Dear all, I seek for help that how to change the unit of "color key" to angstrom. As the default value displaied in "color key" is just number, I wonder what it means. Any reply will be greatly appreciated. -- Regards! C.J.
Dear CJ, The units depend on what you are trying to show with color. If you started Color Key with the button in the Surface Color tool and in that tool, you were coloring by distance (radius, cylinder radius, or height), the units are whatever distance units are in your structure data. That is usually angstroms, but it could be nanometers for some density maps. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.h...> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolor...> If you mean you want to display an angstrom symbol, that can be done with the 2D Labels tool, which is another tab on the same dialog as Color Key. You can just make a symbol label and then drag it to wherever you want. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.h...> There is an example of putting an angstrom symbol over a color key in this image tutorial: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/bfactor.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 Dec 15, 2010, at 6:36 PM, C.J. wrote:
Dear all, I seek for help that how to change the unit of "color key" to angstrom. As the default value displaied in "color key" is just number, I wonder what it means. Any reply will be greatly appreciated. -- Regards! C.J.
Thanks. But I don't know clearlly how to set these paremeters to creat a color key with unit of "Angstrom" automatically. More help will be appreciated. 2010/12/16 Elaine Meng <meng@cgl.ucsf.edu>:
Dear CJ, The units depend on what you are trying to show with color. If you started Color Key with the button in the Surface Color tool and in that tool, you were coloring by distance (radius, cylinder radius, or height), the units are whatever distance units are in your structure data. That is usually angstroms, but it could be nanometers for some density maps. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.h...> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolor...>
If you mean you want to display an angstrom symbol, that can be done with the 2D Labels tool, which is another tab on the same dialog as Color Key. You can just make a symbol label and then drag it to wherever you want. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.h...>
There is an example of putting an angstrom symbol over a color key in this image tutorial: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/bfactor.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 Dec 15, 2010, at 6:36 PM, C.J. wrote:
Dear all, I seek for help that how to change the unit of "color key" to angstrom. As the default value displaied in "color key" is just number, I wonder what it means. Any reply will be greatly appreciated. -- Regards! C.J.
-- Regards! C.J.
Hi CJ, If your structure and/or map data is in angstrom cooordinates, and you are coloring by distance in Surface Color, and you start Color Key from the button in Surface Color, it is already automatically in angstrom units. Elaine On Dec 15, 2010, at 7:21 PM, C.J. wrote:
Thanks.
But I don't know clearlly how to set these paremeters to creat a color key with unit of "Angstrom" automatically. More help will be appreciated.
2010/12/16 Elaine Meng <meng@cgl.ucsf.edu>:
Dear CJ, The units depend on what you are trying to show with color. If you started Color Key with the button in the Surface Color tool and in that tool, you were coloring by distance (radius, cylinder radius, or height), the units are whatever distance units are in your structure data. That is usually angstroms, but it could be nanometers for some density maps. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.h...> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolor...>
If you mean you want to display an angstrom symbol, that can be done with the 2D Labels tool, which is another tab on the same dialog as Color Key. You can just make a symbol label and then drag it to wherever you want. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.h...>
There is an example of putting an angstrom symbol over a color key in this image tutorial: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/bfactor.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 Dec 15, 2010, at 6:36 PM, C.J. wrote:
Dear all, I seek for help that how to change the unit of "color key" to angstrom. As the default value displaied in "color key" is just number, I wonder what it means. Any reply will be greatly appreciated. -- Regards! C.J.
-- Regards! C.J.
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Dear Dr. Elaine, I am afraid that my structure is not in angstrom coordinates. So, any way to change the color key? Thanks all the same. 2010/12/17 Elaine Meng <meng@cgl.ucsf.edu>:
Hi CJ, If your structure and/or map data is in angstrom cooordinates, and you are coloring by distance in Surface Color, and you start Color Key from the button in Surface Color, it is already automatically in angstrom units. Elaine
On Dec 15, 2010, at 7:21 PM, C.J. wrote:
Thanks.
But I don't know clearlly how to set these paremeters to creat a color key with unit of "Angstrom" automatically. More help will be appreciated.
2010/12/16 Elaine Meng <meng@cgl.ucsf.edu>:
Dear CJ, The units depend on what you are trying to show with color. If you started Color Key with the button in the Surface Color tool and in that tool, you were coloring by distance (radius, cylinder radius, or height), the units are whatever distance units are in your structure data. That is usually angstroms, but it could be nanometers for some density maps. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.h...> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfcolor/surfcolor...>
If you mean you want to display an angstrom symbol, that can be done with the 2D Labels tool, which is another tab on the same dialog as Color Key. You can just make a symbol label and then drag it to wherever you want. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.h...>
There is an example of putting an angstrom symbol over a color key in this image tutorial: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/bfactor.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 Dec 15, 2010, at 6:36 PM, C.J. wrote:
Dear all, I seek for help that how to change the unit of "color key" to angstrom. As the default value displaied in "color key" is just number, I wonder what it means. Any reply will be greatly appreciated. -- Regards! C.J.
