Can ChimeraX morph between two surfaces?
Dear ChimeraX team, 1. Can ChimeraX morph between two surfaces (surfaces generated from two PDBs, not maps)? 2. During morphing, can the color also change gradually from one color (one conformation colored in red) to another color (another conformation colored in blue)? 3. The following command works if #1 has only one chain. morph #2 #1/L frames 10 When there are several chains in #1, ChimeraX stopped with an error (ValueError: models have different number of chains). Thanks in advance! Steve -- Steve Chou
Hi Steve, Yes, you have to have equal numbers of chains in the two structures on either end of a morph. This is in the “Limitations" <http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#limitations> You cannot morph only the surfaces; instead you would morph the atomic structures and then show surface for the trajectory as it morphs (in effect, you would just see the surface morphing). I can’t think of any easy way to gradually change the color of the surface over the trajectory, though. A somewhat tedious way would be to save the trajectory as a multi-model PDB file, then reopen (it would show all the frames at the same time like an NMR ensemble), then “rainbow” with your desired palette, say red->blue, then surface each one, then show each one in trajectory order, hiding the others. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 14, 2019, at 9:13 AM, Steve Chou <stevezchou@gmail.com> wrote:
Dear ChimeraX team, 1. Can ChimeraX morph between two surfaces (surfaces generated from two PDBs, not maps)? 2. During morphing, can the color also change gradually from one color (one conformation colored in red) to another color (another conformation colored in blue)? 3. The following command works if #1 has only one chain. morph #2 #1/L frames 10 When there are several chains in #1, ChimeraX stopped with an error (ValueError: models have different number of chains). Thanks in advance! Steve -- Steve Chou
Dear Elaine, Thanks for your fast reply. I (1) saved the trajectory as a multi-model PDB file (11 models, like an NMR ensemble), (2) loaded the ensemble PDB back to ChimeraX, (3) rendered each model as a surface, then (4) tried to color the surfaces as a rainbow, but the last step [step: (4)] only produces red surfaces, not a rainbow. *rainbow chain palette red:blue* *rainbow polymers palette red:blue* Steve On Thu, Feb 14, 2019 at 12:25 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Steve, Yes, you have to have equal numbers of chains in the two structures on either end of a morph. This is in the “Limitations" <http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#limitations>
You cannot morph only the surfaces; instead you would morph the atomic structures and then show surface for the trajectory as it morphs (in effect, you would just see the surface morphing).
I can’t think of any easy way to gradually change the color of the surface over the trajectory, though. A somewhat tedious way would be to save the trajectory as a multi-model PDB file, then reopen (it would show all the frames at the same time like an NMR ensemble), then “rainbow” with your desired palette, say red->blue, then surface each one, then show each one in trajectory order, hiding the others. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 14, 2019, at 9:13 AM, Steve Chou <stevezchou@gmail.com> wrote:
Dear ChimeraX team, 1. Can ChimeraX morph between two surfaces (surfaces generated from two PDBs, not maps)? 2. During morphing, can the color also change gradually from one color (one conformation colored in red) to another color (another conformation colored in blue)? 3. The following command works if #1 has only one chain. morph #2 #1/L frames 10 When there are several chains in #1, ChimeraX stopped with an error (ValueError: models have different number of chains). Thanks in advance! Steve -- Steve Chou
-- Steve Chou
Hi Steve, You want “rainbow structures”: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#sequential> Best, Elaine
On Feb 14, 2019, at 12:21 PM, Steve Chou <stevezchou@gmail.com> wrote:
Dear Elaine, Thanks for your fast reply. I (1) saved the trajectory as a multi-model PDB file (11 models, like an NMR ensemble), (2) loaded the ensemble PDB back to ChimeraX, (3) rendered each model as a surface, then (4) tried to color the surfaces as a rainbow, but the last step [step: (4)] only produces red surfaces, not a rainbow. rainbow chain palette red:blue rainbow polymers palette red:blue Steve
On Thu, Feb 14, 2019 at 12:25 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Steve, Yes, you have to have equal numbers of chains in the two structures on either end of a morph. This is in the “Limitations" <http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#limitations>
You cannot morph only the surfaces; instead you would morph the atomic structures and then show surface for the trajectory as it morphs (in effect, you would just see the surface morphing).
