Greeting there, I am trying to get coordinate for fulcrum selection in cryoSPARC. I use volume tracer place a marker on the position of map density I wanted, with the maker selected, I use getcrd command report the coordinate in xyz in Angstroms, when I divide the values by the pixel size, the xyz in voxels are make no sense, as they are larger than my volume size. Like my volume size is 1024^3, got coordinates in Angstroms 2100,2100,2000, my pixel size is 1.475. Could you please anyone help me out? Do I did something wrong? Thanks and best, Yanhe
Hi Yanhe, As I understand it, you cannot tell the location of your volume from its size. It might be placed at some other coordinates, not 0,0,0. You can use Volume Viewer menu Features... Coordinates to see the origin index (volume grid indices that would be at zero) and voxel size, and click "Center" if you want to center the volume grid at 0,0,0. <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html> <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#coordinates> Also consider that "getcrd" gives the coordinates in the atomic model's coordinate system, which is not necessarily the same as the volume model's coordinate system (if they were moved separately, like for fitting), or if you use the "xformed" keyword, it gives the coordinates in the screen/laboratory coordinate system (X and Y in plane of screen, Z coming in/out of screen), which is also not the same as the volume model coordinate system. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/getcrd.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 9, 2023, at 12:53 PM, Yanhe Zhao via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Greeting there,
I am trying to get coordinate for fulcrum selection in cryoSPARC. I use volume tracer place a marker on the position of map density I wanted, with the maker selected, I use getcrd command report the coordinate in xyz in Angstroms, when I divide the values by the pixel size, the xyz in voxels are make no sense, as they are larger than my volume size. Like my volume size is 1024^3, got coordinates in Angstroms 2100,2100,2000, my pixel size is 1.475. Could you please anyone help me out? Do I did something wrong?
Thanks and best, Yanhe
Dear Elaine, Thanks a lot for the information. Your are right, my volume was placed on other coordinates, and I have it saved and open by chimera again. After I click center, the origin index is not 0, so I edited it to 0 and press enter, then save the volume. So right now the volume is center at 0,0,0. Am I doing right thing? Thanks and cheers, Yanhe Elaine Meng <meng@cgl.ucsf.edu> 于2023年6月9日周五 15:16写道：
Hi Yanhe, As I understand it, you cannot tell the location of your volume from its size. It might be placed at some other coordinates, not 0,0,0.
You can use Volume Viewer menu Features... Coordinates to see the origin index (volume grid indices that would be at zero) and voxel size, and click "Center" if you want to center the volume grid at 0,0,0.
< https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/fram...
< https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volu...
Also consider that "getcrd" gives the coordinates in the atomic model's coordinate system, which is not necessarily the same as the volume model's coordinate system (if they were moved separately, like for fitting), or if you use the "xformed" keyword, it gives the coordinates in the screen/laboratory coordinate system (X and Y in plane of screen, Z coming in/out of screen), which is also not the same as the volume model coordinate system.
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/getcrd.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 9, 2023, at 12:53 PM, Yanhe Zhao via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
Greeting there,
I am trying to get coordinate for fulcrum selection in cryoSPARC. I use volume tracer place a marker on the position of map density I wanted, with the maker selected, I use getcrd command report the coordinate in xyz in Angstroms, when I divide the values by the pixel size, the xyz in voxels are make no sense, as they are larger than my volume size. Like my volume size is 1024^3, got coordinates in Angstroms 2100,2100,2000, my pixel size is 1.475. Could you please anyone help me out? Do I did something wrong?
Thanks and best, Yanhe
Hi Yanhe, I don't know what you want, so I don't know if you are doing the right thing. If you edit origin index to 0,0,0 the map is not centered at 0,0,0. Origin index is which i,j,k grid point of the map is at xyz 0,0,0. So if you change it to 1,1,1 that means the corner of the map grid (grid point 1,1,1) is at xyz 0,0,0. If you want map center at 0,0,0 then click the "center" button. Here is the help
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html> <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#coordinates>
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 9, 2023, at 2:33 PM, Yanhe Zhao via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Elaine,
Thanks a lot for the information. Your are right, my volume was placed on other coordinates, and I have it saved and open by chimera again. After I click center, the origin index is not 0, so I edited it to 0 and press enter, then save the volume. So right now the volume is center at 0,0,0. Am I doing right thing?
