extract parts of a map based on 'volume data gradient norm'
Hi, I want to segment a map based on differences in 'volume data gradient norm' which I can adjust as to color the part of the volume I am interested in in blue and the one I want to get rid of in red. Is there a way of doing so? I admit that I never used the segger tool and do not know whether it would be appropriate for this task. The final aim is it to write out the blue volume! Thanks for hints, bw, 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, If I understand correctly, you have two maps, the original volume (density) and then another with gradient norm that is used to color the first. In that case, you could show an isosurface of the gradient norm values, then use the “mask” command to mask the original density map by the gradient-norm isosurface (i.e. zero out parts inside or outside the isosurface): <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mask.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 14, 2018, at 10:43 PM, Dieter Blaas <dieter.blaas@meduniwien.ac.at> wrote:
Hi, I want to segment a map based on differences in 'volume data gradient norm' which I can adjust as to color the part of the volume I am interested in in blue and the one I want to get rid of in red. Is there a way of doing so? I admit that I never used the segger tool and do not know whether it would be appropriate for this task. The final aim is it to write out the blue volume!
Thanks for hints, bw, Dieter
Dear Elaine, thank you! I am sorry, but I do not understand: how do I get the isosurface? What is the command? Carefully adjusting the boundaries of the gradient norm, I got a blue and a red part. How can I make an isosurface of one of them? Is this a function in the GUI or do I have to use the command line? Can you please give an example of how to proceed! Thank you very much, bw 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 ------------------------------------------------------------------------ Am 15.06.2018 um 18:56 schrieb Elaine Meng:
Hi Dieter, If I understand correctly, you have two maps, the original volume (density) and then another with gradient norm that is used to color the first.
In that case, you could show an isosurface of the gradient norm values, then use the “mask” command to mask the original density map by the gradient-norm isosurface (i.e. zero out parts inside or outside the isosurface):
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mask.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 14, 2018, at 10:43 PM, Dieter Blaas <dieter.blaas@meduniwien.ac.at> wrote:
Hi, I want to segment a map based on differences in 'volume data gradient norm' which I can adjust as to color the part of the volume I am interested in in blue and the one I want to get rid of in red. Is there a way of doing so? I admit that I never used the segger tool and do not know whether it would be appropriate for this task. The final aim is it to write out the blue volume!
Thanks for hints, bw, Dieter
Dear Dieter, An isosurface is just the surface of a density map showing a certain level, i.e. the “surface” display in Volume Viewer. Do you have one map or two maps? I tried to ask that by saying “if I understand correctly” in my previous message. I thought you were just coloring the isosurface of one density map by the values in a second map, where the second map is gradient norm map. It might help if you attached a picture of the display and Volume Viewer dialog. “blue part” and “red part” are ambiguous. Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 15, 2018, at 2:51 PM, Dieter Blaas <dieter.blaas@meduniwien.ac.at> wrote:
Dear Elaine, thank you! I am sorry, but I do not understand: how do I get the isosurface? What is the command? Carefully adjusting the boundaries of the gradient norm, I got a blue and a red part. How can I make an isosurface of one of them? Is this a function in the GUI or do I have to use the command line? Can you please give an example of how to proceed!
Thank you very much, bw Dieter
Dear Elaine, thanks a lot! Here it is! I open a volume, colour it according to 'gradient norm' and would like to save the red or the blue part of the whole (not just the half of the virus shown! bw Dieter On 2018-06-16 00:06, Elaine Meng wrote:
Dear Dieter, An isosurface is just the surface of a density map showing a certain level, i.e. the “surface” display in Volume Viewer.
Do you have one map or two maps? I tried to ask that by saying “if I understand correctly” in my previous message. I thought you were just coloring the isosurface of one density map by the values in a second map, where the second map is gradient norm map.
It might help if you attached a picture of the display and Volume Viewer dialog. “blue part” and “red part” are ambiguous. Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 15, 2018, at 2:51 PM, Dieter Blaas <dieter.blaas@meduniwien.ac.at> wrote:
Dear Elaine, thank you! I am sorry, but I do not understand: how do I get the isosurface? What is the command? Carefully adjusting the boundaries of the gradient norm, I got a blue and a red part. How can I make an isosurface of one of them? Is this a function in the GUI or do I have to use the command line? Can you please give an example of how to proceed!
