Segment Maps In ChimeraX
Dear ChimeraX User Group, I'm trying to segment a map using an atomic model as a reference. To make my life easier for many of the operations I use in my work, I centered all of my structures to the origin of the session. However, when I want to segment out parts of my density, the original coordinates of the map are used for the various regions. I, therefore, can't use my centered structures as a reference as I had originally planned. I don't know if this is a bug or if this is intentionally programmed, but I am having a difficult time re-aligning the segmentation to my origin-based coordinate system. Is there a better way to do what I am trying to do or am I out of luck? Thank you. Shosholoza, Jonathan Myers
Hi Jonathan, Our volume expert is away this week but I will try to answer. I'm not sure what you mean by "centered all of my structures" ... does structures mean atomic structures or maps? Just moving maps (or atomic structures) will not change their inherent coordinates, only how they are placed relative to the camera. If the movement is a translation you can actually do it by modifying the map origin location (Tools... Volume Data... Map Coordinates). Actually you have to do it by changing origin index, which is not the location of the map origin in X,Y,Z but the grid indices that should be placed at 0,0,0 in X,Y,Z. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/mapcoords.html> If that is what you already did, it may be a bug if a subsequent segmentation does not reflect it. However, you could try saving the map to a file after changing origin index and then reopening the file prior to segmentation and seeing if that helps. If you also did rotations of the map to put it where you want, then you would have to re-sample the map on a new grid to have it saved in the rotated state. Basically it is much simpler if you have maps and structures superimposed to save the atomic structures in their positions relative to the map than vice versa, since saving the atomic structures with new coordinates does not require resampling. See <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#afterfitting> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 18, 2022, at 2:18 PM, Myers, Jonathan via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX User Group,
I'm trying to segment a map using an atomic model as a reference. To make my life easier for many of the operations I use in my work, I centered all of my structures to the origin of the session. However, when I want to segment out parts of my density, the original coordinates of the map are used for the various regions. I, therefore, can't use my centered structures as a reference as I had originally planned. I don't know if this is a bug or if this is intentionally programmed, but I am having a difficult time re-aligning the segmentation to my origin-based coordinate system.
Is there a better way to do what I am trying to do or am I out of luck? Thank you.
Shosholoza,
Jonathan Myers
Dear Elaine, I apologize for the late thanks. Thank you for the help. It looks like the Map Coordinates attributes are the parameters that I wanted to change. I also performed rotations so I would need to resample the map. I have the atomic structures exactly where I want them from another map so I would need to resample the map since the atomic structures are essentially fixed in 3D space. While looking around the documentation, I came across the map resampling function but I didn't know that is would be necessary. Shosholoza, Jonathan Myers ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Thursday, August 18, 2022 6:20:49 PM To: Myers, Jonathan Cc: chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Segment Maps In ChimeraX Hi Jonathan, Our volume expert is away this week but I will try to answer. I'm not sure what you mean by "centered all of my structures" ... does structures mean atomic structures or maps? Just moving maps (or atomic structures) will not change their inherent coordinates, only how they are placed relative to the camera. If the movement is a translation you can actually do it by modifying the map origin location (Tools... Volume Data... Map Coordinates). Actually you have to do it by changing origin index, which is not the location of the map origin in X,Y,Z but the grid indices that should be placed at 0,0,0 in X,Y,Z. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/mapcoords.html> If that is what you already did, it may be a bug if a subsequent segmentation does not reflect it. However, you could try saving the map to a file after changing origin index and then reopening the file prior to segmentation and seeing if that helps. If you also did rotations of the map to put it where you want, then you would have to re-sample the map on a new grid to have it saved in the rotated state. Basically it is much simpler if you have maps and structures superimposed to save the atomic structures in their positions relative to the map than vice versa, since saving the atomic structures with new coordinates does not require resampling. See <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#afterfitting> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 18, 2022, at 2:18 PM, Myers, Jonathan via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX User Group,
I'm trying to segment a map using an atomic model as a reference. To make my life easier for many of the operations I use in my work, I centered all of my structures to the origin of the session. However, when I want to segment out parts of my density, the original coordinates of the map are used for the various regions. I, therefore, can't use my centered structures as a reference as I had originally planned. I don't know if this is a bug or if this is intentionally programmed, but I am having a difficult time re-aligning the segmentation to my origin-based coordinate system.
Is there a better way to do what I am trying to do or am I out of luck? Thank you.
Shosholoza,
Jonathan Myers
Hi Jonathan, Sounds like there might be a bug here but you left out so many details there is no way to tell. How are you segmenting the density? You would have to explain all the steps. Tom
On Aug 18, 2022, at 2:18 PM, Myers, Jonathan via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX User Group,
I'm trying to segment a map using an atomic model as a reference. To make my life easier for many of the operations I use in my work, I centered all of my structures to the origin of the session. However, when I want to segment out parts of my density, the original coordinates of the map are used for the various regions. I, therefore, can't use my centered structures as a reference as I had originally planned. I don't know if this is a bug or if this is intentionally programmed, but I am having a difficult time re-aligning the segmentation to my origin-based coordinate system.
Is there a better way to do what I am trying to do or am I out of luck? Thank you.
Shosholoza,
Jonathan Myers _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
participants (3)
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Elaine Meng -
Myers, Jonathan -
Tom Goddard