-- Regards! C.J.
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- Regards! C.J.
Hi CJ, If you know what distance units are in your structure, you can simply apply the conversion factor to the values in the Color Key dialog. In other words, if your structure is in nanometer units, you can just manually type new values into the Color Key dialog that are 10x the values that were there initially. If the values from the structure are 10 and 50 (nanometers), you can just manually edit the values in the Color Key dialog to 100 and 500, then they will be in angstroms. If your structure is in grid units where the grid points are spaced 1.582 angstroms apart, then you would multiply by 1.582 instead. (etc.) Best, 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 Dec 16, 2010, at 5:17 PM, C.J. wrote:
Dear Dr. Elaine,
I am afraid that my structure is not in angstrom coordinates. So, any way to change the color key? Thanks all the same.
2010/12/17 Elaine Meng <meng@cgl.ucsf.edu>:
Hi CJ, If your structure and/or map data is in angstrom cooordinates, and you are coloring by distance in Surface Color, and you start Color Key from the button in Surface Color, it is already automatically in angstrom units. Elaine
Thanks, but can I change the distance unit of color key in Chimera? Or I have to modify the pdb structure file to change that? 2010/12/18 Elaine Meng <meng@cgl.ucsf.edu>:
Hi CJ, If you know what distance units are in your structure, you can simply apply the conversion factor to the values in the Color Key dialog. In other words, if your structure is in nanometer units, you can just manually type new values into the Color Key dialog that are 10x the values that were there initially. If the values from the structure are 10 and 50 (nanometers), you can just manually edit the values in the Color Key dialog to 100 and 500, then they will be in angstroms. If your structure is in grid units where the grid points are spaced 1.582 angstroms apart, then you would multiply by 1.582 instead. (etc.) Best, 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 Dec 16, 2010, at 5:17 PM, C.J. wrote:
Dear Dr. Elaine,
I am afraid that my structure is not in angstrom coordinates. So, any way to change the color key? Thanks all the same.
2010/12/17 Elaine Meng <meng@cgl.ucsf.edu>:
Hi CJ, If your structure and/or map data is in angstrom cooordinates, and you are coloring by distance in Surface Color, and you start Color Key from the button in Surface Color, it is already automatically in angstrom units. Elaine
-- Regards! C.J.
Hi CJ, My previous reply (12/18 below) already explained how to change the units in the color key. I can' t think of any other way to explain this, sorry. If your structure is from the PDB, however, it is already in angstrom units. Elaine On Dec 20, 2010, at 7:44 PM, C.J. wrote:
Thanks, but can I change the distance unit of color key in Chimera? Or I have to modify the pdb structure file to change that?
2010/12/18 Elaine Meng <meng@cgl.ucsf.edu>:
Hi CJ, If you know what distance units are in your structure, you can simply apply the conversion factor to the values in the Color Key dialog. In other words, if your structure is in nanometer units, you can just manually type new values into the Color Key dialog that are 10x the values that were there initially. If the values from the structure are 10 and 50 (nanometers), you can just manually edit the values in the Color Key dialog to 100 and 500, then they will be in angstroms. If your structure is in grid units where the grid points are spaced 1.582 angstroms apart, then you would multiply by 1.582 instead. (etc.) Best, 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 Dec 16, 2010, at 5:17 PM, C.J. wrote:
Dear Dr. Elaine,
I am afraid that my structure is not in angstrom coordinates. So, any way to change the color key? Thanks all the same.
2010/12/17 Elaine Meng <meng@cgl.ucsf.edu>:
Hi CJ, If your structure and/or map data is in angstrom cooordinates, and you are coloring by distance in Surface Color, and you start Color Key from the button in Surface Color, it is already automatically in angstrom units. Elaine
-- Regards! C.J.
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Dear Elaine, Thanks for explaining that for many times Regards! CJ 2010/12/22 Elaine Meng <meng@cgl.ucsf.edu>:
Hi CJ, My previous reply (12/18 below) already explained how to change the units in the color key. I can' t think of any other way to explain this, sorry. If your structure is from the PDB, however, it is already in angstrom units. Elaine
On Dec 20, 2010, at 7:44 PM, C.J. wrote:
Thanks, but can I change the distance unit of color key in Chimera? Or I have to modify the pdb structure file to change that?
2010/12/18 Elaine Meng <meng@cgl.ucsf.edu>:
Hi CJ, If you know what distance units are in your structure, you can simply apply the conversion factor to the values in the Color Key dialog. In other words, if your structure is in nanometer units, you can just manually type new values into the Color Key dialog that are 10x the values that were there initially. If the values from the structure are 10 and 50 (nanometers), you can just manually edit the values in the Color Key dialog to 100 and 500, then they will be in angstroms. If your structure is in grid units where the grid points are spaced 1.582 angstroms apart, then you would multiply by 1.582 instead. (etc.) Best, 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 Dec 16, 2010, at 5:17 PM, C.J. wrote:
Dear Dr. Elaine,
I am afraid that my structure is not in angstrom coordinates. So, any way to change the color key? Thanks all the same.