Thank you very much, bw Dieter
-- Dr. Dieter Blaas Max F. Perutz Laboratories, Inst. Med. Biochem., Med. Univ. Vienna Dr. Bohr Gasse 9/3 A-1030 Vienna, Austria Tel. 0043 1 4277 61630 Fax 0043 1 4277 9616
Hi Dieter, This cannot be done easily. To do it you would want a a gradient norm map, then you could mask your map setting all the values to zero where the gradient norm is small. The surface color tool you are using does not compute a gradient norm map — it just computes gradient norm values on the surface which is not good enough for your use. Even if you get the gradient norm map, I see lots of red in the blue region so masking is going zero many grid points in the interior of the virus. You could try to smooth (Gaussian filter) the gradient norm map to avoid that. Finally it is possible to get the gradient norm (squared) by just using "vop subtract”, “vop multiply” and “vop add”. There are a lot of steps to it — basically you do a center difference along each axis, in other words take 2 copies of the map shift one by 1 voxel along -x and the other by 1 voxel in the +x direction, then subtract them. Do the same along y and z axes. The 3 resulting maps give you the 3 components of the gradient vector. Square each component (vop multiply map times itself), then sum the 3 squared components and you have the norm squared. There is no square-root operator so hopefully the norm squared would suffice. Tom
On Jun 15, 2018, at 10:23 PM, Blaas Dieter <dieter.blaas@meduniwien.ac.at> wrote:
Dear Elaine, thanks a lot! Here it is! I open a volume, colour it according to 'gradient norm' and would like to save the red or the blue part of the whole (not just the half of the virus shown! bw Dieter
On 2018-06-16 00:06, Elaine Meng wrote:
Dear Dieter, An isosurface is just the surface of a density map showing a certain level, i.e. the “surface” display in Volume Viewer. Do you have one map or two maps? I tried to ask that by saying “if I understand correctly” in my previous message. I thought you were just coloring the isosurface of one density map by the values in a second map, where the second map is gradient norm map. It might help if you attached a picture of the display and Volume Viewer dialog. “blue part” and “red part” are ambiguous. Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 15, 2018, at 2:51 PM, Dieter Blaas <dieter.blaas@meduniwien.ac.at> wrote: Dear Elaine, thank you! I am sorry, but I do not understand: how do I get the isosurface? What is the command? Carefully adjusting the boundaries of the gradient norm, I got a blue and a red part. How can I make an isosurface of one of them? Is this a function in the GUI or do I have to use the command line? Can you please give an example of how to proceed! Thank you very much, bw Dieter
-- Dr. Dieter Blaas Max F. Perutz Laboratories, Inst. Med. Biochem., Med. Univ. Vienna Dr. Bohr Gasse 9/3 A-1030 Vienna, Austria Tel. 0043 1 4277 61630 Fax 0043 1 4277 9616<chimera-question.png>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
Dear Tom, thank you very much for these explanations. I shall try in the next days and report! bw 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 ------------------------------------------------------------------------ Am 18.06.2018 um 19:48 schrieb Tom Goddard:
Hi Dieter,
This cannot be done easily. To do it you would want a a gradient norm map, then you could mask your map setting all the values to zero where the gradient norm is small. The surface color tool you are using does not compute a gradient norm map — it just computes gradient norm values on the surface which is not good enough for your use. Even if you get the gradient norm map, I see lots of red in the blue region so masking is going zero many grid points in the interior of the virus. You could try to smooth (Gaussian filter) the gradient norm map to avoid that. Finally it is possible to get the gradient norm (squared) by just using "vop subtract”, “vop multiply” and “vop add”. There are a lot of steps to it — basically you do a center difference along each axis, in other words take 2 copies of the map shift one by 1 voxel along -x and the other by 1 voxel in the +x direction, then subtract them. Do the same along y and z axes. The 3 resulting maps give you the 3 components of the gradient vector. Square each component (vop multiply map times itself), then sum the 3 squared components and you have the norm squared. There is no square-root operator so hopefully the norm squared would suffice.
Tom
On Jun 15, 2018, at 10:23 PM, Blaas Dieter <dieter.blaas@meduniwien.ac.at <mailto:dieter.blaas@meduniwien.ac.at>> wrote:
Dear Elaine, thanks a lot! Here it is! I open a volume, colour it according to 'gradient norm' and would like to save the red or the blue part of the whole (not just the half of the virus shown! bw Dieter
On 2018-06-16 00:06, Elaine Meng wrote:
Dear Dieter, An isosurface is just the surface of a density map showing a certain level, i.e. the “surface” display in Volume Viewer. Do you have one map or two maps? I tried to ask that by saying “if I understand correctly” in my previous message. I thought you were just coloring the isosurface of one density map by the values in a second map, where the second map is gradient norm map. It might help if you attached a picture of the display and Volume Viewer dialog. “blue part” and “red part” are ambiguous. Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 15, 2018, at 2:51 PM, Dieter Blaas <dieter.blaas@meduniwien.ac.at <mailto:dieter.blaas@meduniwien.ac.at>> wrote: Dear Elaine, thank you! I am sorry, but I do not understand: how do I get the isosurface? What is the command? Carefully adjusting the boundaries of the gradient norm, I got a blue and a red part. How can I make an isosurface of one of them? Is this a function in the GUI or do I have to use the command line? Can you please give an example of how to proceed! Thank you very much, bw Dieter
-- Dr. Dieter Blaas Max F. Perutz Laboratories, Inst. Med. Biochem., Med. Univ. Vienna Dr. Bohr Gasse 9/3 A-1030 Vienna, Austria Tel. 0043 1 4277 61630 Fax 0043 1 4277 9616<chimera-question.png>_______________________________________________ Chimera-users mailing list:Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription:http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (4)
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Blaas Dieter -
Dieter Blaas
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Elaine Meng -
Tom Goddard