Symmetry operation calculations for multimeric fibrillar assemblies
Dear Chimera support team, I am trying to deposit to the PDB an X-ray crystal structure I solved, and came across with the need to calculate its biological assembly, which is pretty tricky in my case, and so I wondered if Chimera could help me with that. I am working on fibrils made out of repeating units of peptides. The asymmetric unit in my structures usually contains only a monomer, whereas the structure of the fibril is obtained by drawing the copies of this monomer along the fibril axis (potentially there are tens of thousands of those copies), based on the unit cell parameters (the copies are packed within the unit cell). After choosing and drawing an arbitrary number of copies along the axis of fibrillation I would like to get the output of the symmetry operations resulting in this desired representation of the fibril, in order to deposit them as the biological assembly of my structure. I would appreciate if you could advice me to how to obtain those symmetry operations so to define my biomt. Thank you in advance, Einav -- Einav Tayeb-Fligelman, PhD The Landau lab Faculty of Biology Technion, Israel Institute of Technology Haifa, Israel E-mail :einavtf@campus.technion.ac.il Tel at the lab:+972-77-8871964 <+972%2077-887-1964>
Dear Einav, In my opinion, it is difficult to try to back-calculate symmetry relationships between copies of a structure in Chimera, and the results are not exact truth especially when you have hand-placed those copies. I doubt it would be suitable for deposition purposes. For example Chimera instructions, see this recent post: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2018-May/014625.html> There is also a “measure symmetry” command to guess the symmetry of a density map (not atomic structures), but it only looks for cyclic, dihedral, tetrahedral, octahedral, and icosahedral symmetries in standard coordinate systems: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#symmetry> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 12, 2018, at 1:47 PM, Einav Tayeb-Fligelman <einavt@gmail.com> wrote:
Dear Chimera support team,
I am trying to deposit to the PDB an X-ray crystal structure I solved, and came across with the need to calculate its biological assembly, which is pretty tricky in my case, and so I wondered if Chimera could help me with that. I am working on fibrils made out of repeating units of peptides. The asymmetric unit in my structures usually contains only a monomer, whereas the structure of the fibril is obtained by drawing the copies of this monomer along the fibril axis (potentially there are tens of thousands of those copies), based on the unit cell parameters (the copies are packed within the unit cell). After choosing and drawing an arbitrary number of copies along the axis of fibrillation I would like to get the output of the symmetry operations resulting in this desired representation of the fibril, in order to deposit them as the biological assembly of my structure. I would appreciate if you could advice me to how to obtain those symmetry operations so to define my biomt.
Thank you in advance, Einav
Dear Elaine, Thank you for your reply. I am not sure what you mean by hand placing the copies. I place the copies by increasing the number of unit cells in a certain direction in the higher order tab, and therefore I thought that The symmetry operations could be extracted... If this information changes your answer somehow please let me know. Best, Einav On Wed, Jun 13, 2018 at 3:34 AM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear Einav, In my opinion, it is difficult to try to back-calculate symmetry relationships between copies of a structure in Chimera, and the results are not exact truth especially when you have hand-placed those copies. I doubt it would be suitable for deposition purposes.
For example Chimera instructions, see this recent post: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2018-May/014625.html>
There is also a “measure symmetry” command to guess the symmetry of a density map (not atomic structures), but it only looks for cyclic, dihedral, tetrahedral, octahedral, and icosahedral symmetries in standard coordinate systems: < http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#symmetry
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 12, 2018, at 1:47 PM, Einav Tayeb-Fligelman <einavt@gmail.com> wrote:
Dear Chimera support team,
I am trying to deposit to the PDB an X-ray crystal structure I solved, and came across with the need to calculate its biological assembly, which is pretty tricky in my case, and so I wondered if Chimera could help me with that. I am working on fibrils made out of repeating units of peptides. The asymmetric unit in my structures usually contains only a monomer, whereas the structure of the fibril is obtained by drawing the copies of this monomer along the fibril axis (potentially there are tens of thousands of those copies), based on the unit cell parameters (the copies are packed within the unit cell). After choosing and drawing an arbitrary number of copies along the axis of fibrillation I would like to get the output of the symmetry operations resulting in this desired representation of the fibril, in order to deposit them as the biological assembly of my structure. I would appreciate if you could advice me to how to obtain those symmetry operations so to define my biomt.
Thank you in advance, Einav
-- Einav Tayeb-Fligelman, PhD The Landau lab Faculty of Biology Technion, Israel Institute of Technology Haifa, Israel E-mail :einavtf@campus.technion.ac.il Tel at the lab:+972-77-8871964 <javascript:void(0);>
Dear Einav, Sorry for my misinterpretation… ignore what I said about hand placement. The instructions in that previous post would still be one way to get the symmetry relationship between copies of a protein, but the process is rather long and complicated. Since then, I was reminded of a less arduous approach: To get the transformation between atomic structures that are similar but displaced from one another (without actually superimposing them), use the “match" command with “move false" and "showMatrix true": <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html> I’m still not completely sure if it will suffice for what is needed to submit the structure, but you can try this and see what you think. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 12, 2018, at 10:16 PM, Einav Tayeb-Fligelman <einavt@gmail.com> wrote:
Dear Elaine, Thank you for your reply. I am not sure what you mean by hand placing the copies. I place the copies by increasing the number of unit cells in a certain direction in the higher order tab, and therefore I thought that The symmetry operations could be extracted... If this information changes your answer somehow please let me know. Best, Einav
On Wed, Jun 13, 2018 at 3:34 AM Elaine Meng <meng@cgl.ucsf.edu> wrote: Dear Einav, In my opinion, it is difficult to try to back-calculate symmetry relationships between copies of a structure in Chimera, and the results are not exact truth especially when you have hand-placed those copies. I doubt it would be suitable for deposition purposes.
