Hi all, I am fairly new to using chimera and was wondering if there is a way to get more control over the path that is calculated when morph map is used for two EM density maps that are different conformations. When I use the tool now it will change the visible density a great deal and rather than rotating only a certain part of the map the result seems quite confusing to look at as the whole structures move. Is there a way to fix some areas while alowing to morph subregeons? Or does anyone have a better idea on how to approach this? the map is a dimer and the change is suposed to be a difference in rotation between the two monomers. Ideally I would show this by fixing two monomers ontop of each other and allowing the other halfs to move. Thank you in advance, Linda
Hi Linda, The Chimera morph map tool just linearly interpolates the density value at each map grid point. So it won’t show a domain rotating if the domain moves a long distance — instead it will just disappear in the starting position and appear at the final position. If the motion is small this ends up looking like a rotation. Your start and end maps must have the same grid alignment for this to work, in other words if you had to move one to align it with the other, then you need to resample the map so it is on the same grid points (vop resample command). For your case to show rotation of one monomer relative to the other you’d be better off fitting to monomer atomic models into the two maps and then use savepos (save position) and reset (restore position) commands to smoothly interpolate the atomic model positions between the two configurations. If you fit the two monomers as chains of a single atomic model then you would instead use the Morph Conformations tool to interpolate. If you really wanted to see the motion using the maps, you could perhaps segment your initial map into two monomer maps, fit the segments to the final map, then use savepos/reset to show the motion of the two pieces. There is not tool in Chimera that intelligently moves the density from one state to another. The “Morph” Map name is misleading since it does an interpolation, not a morph. Tom
On Apr 13, 2016, at 7:16 AM, Franken, L.E. wrote:
Hi all, I am fairly new to using chimera and was wondering if there is a way to get more control over the path that is calculated when morph map is used for two EM density maps that are different conformations. When I use the tool now it will change the visible density a great deal and rather than rotating only a certain part of the map the result seems quite confusing to look at as the whole structures move. Is there a way to fix some areas while alowing to morph subregeons? Or does anyone have a better idea on how to approach this? the map is a dimer and the change is suposed to be a difference in rotation between the two monomers. Ideally I would show this by fixing two monomers ontop of each other and allowing the other halfs to move.
Thank you in advance, Linda
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Hi Tom, Thank you for you clear explanation, I managed by fitting 2 structures and the movie now shows what I intended, but because of the high resolution structures it feels rather over-interpreted (my maps are around 20A), would there be a way to filter the morph back to 15A density maps and show that? Best wishes, Linda On Wed, Apr 13, 2016 at 8:16 PM, Tom Goddard <goddard@sonic.net> wrote:
Hi Linda,
The Chimera morph map tool just linearly interpolates the density value at each map grid point. So it won’t show a domain rotating if the domain moves a long distance — instead it will just disappear in the starting position and appear at the final position. If the motion is small this ends up looking like a rotation. Your start and end maps must have the same grid alignment for this to work, in other words if you had to move one to align it with the other, then you need to resample the map so it is on the same grid points (vop resample command).
For your case to show rotation of one monomer relative to the other you’d be better off fitting to monomer atomic models into the two maps and then use savepos (save position) and reset (restore position) commands to smoothly interpolate the atomic model positions between the two configurations. If you fit the two monomers as chains of a single atomic model then you would instead use the Morph Conformations tool to interpolate. If you really wanted to see the motion using the maps, you could perhaps segment your initial map into two monomer maps, fit the segments to the final map, then use savepos/reset to show the motion of the two pieces. There is not tool in Chimera that intelligently moves the density from one state to another. The “Morph” Map name is misleading since it does an interpolation, not a morph.
Tom
On Apr 13, 2016, at 7:16 AM, Franken, L.E. wrote:
Hi all, I am fairly new to using chimera and was wondering if there is a way to get more control over the path that is calculated when morph map is used for two EM density maps that are different conformations. When I use the tool now it will change the visible density a great deal and rather than rotating only a certain part of the map the result seems quite confusing to look at as the whole structures move. Is there a way to fix some areas while alowing to morph subregeons? Or does anyone have a better idea on how to approach this? the map is a dimer and the change is suposed to be a difference in rotation between the two monomers. Ideally I would show this by fixing two monomers ontop of each other and allowing the other halfs to move.
Thank you in advance, Linda
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Hi Linda, You can make a 15 Angstrom resolution map calculated from the atomic model using “molmap #0 15” where #0 is the atomic model. Then use savepos and reset commands as described earlier to interpolate. To place the calculated map (say #1) aligned with the ending position atomic model (say #2) use "matrixcopy #2 #1”. Another approach if you have the initial and final atomic model as single PDBs rather than one PDB each domain and you use the Morph Conformations tool to morph between them, you can compute the map from the atomic model at every interpolation step with a command like “molmap #1 15 modelId #2”. You would use this with the “perframe” command to run molmap at every frame of the movie. And you would play the atomic morph (with the atomic model hidden) using the coordset command. Tom
On Apr 14, 2016, at 6:12 AM, Franken, L.E. <l.e.franken@rug.nl> wrote:
Hi Tom, Thank you for you clear explanation, I managed by fitting 2 structures and the movie now shows what I intended, but because of the high resolution structures it feels rather over-interpreted (my maps are around 20A), would there be a way to filter the morph back to 15A density maps and show that?
Best wishes, Linda
On Wed, Apr 13, 2016 at 8:16 PM, Tom Goddard <goddard@sonic.net <mailto:goddard@sonic.net>> wrote: Hi Linda,
The Chimera morph map tool just linearly interpolates the density value at each map grid point. So it won’t show a domain rotating if the domain moves a long distance — instead it will just disappear in the starting position and appear at the final position. If the motion is small this ends up looking like a rotation. Your start and end maps must have the same grid alignment for this to work, in other words if you had to move one to align it with the other, then you need to resample the map so it is on the same grid points (vop resample command).
For your case to show rotation of one monomer relative to the other you’d be better off fitting to monomer atomic models into the two maps and then use savepos (save position) and reset (restore position) commands to smoothly interpolate the atomic model positions between the two configurations. If you fit the two monomers as chains of a single atomic model then you would instead use the Morph Conformations tool to interpolate. If you really wanted to see the motion using the maps, you could perhaps segment your initial map into two monomer maps, fit the segments to the final map, then use savepos/reset to show the motion of the two pieces. There is not tool in Chimera that intelligently moves the density from one state to another. The “Morph” Map name is misleading since it does an interpolation, not a morph.
Tom
On Apr 13, 2016, at 7:16 AM, Franken, L.E. wrote:
Hi all, I am fairly new to using chimera and was wondering if there is a way to get more control over the path that is calculated when morph map is used for two EM density maps that are different conformations. When I use the tool now it will change the visible density a great deal and rather than rotating only a certain part of the map the result seems quite confusing to look at as the whole structures move. Is there a way to fix some areas while alowing to morph subregeons? Or does anyone have a better idea on how to approach this? the map is a dimer and the change is suposed to be a difference in rotation between the two monomers. Ideally I would show this by fixing two monomers ontop of each other and allowing the other halfs to move.
Thank you in advance, Linda
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Franken, L.E. -
Tom Goddard