Dear Chimera users, I am trying to visualize the interface surface of my two monomers. Is there anyway to show the interacting surface from Chimera by using the EM map? Or should I do it from PDB coordinates? Best, Yangqi -- Yangqi Gu Graduate Student Malvankar Lab Yale University, West Campus
Dear Yangqi I may not understand your question completely, but from the atomic coordinates, you can just show the surfaces of each monomer and color the interface where the two surfaces are close to each other. For example, see this image tutorial: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/openbook.html> As in that tutorial, if both monomers are in one file, to get separate surfaces instead of one combined surface, you may need to use “split” or put them in separate files first (the other way is to use the “surfcat” command if you’d rather keep them as one model0. However, there are lots of ways to find and/or visualize an interface, such as by H-bonds or contacts. See FindHBond (or findhbond command), Find Clashes/Contacts (or findclash command, which is used in the tutorial above), and the Structure Analysis tutorial with examples of using those tools. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbon...> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclas...> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html> Additional related features that may interest you: - command “measure contactArea” which also shows a colored surface patch similar to that in the first tutorial above <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#contactA...> - Intersurf tool: shows a single “interaction surface” <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/intersurf/intersur...> I don’t know how you would use an EM map to visualize an interface surface. 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 14, 2018, at 12:02 PM, Yangqi Gu <yangqi.gu@yale.edu> wrote:
Dear Chimera users, I am trying to visualize the interface surface of my two monomers. Is there anyway to show the interacting surface from Chimera by using the EM map? Or should I do it from PDB coordinates? Best, Yangqi
Hi Elaine, Thank you for your reply. I guess my question is essentially to calculate the surface area. I am just wondering if we could extract that information from EM potential map. Such as inserting a plane where the interface locates and calculate the projection to the plane from the 3D volume. But I guess based on atom coordinates will be much more accurate. Best, Yangqi On Friday, September 14, 2018, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear Yangqi I may not understand your question completely, but from the atomic coordinates, you can just show the surfaces of each monomer and color the interface where the two surfaces are close to each other. For example, see this image tutorial: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/openbook.html>
As in that tutorial, if both monomers are in one file, to get separate surfaces instead of one combined surface, you may need to use “split” or put them in separate files first (the other way is to use the “surfcat” command if you’d rather keep them as one model0.
However, there are lots of ways to find and/or visualize an interface, such as by H-bonds or contacts. See FindHBond (or findhbond command), Find Clashes/Contacts (or findclash command, which is used in the tutorial above), and the Structure Analysis tutorial with examples of using those tools. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/ findhbond.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findclash/ findclash.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html>
Additional related features that may interest you:
- command “measure contactArea” which also shows a colored surface patch similar to that in the first tutorial above <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ measure.html#contactArea>
- Intersurf tool: shows a single “interaction surface” <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/intersurf/ intersurf.html>
I don’t know how you would use an EM map to visualize an interface surface. 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 14, 2018, at 12:02 PM, Yangqi Gu <yangqi.gu@yale.edu> wrote:
Dear Chimera users, I am trying to visualize the interface surface of my two monomers. Is there anyway to show the interacting surface from Chimera by using the EM map? Or should I do it from PDB coordinates? Best, Yangqi
-- Yangqi Gu Graduate Student Malvankar Lab Yale University, West Campus
Hi Yangqi, Oh you said visualize, so I didn’t answer about measuring the area. To measure the area based on molecular surfaces calculated from the atoms, see command measure buriedArea <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#buriedAr...> If you want a specific answer, make sure to ask a specific question! :-) 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 14, 2018, at 1:41 PM, Yangqi Gu <yangqi.gu@yale.edu> wrote:
Hi Elaine, Thank you for your reply. I guess my question is essentially to calculate the surface area. I am just wondering if we could extract that information from EM potential map. Such as inserting a plane where the interface locates and calculate the projection to the plane from the 3D volume. But I guess based on atom coordinates will be much more accurate. Best, Yangqi
On Friday, September 14, 2018, Elaine Meng <meng@cgl.ucsf.edu> wrote: Dear Yangqi I may not understand your question completely, but from the atomic coordinates, you can just show the surfaces of each monomer and color the interface where the two surfaces are close to each other. For example, see this image tutorial: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/openbook.html>
As in that tutorial, if both monomers are in one file, to get separate surfaces instead of one combined surface, you may need to use “split” or put them in separate files first (the other way is to use the “surfcat” command if you’d rather keep them as one model0.
However, there are lots of ways to find and/or visualize an interface, such as by H-bonds or contacts. See FindHBond (or findhbond command), Find Clashes/Contacts (or findclash command, which is used in the tutorial above), and the Structure Analysis tutorial with examples of using those tools. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbon...> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclas...> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html>
Additional related features that may interest you:
- command “measure contactArea” which also shows a colored surface patch similar to that in the first tutorial above <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#contactA...>
- Intersurf tool: shows a single “interaction surface” <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/intersurf/intersur...>
I don’t know how you would use an EM map to visualize an interface surface. 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 14, 2018, at 12:02 PM, Yangqi Gu <yangqi.gu@yale.edu> wrote:
Dear Chimera users, I am trying to visualize the interface surface of my two monomers. Is there anyway to show the interacting surface from Chimera by using the EM map? Or should I do it from PDB coordinates? Best, Yangqi
Thank you very much! Best, Yangqi On Friday, September 14, 2018, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Yangqi, Oh you said visualize, so I didn’t answer about measuring the area. To measure the area based on molecular surfaces calculated from the atoms, see command
measure buriedArea <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ measure.html#buriedArea>
If you want a specific answer, make sure to ask a specific question! :-) 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 14, 2018, at 1:41 PM, Yangqi Gu <yangqi.gu@yale.edu> wrote:
Hi Elaine, Thank you for your reply. I guess my question is essentially to calculate the surface area. I am just wondering if we could extract that information from EM potential map. Such as inserting a plane where the interface locates and calculate the projection to the plane from the 3D volume. But I guess based on atom coordinates will be much more accurate. Best, Yangqi
On Friday, September 14, 2018, Elaine Meng <meng@cgl.ucsf.edu> wrote: Dear Yangqi I may not understand your question completely, but from the atomic coordinates, you can just show the surfaces of each monomer and color the interface where the two surfaces are close to each other. For example, see this image tutorial: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/ tutorials/openbook.html>
As in that tutorial, if both monomers are in one file, to get separate surfaces instead of one combined surface, you may need to use “split” or put them in separate files first (the other way is to use the “surfcat” command if you’d rather keep them as one model0.
However, there are lots of ways to find and/or visualize an interface, such as by H-bonds or contacts. See FindHBond (or findhbond command), Find Clashes/Contacts (or findclash command, which is used in the tutorial above), and the Structure Analysis tutorial with examples of using those tools. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/ findhbond.html> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findclash/ findclash.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/ tutorials/squalene.html>
Additional related features that may interest you:
- command “measure contactArea” which also shows a colored surface patch similar to that in the first tutorial above <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ measure.html#contactArea>
- Intersurf tool: shows a single “interaction surface” <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/intersurf/ intersurf.html>
I don’t know how you would use an EM map to visualize an interface surface. 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 14, 2018, at 12:02 PM, Yangqi Gu <yangqi.gu@yale.edu> wrote:
Dear Chimera users, I am trying to visualize the interface surface of my two monomers. Is there anyway to show the interacting surface from Chimera by using the EM map? Or should I do it from PDB coordinates? Best, Yangqi
-- Yangqi Gu Graduate Student Malvankar Lab Yale University, West Campus
participants (2)
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Elaine Meng -
Yangqi Gu