Thanks and cheers, Yanhe
Elaine Meng <meng@cgl.ucsf.edu> 于2023年6月9日周五 15:16写道： Hi Yanhe, As I understand it, you cannot tell the location of your volume from its size. It might be placed at some other coordinates, not 0,0,0.
You can use Volume Viewer menu Features... Coordinates to see the origin index (volume grid indices that would be at zero) and voxel size, and click "Center" if you want to center the volume grid at 0,0,0.
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html> <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#coordinates>
Also consider that "getcrd" gives the coordinates in the atomic model's coordinate system, which is not necessarily the same as the volume model's coordinate system (if they were moved separately, like for fitting), or if you use the "xformed" keyword, it gives the coordinates in the screen/laboratory coordinate system (X and Y in plane of screen, Z coming in/out of screen), which is also not the same as the volume model coordinate system.
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/getcrd.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 9, 2023, at 12:53 PM, Yanhe Zhao via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Greeting there,
I am trying to get coordinate for fulcrum selection in cryoSPARC. I use volume tracer place a marker on the position of map density I wanted, with the maker selected, I use getcrd command report the coordinate in xyz in Angstroms, when I divide the values by the pixel size, the xyz in voxels are make no sense, as they are larger than my volume size. Like my volume size is 1024^3, got coordinates in Angstroms 2100,2100,2000, my pixel size is 1.475. Could you please anyone help me out? Do I did something wrong?
Thanks and best, Yanhe
Dear Elaine, Thank you so much for your answer. I thought I got it now. Thanks and cheers, Yanhe Elaine Meng <meng@cgl.ucsf.edu> 于2023年6月9日周五 16:44写道：
Hi Yanhe, I don't know what you want, so I don't know if you are doing the right thing.
If you edit origin index to 0,0,0 the map is not centered at 0,0,0. Origin index is which i,j,k grid point of the map is at xyz 0,0,0. So if you change it to 1,1,1 that means the corner of the map grid (grid point 1,1,1) is at xyz 0,0,0. If you want map center at 0,0,0 then click the "center" button. Here is the help
< https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/fram...
< https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volu...
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 9, 2023, at 2:33 PM, Yanhe Zhao via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
Dear Elaine,
Thanks a lot for the information. Your are right, my volume was placed on other coordinates, and I have it saved and open by chimera again. After I click center, the origin index is not 0, so I edited it to 0 and press enter, then save the volume. So right now the volume is center at 0,0,0. Am I doing right thing?
Thanks and cheers, Yanhe
Elaine Meng <meng@cgl.ucsf.edu> 于2023年6月9日周五 15:16写道： Hi Yanhe, As I understand it, you cannot tell the location of your volume from its size. It might be placed at some other coordinates, not 0,0,0.
You can use Volume Viewer menu Features... Coordinates to see the origin index (volume grid indices that would be at zero) and voxel size, and click "Center" if you want to center the volume grid at 0,0,0.
< https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/fram...
< https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volu...
Also consider that "getcrd" gives the coordinates in the atomic model's coordinate system, which is not necessarily the same as the volume model's coordinate system (if they were moved separately, like for fitting), or if you use the "xformed" keyword, it gives the coordinates in the screen/laboratory coordinate system (X and Y in plane of screen, Z coming in/out of screen), which is also not the same as the volume model coordinate system.
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/getcrd.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 9, 2023, at 12:53 PM, Yanhe Zhao via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:
Greeting there,
I am trying to get coordinate for fulcrum selection in cryoSPARC. I use volume tracer place a marker on the position of map density I wanted, with the maker selected, I use getcrd command report the coordinate in xyz in Angstroms, when I divide the values by the pixel size, the xyz in voxels are make no sense, as they are larger than my volume size. Like my volume size is 1024^3, got coordinates in Angstroms 2100,2100,2000, my pixel size is 1.475. Could you please anyone help me out? Do I did something wrong?
Thanks and best, Yanhe
participants (2)
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Elaine Meng -
Yanhe Zhao