Morph map parts transformation in a complex
Dear user group, I am trying to do volume morph to transform different parts of a complex into another part of the same complex. Because I did drag and fit each segmented parts, the map positions are no longer the same and I have this error: Map positions are not the same. Is there a way to do the map morph to transform different map parts in the complex? Many thanks! Hong
Hi Hong, As mentioned in the volume morph" help, <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#morph <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#morph>> "the input maps should have the same grids: dimensions, spacing, and numbers of points. Note volume resample can be used to make a copy of one map that has the same grid as another." Here is the "volume resample" help, with explanation that you can lose some resolution from resampling: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#resample <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#resample>> There is also a "volume add" if you are just trying to put different parts together, rather than morphing: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#add <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#add>> 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 5:36 PM, HONG ZHAN via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear user group,
I am trying to do volume morph to transform different parts of a complex into another part of the same complex. Because I did drag and fit each segmented parts, the map positions are no longer the same and I have this error: Map positions are not the same.
Is there a way to do the map morph to transform different map parts in the complex?
Many thanks! Hong
Thank you Elaine for the quick response! I did use the volume resample, but I misunderstood the onGrid pointer… I made it! The volume morph dissolves one part of the complex and appears the other, but I want to have a "movement movie", like using morph for atomic models, one part of the complex flies out and fit into the other part, is there any functions I missed? Thanks! Hong On Aug 18, 2022, at 8:14 PM, Elaine Meng <meng@cgl.ucsf.edu<mailto:meng@cgl.ucsf.edu>> wrote: Hi Hong, As mentioned in the volume morph" help, <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#morph> "the input maps should have the same grids: dimensions, spacing, and numbers of points. Note volume resample can be used to make a copy of one map that has the same grid as another." Here is the "volume resample" help, with explanation that you can lose some resolution from resampling: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#resample> There is also a "volume add" if you are just trying to put different parts together, rather than morphing: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#add> 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 5:36 PM, HONG ZHAN via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Dear user group, I am trying to do volume morph to transform different parts of a complex into another part of the same complex. Because I did drag and fit each segmented parts, the map positions are no longer the same and I have this error: Map positions are not the same. Is there a way to do the map morph to transform different map parts in the complex? Many thanks! Hong
Hi Hong, The volume morph capability just linearly interpolates map values at each grid point to go from one map to another. So if some density moves to an entirely new location it does not appear to move during the volume morph, it simply vanishes from the starting location and appears in the ending location. If you want to shown a volume move you may instead want the mobile part to be a separate map. You fit it to the starting position and record that position with the command "view name pos1" command, then fit it to the final position and save that position with another "view name pos2". Then you could use the command "fly 100 pos1 pos2" to move have the map fly between the two positions over 100 frames. This does not change the shape of the mobile density it just moves it. If you wanted to change its shape while it flies to the new location you could use the "volume morph" command to change its shape while the fly command moves it. Tom
On Aug 18, 2022, at 6:46 PM, HONG ZHAN via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Thank you Elaine for the quick response! I did use the volume resample, but I misunderstood the onGrid pointer… I made it!
The volume morph dissolves one part of the complex and appears the other, but I want to have a "movement movie", like using morph for atomic models, one part of the complex flies out and fit into the other part, is there any functions I missed?
Thanks!
Hong
On Aug 18, 2022, at 8:14 PM, Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote:
Hi Hong, As mentioned in the volume morph" help, <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#morph <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#morph>>
"the input maps should have the same grids: dimensions, spacing, and numbers of points. Note volume resample can be used to make a copy of one map that has the same grid as another."
Here is the "volume resample" help, with explanation that you can lose some resolution from resampling: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#resample <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#resample>>
There is also a "volume add" if you are just trying to put different parts together, rather than morphing: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#add <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#add>>
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 5:36 PM, HONG ZHAN via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Dear user group,
I am trying to do volume morph to transform different parts of a complex into another part of the same complex. Because I did drag and fit each segmented parts, the map positions are no longer the same and I have this error: Map positions are not the same.
Is there a way to do the map morph to transform different map parts in the complex?
Many thanks! Hong
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Super thanks Tom! it is what I want . Best, Hong ________________________________ From: Tom Goddard <goddard@sonic.net> Sent: Monday, August 22, 2022 6:25 PM To: HONG ZHAN <hzhan3@wisc.edu> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Morph map parts transformation in a complex Hi Hong, The volume morph capability just linearly interpolates map values at each grid point to go from one map to another. So if some density moves to an entirely new location it does not appear to move during the volume morph, it simply vanishes from the starting location and appears in the ending location. If you want to shown a volume move you may instead want the mobile part to be a separate map. You fit it to the starting position and record that position with the command "view name pos1" command, then fit it to the final position and save that position with another "view name pos2". Then you could use the command "fly 100 pos1 pos2" to move have the map fly between the two positions over 100 frames. This does not change the shape of the mobile density it just moves it. If you wanted to change its shape while it flies to the new location you could use the "volume morph" command to change its shape while the fly command moves it. Tom On Aug 18, 2022, at 6:46 PM, HONG ZHAN via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Thank you Elaine for the quick response! I did use the volume resample, but I misunderstood the onGrid pointer… I made it! The volume morph dissolves one part of the complex and appears the other, but I want to have a "movement movie", like using morph for atomic models, one part of the complex flies out and fit into the other part, is there any functions I missed? Thanks! Hong On Aug 18, 2022, at 8:14 PM, Elaine Meng <meng@cgl.ucsf.edu<mailto:meng@cgl.ucsf.edu>> wrote: Hi Hong, As mentioned in the volume morph" help, <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#morph> "the input maps should have the same grids: dimensions, spacing, and numbers of points. Note volume resample can be used to make a copy of one map that has the same grid as another." Here is the "volume resample" help, with explanation that you can lose some resolution from resampling: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#resample> There is also a "volume add" if you are just trying to put different parts together, rather than morphing: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#add> 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 5:36 PM, HONG ZHAN via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Dear user group, I am trying to do volume morph to transform different parts of a complex into another part of the same complex. Because I did drag and fit each segmented parts, the map positions are no longer the same and I have this error: Map positions are not the same. Is there a way to do the map morph to transform different map parts in the complex? Many thanks! Hong _______________________________________________ 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
participants (3)
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Elaine Meng -
HONG ZHAN -
Tom Goddard