I can’t think of any easy way to gradually change the color of the surface over the trajectory, though. A somewhat tedious way would be to save the trajectory as a multi-model PDB file, then reopen (it would show all the frames at the same time like an NMR ensemble), then “rainbow” with your desired palette, say red->blue, then surface each one, then show each one in trajectory order, hiding the others. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 14, 2019, at 9:13 AM, Steve Chou <stevezchou@gmail.com> wrote:
Dear ChimeraX team, 1. Can ChimeraX morph between two surfaces (surfaces generated from two PDBs, not maps)? 2. During morphing, can the color also change gradually from one color (one conformation colored in red) to another color (another conformation colored in blue)? 3. The following command works if #1 has only one chain. morph #2 #1/L frames 10 When there are several chains in #1, ChimeraX stopped with an error (ValueError: models have different number of chains). Thanks in advance! Steve -- Steve Chou
-- Steve Chou
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Thanks, Elaine! You command "rainbow structures" works beautifully. There is "a Mg ion" and "a water molecule" in the two conformations. (1) If the two conformations have exactly the same compositions (by shifting the structure), the "Mg ion" and the "water molecule" do not follow the same path as the protein. They move but separate from the protein. (2) If the two conformations have slightly different compositions, the "Mg ion" and the "water molecule" do not show up in the morphed pdb ensemble. Is there a way to morph the specific components properly? Steve On Thu, Feb 14, 2019 at 3:25 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Steve, You want “rainbow structures”:
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#sequential>
Best, Elaine
On Feb 14, 2019, at 12:21 PM, Steve Chou <stevezchou@gmail.com> wrote:
Dear Elaine, Thanks for your fast reply. I (1) saved the trajectory as a multi-model PDB file (11 models, like an NMR ensemble), (2) loaded the ensemble PDB back to ChimeraX, (3) rendered each model as a surface, then (4) tried to color the surfaces as a rainbow, but the last step [step: (4)] only produces red surfaces, not a rainbow. rainbow chain palette red:blue rainbow polymers palette red:blue Steve
On Thu, Feb 14, 2019 at 12:25 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Steve, Yes, you have to have equal numbers of chains in the two structures on either end of a morph. This is in the “Limitations" <http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#limitations
You cannot morph only the surfaces; instead you would morph the atomic structures and then show surface for the trajectory as it morphs (in effect, you would just see the surface morphing).
I can’t think of any easy way to gradually change the color of the surface over the trajectory, though. A somewhat tedious way would be to save the trajectory as a multi-model PDB file, then reopen (it would show all the frames at the same time like an NMR ensemble), then “rainbow” with your desired palette, say red->blue, then surface each one, then show each one in trajectory order, hiding the others. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 14, 2019, at 9:13 AM, Steve Chou <stevezchou@gmail.com> wrote:
Dear ChimeraX team, 1. Can ChimeraX morph between two surfaces (surfaces generated from two PDBs, not maps)? 2. During morphing, can the color also change gradually from one color (one conformation colored in red) to another color (another conformation colored in blue)? 3. The following command works if #1 has only one chain. morph #2 #1/L frames 10 When there are several chains in #1, ChimeraX stopped with an error (ValueError: models have different number of chains). Thanks in advance! Steve -- Steve Chou
-- Steve Chou
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
-- Steve Chou
Hi Steve, Actually I’m surprised the Mg and water were included (even if present at both ends) because I thought they had to be tethered by a bond or pseudobond (like a distance measurement) to the biopolymer chain, as described here under “Atoms in Common”: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#pairing> For the case where composition changes, you could add in a fake Mg ion and water to the structure that’s missing them, but you’d have to decide where to put them. Also it was my understanding that they had to be tethered to the biopolymer chain (e.g. add distance measurement, which can then be hidden), but maybe that requirement has changed, or the Mg does already have a metal-coordination pseudobond to the biopolymer. Or if you don’t care if the Mg or water move during the morph, you could just display those atoms from the original model (that was input to morphing) even though they are not present in the trajectory. Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 14, 2019, at 12:51 PM, Steve Chou <stevezchou@gmail.com> wrote:
Thanks, Elaine! You command "rainbow structures" works beautifully. There is "a Mg ion" and "a water molecule" in the two conformations. (1) If the two conformations have exactly the same compositions (by shifting the structure), the "Mg ion" and the "water molecule" do not follow the same path as the protein. They move but separate from the protein. (2) If the two conformations have slightly different compositions, the "Mg ion" and the "water molecule" do not show up in the morphed pdb ensemble. Is there a way to morph the specific components properly? Steve
participants (2)
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Elaine Meng -
Steve Chou