Dear USCF Chimera developers, I got a question here, how to find the barycenter of a model in UCSF Chimera? And the Model has a C2 symmetry, I can only find the symmetry axis. Best regards, Mingliang Jin NCPSS, SIBCB, CAS
Dear Mingliang Jin, (1) to find center of mass, see command “measure center”: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#center> If your model is an atomic structure, another possibility is “define centroid” with “massWeighting true” (otherwise it will find the center of geometry, treating all atoms equally): <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html#centroid> (2) to find C2 symmetry axis of an atomic structure (not a map), you could try opening two copies of the structure, matching one half in one copy to the OTHER half in the other copy, and then measuring the axis of rotation between the two copies. See this previous post with example commands for the structure 5hvp: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2017-April/013290.html> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 11, 2017, at 1:26 AM, mljin <jinmingliang2013@sibcb.ac.cn> wrote:
Dear USCF Chimera developers,
I got a question here, how to find the barycenter of a model in UCSF Chimera? And the Model has a C2 symmetry, I can only find the symmetry axis.
Best regards, Mingliang Jin
NCPSS, SIBCB, CAS
Dear Elaine, Thank you very much for this, the measure center and the way to find the axis is quite useful for my model! Thanks! Best regards! Mingliang
在 2017年9月12日，上午12:57，Elaine Meng <meng@cgl.ucsf.edu> 写道：
Dear Mingliang Jin,
(1) to find center of mass, see command “measure center”: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#center>
If your model is an atomic structure, another possibility is “define centroid” with “massWeighting true” (otherwise it will find the center of geometry, treating all atoms equally): <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html#centroid>
(2) to find C2 symmetry axis of an atomic structure (not a map), you could try opening two copies of the structure, matching one half in one copy to the OTHER half in the other copy, and then measuring the axis of rotation between the two copies. See this previous post with example commands for the structure 5hvp: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2017-April/013290.html>
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 11, 2017, at 1:26 AM, mljin <jinmingliang2013@sibcb.ac.cn> wrote:
Dear USCF Chimera developers,
I got a question here, how to find the barycenter of a model in UCSF Chimera? And the Model has a C2 symmetry, I can only find the symmetry axis.
Best regards, Mingliang Jin
NCPSS, SIBCB, CAS
Dear Elaine, I got another question here, I have two models, these two model are the same molecule but with different conformation. This molecule composes several subunits. And the conformation change include not only like subunit rigid body rotation but also a self movement, I would like to do a morph between these two, but actually I do not know how to put these two molecule in the Chimera, I mean the relative position, by which I can do morph and study the rigid body rotation and movement. I try to find the axis and the center of mass by your advice, however, I still need another valve to fix it in right position, because I only have a axis and a center, still lack a third vale, does there any method to solve this? Best regard! Mingliang
在 2017年9月12日，上午12:57，Elaine Meng <meng@cgl.ucsf.edu> 写道：
Dear Mingliang Jin,
(1) to find center of mass, see command “measure center”: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#center>
If your model is an atomic structure, another possibility is “define centroid” with “massWeighting true” (otherwise it will find the center of geometry, treating all atoms equally): <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html#centroid>
(2) to find C2 symmetry axis of an atomic structure (not a map), you could try opening two copies of the structure, matching one half in one copy to the OTHER half in the other copy, and then measuring the axis of rotation between the two copies. See this previous post with example commands for the structure 5hvp: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2017-April/013290.html>
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 11, 2017, at 1:26 AM, mljin <jinmingliang2013@sibcb.ac.cn> wrote:
Dear USCF Chimera developers,
I got a question here, how to find the barycenter of a model in UCSF Chimera? And the Model has a C2 symmetry, I can only find the symmetry axis.
Best regards, Mingliang Jin
NCPSS, SIBCB, CAS
Hi Mingliang, I’m not sure I really understand your question, but seems like you just need a method to superimpose one atomic structure on the other, instead of trying to use the axis and center. Here is a discussion of the different ways in Chimera to superimpose atomic structures (I assume your structures are really made of atoms, not just the shapes in your picture): <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> For example, if it’s a multisubunit protein complex, you could try MatchMaker (or command matchmaker) to superimpose using specified pairs of chains between the two structures. The links in that page lead to more information on each method. You can try using different options and/or sets of chain pairs and just see which one gives you a superposition suitable for input to the Morph Conformations tool. If none of the semi-automated approaches seem to give what you want, you could even do it by just moving one structure relative to the other with the mouse. You can freeze/unfreeze structures for mouse movement. See “Structures can be superimposed manually…” in the page linked above. Also note that for Morph Conformations, the structures must have the same numbers of chains and they will be either paired by chain ID if they contain all the same IDs as each other, or by the order of the chains in the input file if some IDs are different. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html#pairing> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 12, 2017, at 6:30 AM, mljin <jinmingliang2013@sibcb.ac.cn> wrote:
Dear Elaine, I got another question here, I have two models, these two model are the same molecule but with different conformation. This molecule composes several subunits. And the conformation change include not only like subunit rigid body rotation but also a self movement, I would like to do a morph between these two, but actually I do not know how to put these two molecule in the Chimera, I mean the relative position, by which I can do morph and study the rigid body rotation and movement. I try to find the axis and the center of mass by your advice, however, I still need another valve to fix it in right position, because I only have a axis and a center, still lack a third vale, does there any method to solve this? Best regard! Mingliang
Dear Elaine, Thank you for your advise! Best regard! Mingliang
在 2017年9月13日，上午12:39，Elaine Meng <meng@cgl.ucsf.edu> 写道：
Hi Mingliang, I’m not sure I really understand your question, but seems like you just need a method to superimpose one atomic structure on the other, instead of trying to use the axis and center. Here is a discussion of the different ways in Chimera to superimpose atomic structures (I assume your structures are really made of atoms, not just the shapes in your picture):
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>
For example, if it’s a multisubunit protein complex, you could try MatchMaker (or command matchmaker) to superimpose using specified pairs of chains between the two structures. The links in that page lead to more information on each method. You can try using different options and/or sets of chain pairs and just see which one gives you a superposition suitable for input to the Morph Conformations tool.
If none of the semi-automated approaches seem to give what you want, you could even do it by just moving one structure relative to the other with the mouse. You can freeze/unfreeze structures for mouse movement. See “Structures can be superimposed manually…” in the page linked above.
Also note that for Morph Conformations, the structures must have the same numbers of chains and they will be either paired by chain ID if they contain all the same IDs as each other, or by the order of the chains in the input file if some IDs are different. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/morph/morph.html#pairing>
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 12, 2017, at 6:30 AM, mljin <jinmingliang2013@sibcb.ac.cn> wrote:
Dear Elaine, I got another question here, I have two models, these two model are the same molecule but with different conformation. This molecule composes several subunits. And the conformation change include not only like subunit rigid body rotation but also a self movement, I would like to do a morph between these two, but actually I do not know how to put these two molecule in the Chimera, I mean the relative position, by which I can do morph and study the rigid body rotation and movement. I try to find the axis and the center of mass by your advice, however, I still need another valve to fix it in right position, because I only have a axis and a center, still lack a third vale, does there any method to solve this? Best regard! Mingliang
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