To whom may concern, This is Yanhe Zhao, from UT Southwestern Medical Center. I was curious that how can I exclude the lipid bilayer to show the transmembrane protein electron density when "zone" could not be used as I have no sequence and pdb information. Thanks a lot in advance for any input. Best regards, Yanhe
Hi Yanhe, I guess you mean you have no atomic structure fitted inside, only the map? Zones are defined using atomic coordinates. However, without any atoms, you can interactively (manually by moving a sphere with the mouse or trackpad) delete parts of the map using the Volume Eraser tool, see: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/voleraser/voleraser.html> It is in the menu, Tools... Volume Data... Volume Eraser. Another possible approach is to try segmenting the map, e.g. menu: Tools... Volume Data... Segger. <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/segger/segment.html> This has many features and controls to group/ungroup segmentation regions, etc., but if you can get the bilayer segmented separately from the protein density, then you can select (Ctrl-click) and hide the regions you don't want to see (Segger menu: Regions... Hide) I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 17, 2021, at 1:00 PM, Yanhe Zhao <yanhezhao1990@gmail.com> wrote:
To whom may concern,
This is Yanhe Zhao, from UT Southwestern Medical Center.
I was curious that how can I exclude the lipid bilayer to show the transmembrane protein electron density when "zone" could not be used as I have no sequence and pdb information. Thanks a lot in advance for any input.
Best regards, Yanhe
Hi Elaine, Sorry for my delay as I was trying the ways you described above. Thanks a lot for that. I have another question as below: How can I have color gradient along the map dimensions? For example along X. Thanks and best, Yanhe Elaine Meng <meng@cgl.ucsf.edu> 于2021年5月17日周一 下午3:14写道：
Hi Yanhe, I guess you mean you have no atomic structure fitted inside, only the map? Zones are defined using atomic coordinates.
However, without any atoms, you can interactively (manually by moving a sphere with the mouse or trackpad) delete parts of the map using the Volume Eraser tool, see:
< https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/voleraser/voleras...
It is in the menu, Tools... Volume Data... Volume Eraser.
Another possible approach is to try segmenting the map, e.g. menu: Tools... Volume Data... Segger. < https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/segger/segment.ht...
This has many features and controls to group/ungroup segmentation regions, etc., but if you can get the bilayer segmented separately from the protein density, then you can select (Ctrl-click) and hide the regions you don't want to see (Segger menu: Regions... Hide)
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 17, 2021, at 1:00 PM, Yanhe Zhao <yanhezhao1990@gmail.com> wrote:
To whom may concern,
This is Yanhe Zhao, from UT Southwestern Medical Center.
I was curious that how can I exclude the lipid bilayer to show the transmembrane protein electron density when "zone" could not be used as I have no sequence and pdb information. Thanks a lot in advance for any input.
Best regards, Yanhe
I'm trying Tools...Volume Data...Surface Color, have not figured out the one I wanted. Any suggestions would be appreciated. Thanks and cheers, Yanhe Elaine Meng <meng@cgl.ucsf.edu> 于2021年5月17日周一 下午3:14写道：
Hi Yanhe, I guess you mean you have no atomic structure fitted inside, only the map? Zones are defined using atomic coordinates.
However, without any atoms, you can interactively (manually by moving a sphere with the mouse or trackpad) delete parts of the map using the Volume Eraser tool, see:
< https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/voleraser/voleras...
It is in the menu, Tools... Volume Data... Volume Eraser.
Another possible approach is to try segmenting the map, e.g. menu: Tools... Volume Data... Segger. < https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/segger/segment.ht...
This has many features and controls to group/ungroup segmentation regions, etc., but if you can get the bilayer segmented separately from the protein density, then you can select (Ctrl-click) and hide the regions you don't want to see (Segger menu: Regions... Hide)
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 17, 2021, at 1:00 PM, Yanhe Zhao <yanhezhao1990@gmail.com> wrote:
To whom may concern,
This is Yanhe Zhao, from UT Southwestern Medical Center.
I was curious that how can I exclude the lipid bilayer to show the transmembrane protein electron density when "zone" could not be used as I have no sequence and pdb information. Thanks a lot in advance for any input.
Best regards, Yanhe
Hi Yanhe, In Surface Color you would choose coloring by "height" which actually means by distance from a plane along its normal; the plane can be in any orientation. You would just need to enter origin and axis values to define the plane. The default values of these are set to color along map Z (axis 0 0 1). To color along X instead, change axis to 1 0 0 . I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 19, 2021, at 6:49 PM, Yanhe Zhao <yanhezhao1990@gmail.com> wrote:
I'm trying Tools...Volume Data...Surface Color, have not figured out the one I wanted. Any suggestions would be appreciated. Thanks and cheers, Yanhe
On May 19, 2021, at 6:42 PM, Yanhe Zhao <yanhezhao1990@gmail.com> wrote:
Hi Elaine,
Sorry for my delay as I was trying the ways you described above. Thanks a lot for that. I have another question as below: How can I have color gradient along the map dimensions? For example along X.
