after you make the selection), not the Icosahedron dialog. Elaine
On Nov 8, 2012, at 12:47 AM, Dieter Blaas wrote:
Hi Elaine, sorry for the wrong subject, but now I stick to it for consistency :-). Thanks a lot for the hint, but unfortunately, neither of them works in my hands (vers. 1.6.2 UBUNTU 10.04):
I cannot find any option for line-width in the Icosahedron Surface dialogue and clicking the line does not select anything (the magnifying glass tells me that nothing is selected). Am I doing anything wrong? best, Dieter
Am 07.11.2012 17:53, schrieb Elaine Meng:
Hi Dieter, You can select the icosahedron (Ctrl-click on a line), click the green magnifying glass icon near the bottom right corner of the Chimera window, and then in the resulting Selection Inspector dialog, change the "line thickness" value (while inspecting "Surface piece"). http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/inspection.html
Alternatively you can specify linewidth directly in the "shape icosahedron" command (instead of using the Icosahedron Surface GUI).... "linewidth" is one of the general options: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html#icosahedron
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 Nov 7, 2012, at 2:57 AM, Dieter Blaas wrote:
Hi, is it possible to change the line thickness in Tools > HighOrderStructure>Icosahedron Surface? Thanks, Dieter
Got it, thanks a lot! Sorry for having been confused.... Dieter
Am 08.11.2012 17:57, schrieb Elaine Meng:
Hi Dieter, Selection is with Ctrl-click, same as if you were selecting an atom or bond. Sounds like your mistake might be clicking instead of Ctrl-clicking. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/selection.html#pickselect
The linewidth setting is in the Selection Inspector dialog opened by clicking the magnifying glass (after you make the selection), not the Icosahedron dialog. Elaine
On Nov 8, 2012, at 12:47 AM, Dieter Blaas wrote:
Hi Elaine, sorry for the wrong subject, but now I stick to it for consistency :-). Thanks a lot for the hint, but unfortunately, neither of them works in my hands (vers. 1.6.2 UBUNTU 10.04):
I cannot find any option for line-width in the Icosahedron Surface dialogue and clicking the line does not select anything (the magnifying glass tells me that nothing is selected). Am I doing anything wrong? best, Dieter
Am 07.11.2012 17:53, schrieb Elaine Meng:
Hi Dieter, You can select the icosahedron (Ctrl-click on a line), click the green magnifying glass icon near the bottom right corner of the Chimera window, and then in the resulting Selection Inspector dialog, change the "line thickness" value (while inspecting "Surface piece"). http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/inspection.html
Alternatively you can specify linewidth directly in the "shape icosahedron" command (instead of using the Icosahedron Surface GUI).... "linewidth" is one of the general options: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/shape.html#icosahedron
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 Nov 7, 2012, at 2:57 AM, Dieter Blaas wrote:
Hi, is it possible to change the line thickness in Tools > HighOrderStructure>Icosahedron Surface? Thanks, Dieter
participants (4)
-
Dieter Blaas -
Elaine Meng -
Reginald McNulty -
Tom Goddard