Dear all, I would like to ask for some information/help for a problem I am facing at the moment: I am currently working on a pentameric protein (C5 symmetric) that undergoes a big conformational change (translational & rotational movement) and would like to utilize the morph function in ChimeraX to come up with a good animation for it. For one single protomer the animation works fine – however, for the full pentamer the subunits follow both directions, clockwise and counterclockwise, during their rotational movement which obviously leads to a lot of clashes and therefore does not look very convincing. Since I tried almost all options listed as parameters for the morph (linear & corkscrew method, cartesian true and false, rates, coreFraction, etc.) and it did not affect the direction of rotation at all, I was wondering whether there are additional values I could modify or any other trick that might equalize the movement? Thank you very much in advance! Best regards, Raphael P.S.: I would be happy to provide data if it might help solving the problem.
Hi Raphael, I agree it can be time-consuming to make a complicated morph trajectory go the way you want, even when it seems like the most sensible way! Unfortunately it does involve a lot of trial and error. I've spent many days trying to do it, and didn't have any luck with changing method or cartesian. What helped in my case of a complicated conformational change of a single-chain protein was: (1) adjusting coreFraction (although you said you already tried that, so maybe it's not helpful in your multimer situation) <https://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html> (2) manually creating one or more intermediate structures between the experimental structures and doing the morph in several stages ...where (2) can be quite effective but also labor-intensive. Since one of the protomers behaves as expected in your current morph, maybe you can save an intermediate conformation from the morph trajectory as a PDB file. Then open that intermediate, delete the other protomers, and use "sym" to generate the symmetrical pentamer from that one correctly behaving monomer. Maybe that is the hard part, because "sym" will need correct specification of the center and axis of symmetry. If the original pentamer structure was from the RCSB PDB, maybe the originally opened mmCIF file has the symmetry information and you can use the option to use the symmetry from that model, opened separately (e.g. "sym #3 symmetry #5 [other options]" if the behaving protomer is model #3 and the original mmCIF is model #5). <https://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html> However, if the behaving protomer from the morph trajectory did not arise from the asymmetric unit monomer in that mmCIF file, it may not work. Maybe you can think of some other way to generate the appropriate C5 symmetric pentamer for the intermediate. Next, you want that pentamer to be a single model. if it is in multiple models, you may need to use "combine" to make it a single model. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html> Then save the single-model intermediate pentamer as PDB just in case you need it later, and do the morphing from start structure -> your manually created intermediate pentamer model -> end structure. Phew! I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 23, 2023, at 7:28 AM, Raphael Bader via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear all,
I would like to ask for some information/help for a problem I am facing at the moment: I am currently working on a pentameric protein (C5 symmetric) that undergoes a big conformational change (translational & rotational movement) and would like to utilize the morph function in ChimeraX to come up with a good animation for it. For one single protomer the animation works fine – however, for the full pentamer the subunits follow both directions, clockwise and counterclockwise, during their rotational movement which obviously leads to a lot of clashes and therefore does not look very convincing. Since I tried almost all options listed as parameters for the morph (linear & corkscrew method, cartesian true and false, rates, coreFraction, etc.) and it did not affect the direction of rotation at all, I was wondering whether there are additional values I could modify or any other trick that might equalize the movement? Thank you very much in advance!
Best regards, Raphael
P.S.: I would be happy to provide data if it might help solving the problem.
Hi Raphael, I'm puzzled by your morph problem. If one monomer of your C5 pentamer morphs correctly, the others should all morph in the same way. One thing that can mess up a multi-chain morph is that the chains are not paired up correctly. If the chains are named A,B,C,D,E in both it will match A with A, B with B, .... If wrong pairing is not your problem I'd be curious to see in more detail what you are talking about. I maintain the ChimeraX morph code and have not seen it misbehave the way you describe. You could send example files directly to me and I will not show them to anyone. Tom
On Oct 23, 2023, at 10:38 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Raphael, I agree it can be time-consuming to make a complicated morph trajectory go the way you want, even when it seems like the most sensible way! Unfortunately it does involve a lot of trial and error. I've spent many days trying to do it, and didn't have any luck with changing method or cartesian. What helped in my case of a complicated conformational change of a single-chain protein was:
(1) adjusting coreFraction (although you said you already tried that, so maybe it's not helpful in your multimer situation)
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html>
(2) manually creating one or more intermediate structures between the experimental structures and doing the morph in several stages
...where (2) can be quite effective but also labor-intensive. Since one of the protomers behaves as expected in your current morph, maybe you can save an intermediate conformation from the morph trajectory as a PDB file. Then open that intermediate, delete the other protomers, and use "sym" to generate the symmetrical pentamer from that one correctly behaving monomer. Maybe that is the hard part, because "sym" will need correct specification of the center and axis of symmetry. If the original pentamer structure was from the RCSB PDB, maybe the originally opened mmCIF file has the symmetry information and you can use the option to use the symmetry from that model, opened separately (e.g. "sym #3 symmetry #5 [other options]" if the behaving protomer is model #3 and the original mmCIF is model #5).
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html>
However, if the behaving protomer from the morph trajectory did not arise from the asymmetric unit monomer in that mmCIF file, it may not work. Maybe you can think of some other way to generate the appropriate C5 symmetric pentamer for the intermediate. Next, you want that pentamer to be a single model. if it is in multiple models, you may need to use "combine" to make it a single model.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html>
Then save the single-model intermediate pentamer as PDB just in case you need it later, and do the morphing from start structure -> your manually created intermediate pentamer model -> end structure. Phew!
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 23, 2023, at 7:28 AM, Raphael Bader via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear all,
I would like to ask for some information/help for a problem I am facing at the moment: I am currently working on a pentameric protein (C5 symmetric) that undergoes a big conformational change (translational & rotational movement) and would like to utilize the morph function in ChimeraX to come up with a good animation for it. For one single protomer the animation works fine – however, for the full pentamer the subunits follow both directions, clockwise and counterclockwise, during their rotational movement which obviously leads to a lot of clashes and therefore does not look very convincing. Since I tried almost all options listed as parameters for the morph (linear & corkscrew method, cartesian true and false, rates, coreFraction, etc.) and it did not affect the direction of rotation at all, I was wondering whether there are additional values I could modify or any other trick that might equalize the movement? Thank you very much in advance!
Best regards, Raphael
P.S.: I would be happy to provide data if it might help solving the problem.
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participants (3)
-
Elaine Meng -
Raphael Bader -
Tom Goddard