Thanks and best, Yanhe
Hi Elaine, Thanks for the quick reply, it helps a lot. How can I show the coordinate axis and know the xyz of one exact position which maybe used as my origin for coloring gradient. Thanks again for your help, Yanhe On Wed, May 19, 2021, 9:08 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Yanhe, In Surface Color you would choose coloring by "height" which actually means by distance from a plane along its normal; the plane can be in any orientation. You would just need to enter origin and axis values to define the plane. The default values of these are set to color along map Z (axis 0 0 1). To color along X instead, change axis to 1 0 0 . I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 19, 2021, at 6:49 PM, Yanhe Zhao <yanhezhao1990@gmail.com> wrote:
I'm trying Tools...Volume Data...Surface Color, have not figured out the one I wanted. Any suggestions would be appreciated. Thanks and cheers, Yanhe
On May 19, 2021, at 6:42 PM, Yanhe Zhao <yanhezhao1990@gmail.com> wrote:
Hi Elaine,
Sorry for my delay as I was trying the ways you described above. Thanks a lot for that. I have another question as below: How can I have color gradient along the map dimensions? For example along X.
Thanks and best, Yanhe
Hi Yanhe, When you first open data after starting Chimera (and before you moved it), its X axis is left-right, Y is up-down, Z is near-far from viewer position. Or you can restore that initial orientation with command: reset <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/reset.html> Another way to see the axes even after you moved everything is to open the axis object file "XYZ-axes.bild" linked to this page (download as plain text, keep .bild at the end of filename, open in Chimera) to display them in 3D: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/bild.html> Look at the text of the XYZ-axes.bild file to see which axis is which color. As for the origin point, either you might already know if you are the person who made the map, or you can use the Volume Viewer tool's menu: Features... Coordinates to show the map origin index (this is NOT the coordinates of the origin but instead, the grid units of the map where the 0,0,0 coordinates are) and voxel size, <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#coordinates> ...and use those values to calculate what origin coordinates you want to use in Surface Color. I hope this helps, Elaine
On May 19, 2021, at 7:50 PM, Yanhe Zhao <yanhezhao1990@gmail.com> wrote:
Hi Elaine, Thanks for the quick reply, it helps a lot. How can I show the coordinate axis and know the xyz of one exact position which maybe used as my origin for coloring gradient. Thanks again for your help, Yanhe
On Wed, May 19, 2021, 9:08 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Yanhe, In Surface Color you would choose coloring by "height" which actually means by distance from a plane along its normal; the plane can be in any orientation. You would just need to enter origin and axis values to define the plane. The default values of these are set to color along map Z (axis 0 0 1). To color along X instead, change axis to 1 0 0 . I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 19, 2021, at 6:49 PM, Yanhe Zhao <yanhezhao1990@gmail.com> wrote:
I'm trying Tools...Volume Data...Surface Color, have not figured out the one I wanted. Any suggestions would be appreciated. Thanks and cheers, Yanhe
On May 19, 2021, at 6:42 PM, Yanhe Zhao <yanhezhao1990@gmail.com> wrote:
Hi Elaine,
Sorry for my delay as I was trying the ways you described above. Thanks a lot for that. I have another question as below: How can I have color gradient along the map dimensions? For example along X.
Thanks and best, Yanhe
Hi Elaine, Thank you so much, that help me a lot and I made it. Have great weekend. Best, Yanhe Elaine Meng <meng@cgl.ucsf.edu> 于2021年5月20日周四 下午12:51写道：
Hi Yanhe, When you first open data after starting Chimera (and before you moved it), its X axis is left-right, Y is up-down, Z is near-far from viewer position. Or you can restore that initial orientation with command: reset <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/reset.html>
Another way to see the axes even after you moved everything is to open the axis object file "XYZ-axes.bild" linked to this page (download as plain text, keep .bild at the end of filename, open in Chimera) to display them in 3D: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/bild.html>
Look at the text of the XYZ-axes.bild file to see which axis is which color.
As for the origin point, either you might already know if you are the person who made the map, or you can use the Volume Viewer tool's menu: Features... Coordinates to show the map origin index (this is NOT the coordinates of the origin but instead, the grid units of the map where the 0,0,0 coordinates are) and voxel size, < https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volu...
...and use those values to calculate what origin coordinates you want to use in Surface Color.
I hope this helps, Elaine
On May 19, 2021, at 7:50 PM, Yanhe Zhao <yanhezhao1990@gmail.com> wrote:
Hi Elaine, Thanks for the quick reply, it helps a lot. How can I show the coordinate axis and know the xyz of one exact position which maybe used as my origin for coloring gradient. Thanks again for your help, Yanhe
On Wed, May 19, 2021, 9:08 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Yanhe, In Surface Color you would choose coloring by "height" which actually means by distance from a plane along its normal; the plane can be in any orientation. You would just need to enter origin and axis values to define the plane. The default values of these are set to color along map Z (axis 0 0 1). To color along X instead, change axis to 1 0 0 . I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 19, 2021, at 6:49 PM, Yanhe Zhao <yanhezhao1990@gmail.com> wrote:
I'm trying Tools...Volume Data...Surface Color, have not figured out the one I wanted. Any suggestions would be appreciated. Thanks and cheers, Yanhe
On May 19, 2021, at 6:42 PM, Yanhe Zhao <yanhezhao1990@gmail.com> wrote:
Hi Elaine,
Sorry for my delay as I was trying the ways you described above. Thanks a lot for that. I have another question as below: How can I have color gradient along the map dimensions? For example along X.
Thanks and best, Yanhe
participants (2)
-
Elaine Meng -
Yanhe Zhao