For example Chimera instructions, see this recent post: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2018-May/014625.html>
There is also a “measure symmetry” command to guess the symmetry of a density map (not atomic structures), but it only looks for cyclic, dihedral, tetrahedral, octahedral, and icosahedral symmetries in standard coordinate systems: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#symmetry>
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 12, 2018, at 1:47 PM, Einav Tayeb-Fligelman <einavt@gmail.com> wrote:
Dear Chimera support team,
I am trying to deposit to the PDB an X-ray crystal structure I solved, and came across with the need to calculate its biological assembly, which is pretty tricky in my case, and so I wondered if Chimera could help me with that. I am working on fibrils made out of repeating units of peptides. The asymmetric unit in my structures usually contains only a monomer, whereas the structure of the fibril is obtained by drawing the copies of this monomer along the fibril axis (potentially there are tens of thousands of those copies), based on the unit cell parameters (the copies are packed within the unit cell). After choosing and drawing an arbitrary number of copies along the axis of fibrillation I would like to get the output of the symmetry operations resulting in this desired representation of the fibril, in order to deposit them as the biological assembly of my structure. I would appreciate if you could advice me to how to obtain those symmetry operations so to define my biomt.
Thank you in advance, Einav
-- Einav Tayeb-Fligelman, PhD The Landau lab Faculty of Biology Technion, Israel Institute of Technology Haifa, Israel E-mail :einavtf@campus.technion.ac.il Tel at the lab:+972-77-8871964 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Thank you very much Elaine, I will give it a try now! Einav On Wed, Jun 13, 2018 at 8:21 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear Einav, Sorry for my misinterpretation… ignore what I said about hand placement.
The instructions in that previous post would still be one way to get the symmetry relationship between copies of a protein, but the process is rather long and complicated. Since then, I was reminded of a less arduous approach:
To get the transformation between atomic structures that are similar but displaced from one another (without actually superimposing them), use the “match" command with “move false" and "showMatrix true": <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/match.html>
I’m still not completely sure if it will suffice for what is needed to submit the structure, but you can try this and see what you think. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 12, 2018, at 10:16 PM, Einav Tayeb-Fligelman <einavt@gmail.com> wrote:
Dear Elaine, Thank you for your reply. I am not sure what you mean by hand placing the copies. I place the copies by increasing the number of unit cells in a certain direction in the higher order tab, and therefore I thought that The symmetry operations could be extracted... If this information changes your answer somehow please let me know. Best, Einav
On Wed, Jun 13, 2018 at 3:34 AM Elaine Meng <meng@cgl.ucsf.edu> wrote: Dear Einav, In my opinion, it is difficult to try to back-calculate symmetry relationships between copies of a structure in Chimera, and the results are not exact truth especially when you have hand-placed those copies. I doubt it would be suitable for deposition purposes.
For example Chimera instructions, see this recent post: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2018-May/014625.html>
There is also a “measure symmetry” command to guess the symmetry of a density map (not atomic structures), but it only looks for cyclic, dihedral, tetrahedral, octahedral, and icosahedral symmetries in standard coordinate systems: < http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#symmetry
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 12, 2018, at 1:47 PM, Einav Tayeb-Fligelman <einavt@gmail.com> wrote:
Dear Chimera support team,
I am trying to deposit to the PDB an X-ray crystal structure I solved, and came across with the need to calculate its biological assembly, which is pretty tricky in my case, and so I wondered if Chimera could help me with that. I am working on fibrils made out of repeating units of peptides. The asymmetric unit in my structures usually contains only a monomer, whereas the structure of the fibril is obtained by drawing the copies of this monomer along the fibril axis (potentially there are tens of thousands of those copies), based on the unit cell parameters (the copies are packed within the unit cell). After choosing and drawing an arbitrary number of copies along the axis of fibrillation I would like to get the output of the symmetry operations resulting in this desired representation of the fibril, in order to deposit them as the biological assembly of my structure. I would appreciate if you could advice me to how to obtain those symmetry operations so to define my biomt.
Thank you in advance, Einav
-- Einav Tayeb-Fligelman, PhD The Landau lab Faculty of Biology Technion, Israel Institute of Technology Haifa, Israel E-mail :einavtf@campus.technion.ac.il Tel at the lab:+972-77-8871964 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- Einav Tayeb-Fligelman, PhD The Landau lab Faculty of Biology Technion, Israel Institute of Technology Haifa, Israel E-mail :einavtf@campus.technion.ac.il Tel at the lab:+972-77-8871964 <javascript:void(0);>
participants (2)
-
Einav Tayeb-Fligelman -
Elaine Meng