2010/12/17 Elaine Meng <meng@cgl.ucsf.edu>:
Hi CJ, If your structure and/or map data is in angstrom cooordinates, and you are coloring by distance in Surface Color, and you start Color Key from the button in Surface Color, it is already automatically in angstrom units. Elaine
-- Regards! C.J.
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- Regards! C.J.
Hi CJ, One more idea: maybe you want Scale Bar (under "Tools... Higher-Order Structure" in the menu) instead of Color Key. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/scalebar/scalebar.h...> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.h...> Scale Bar is just a stick with measured length, without any relationship to color. Color Key shows what colors are used for what values, which could be distances or some other thing like B-factors. If you start it from some other tool (Surface Color, Render by Attribute) the values will be the same thing that is shown in that other tool. Best, Elaine On Dec 22, 2010, at 2:17 AM, C.J. wrote:
Dear Elaine,
Thanks for explaining that for many times
Regards! CJ
2010/12/22 Elaine Meng <meng@cgl.ucsf.edu>:
Hi CJ, My previous reply (12/18 below) already explained how to change the units in the color key. I can' t think of any other way to explain this, sorry. If your structure is from the PDB, however, it is already in angstrom units. Elaine
On Dec 20, 2010, at 7:44 PM, C.J. wrote:
Thanks, but can I change the distance unit of color key in Chimera? Or I have to modify the pdb structure file to change that?
2010/12/18 Elaine Meng <meng@cgl.ucsf.edu>:
Hi CJ, If you know what distance units are in your structure, you can simply apply the conversion factor to the values in the Color Key dialog. In other words, if your structure is in nanometer units, you can just manually type new values into the Color Key dialog that are 10x the values that were there initially. If the values from the structure are 10 and 50 (nanometers), you can just manually edit the values in the Color Key dialog to 100 and 500, then they will be in angstroms. If your structure is in grid units where the grid points are spaced 1.582 angstroms apart, then you would multiply by 1.582 instead. (etc.) Best, 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 Dec 16, 2010, at 5:17 PM, C.J. wrote:
Dear Dr. Elaine,
I am afraid that my structure is not in angstrom coordinates. So, any way to change the color key? Thanks all the same.
2010/12/17 Elaine Meng <meng@cgl.ucsf.edu>:
Hi CJ, If your structure and/or map data is in angstrom cooordinates, and you are coloring by distance in Surface Color, and you start Color Key from the button in Surface Color, it is already automatically in angstrom units. Elaine
Dear Elaine, Thank you against! Regards! CJ 2010/12/23 Elaine Meng <meng@cgl.ucsf.edu>:
Hi CJ, One more idea: maybe you want Scale Bar (under "Tools... Higher-Order Structure" in the menu) instead of Color Key.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/scalebar/scalebar.h...> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.h...>
Scale Bar is just a stick with measured length, without any relationship to color.
Color Key shows what colors are used for what values, which could be distances or some other thing like B-factors. If you start it from some other tool (Surface Color, Render by Attribute) the values will be the same thing that is shown in that other tool. Best, Elaine
On Dec 22, 2010, at 2:17 AM, C.J. wrote:
Dear Elaine,
Thanks for explaining that for many times
Regards! CJ
2010/12/22 Elaine Meng <meng@cgl.ucsf.edu>:
Hi CJ, My previous reply (12/18 below) already explained how to change the units in the color key. I can' t think of any other way to explain this, sorry. If your structure is from the PDB, however, it is already in angstrom units. Elaine
On Dec 20, 2010, at 7:44 PM, C.J. wrote:
Thanks, but can I change the distance unit of color key in Chimera? Or I have to modify the pdb structure file to change that?
2010/12/18 Elaine Meng <meng@cgl.ucsf.edu>:
Hi CJ, If you know what distance units are in your structure, you can simply apply the conversion factor to the values in the Color Key dialog. In other words, if your structure is in nanometer units, you can just manually type new values into the Color Key dialog that are 10x the values that were there initially. If the values from the structure are 10 and 50 (nanometers), you can just manually edit the values in the Color Key dialog to 100 and 500, then they will be in angstroms. If your structure is in grid units where the grid points are spaced 1.582 angstroms apart, then you would multiply by 1.582 instead. (etc.) Best, 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 Dec 16, 2010, at 5:17 PM, C.J. wrote:
Dear Dr. Elaine,
I am afraid that my structure is not in angstrom coordinates. So, any way to change the color key? Thanks all the same.
2010/12/17 Elaine Meng <meng@cgl.ucsf.edu>: > Hi CJ, > If your structure and/or map data is in angstrom cooordinates, and you are coloring by distance in Surface Color, and you start Color Key from the button in Surface Color, it is already automatically in angstrom units. > Elaine
-- Regards! C.J.
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Elaine Meng