Re: [chimerax-users] Chimera X -showing electrostatic potential
Dear Yi Shi, The structure is nice work, and worth showing off! We are fine so far... I hope you are well too.
To color a surface by electrostatic potential in ChimeraX, currently you need to use a separate program to generate the electrostatic potential map, for example the APBS web server or the DelPhi web server mentioned/linked to the Chimera tutorial here: http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html#esp2
After you generate the map (e.g. a .dx file, .phi file, or .cube file) http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#volume
... then you can open it in ChimeraX and use it for coloring the protein molecular surface with the ChimeraX "color electrostatic" command: http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#map
If you open a .cube file it will automatically show as isosurfaces. However, you can hide the isosurfaces such as by clicking the "eye" icon in the Volume Viewer panel, and then carry on with using the coloring command as mentioned above. Of course, you need to open the protein structure and then display the protein's molecular surface first, e.g. with the "surface" command, Actions menu, or Molecule Display icon. http://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.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 May 5, 2020, at 7:14 PM, Yi Shi yi.shi@pitt.edu wrote:
Dear Elaine,
Hope this finds you, your family and colleagues safe and well.
We have a question about Chimera X software that you and your colleagues developed. Do you know how to show the electrostatic potential using Chimera X? Do we need some external software to do this?
BTW, the software that you developed was amazing that we really enjoy it. And thanks a million for using our Nup84 hybrid structure for the cover of your paper in Protein Science. Absolutely beautiful work!
Thanks in advance. Yi
Yi Shi Ph.D. Assistant Professor Department of Cell Biology Program for Integrative Systems Biology Pitt/ CMU Program in Computational Biology University of Pittsburgh School of Medicine BST3 9049 3500 5th Avenue Pittsburgh PA 15213 412-383-3242 (office) 412-383-3243 (lab) www.shi-lab.org
Awesome, thanks!!! Yi
On Tue, May 5, 2020 at 10:45 PM Elaine Meng meng@cgl.ucsf.edu wrote:
Dear Yi Shi, The structure is nice work, and worth showing off! We are fine so far... I hope you are well too.
To color a surface by electrostatic potential in ChimeraX, currently you need to use a separate program to generate the electrostatic potential map, for example the APBS web server or the DelPhi web server mentioned/linked to the Chimera tutorial here: < http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html#esp...
After you generate the map (e.g. a .dx file, .phi file, or .cube file) http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#volume
... then you can open it in ChimeraX and use it for coloring the protein molecular surface with the ChimeraX "color electrostatic" command: http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#map
If you open a .cube file it will automatically show as isosurfaces. However, you can hide the isosurfaces such as by clicking the "eye" icon in the Volume Viewer panel, and then carry on with using the coloring command as mentioned above. Of course, you need to open the protein structure and then display the protein's molecular surface first, e.g. with the "surface" command, Actions menu, or Molecule Display icon. http://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.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 May 5, 2020, at 7:14 PM, Yi Shi yi.shi@pitt.edu wrote:
Dear Elaine,
Hope this finds you, your family and colleagues safe and well.
We have a question about Chimera X software that you and your colleagues
developed. Do you know how to show the electrostatic potential using Chimera X? Do we need some external software to do this?
BTW, the software that you developed was amazing that we really enjoy
it. And thanks a million for using our Nup84 hybrid structure for the cover of your paper in Protein Science. Absolutely beautiful work!
Thanks in advance. Yi
Yi Shi Ph.D. Assistant Professor Department of Cell Biology Program for Integrative Systems Biology Pitt/ CMU Program in Computational Biology University of Pittsburgh School of Medicine BST3 9049 3500 5th Avenue Pittsburgh PA 15213 412-383-3242 (office) 412-383-3243 (lab) www.shi-lab.org
I forgot to mention that coloring the surface by electrostatic potential is also covered in a ChimeraX tutorial here:
http://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html#esp
If you open this tutorial in the ChimeraX browser, such as with command:
open http://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html#esp
... then clicking the links will execute the commands in ChimeraX!
Elaine
On May 5, 2020, at 7:50 PM, Yi Shi wally.yis@gmail.com wrote:
Awesome, thanks!!! Yi
On Tue, May 5, 2020 at 10:45 PM Elaine Meng meng@cgl.ucsf.edu wrote: Dear Yi Shi, The structure is nice work, and worth showing off! We are fine so far... I hope you are well too.
To color a surface by electrostatic potential in ChimeraX, currently you need to use a separate program to generate the electrostatic potential map, for example the APBS web server or the DelPhi web server mentioned/linked to the Chimera tutorial here: http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html#esp2
After you generate the map (e.g. a .dx file, .phi file, or .cube file) http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#volume
... then you can open it in ChimeraX and use it for coloring the protein molecular surface with the ChimeraX "color electrostatic" command: http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#map
If you open a .cube file it will automatically show as isosurfaces. However, you can hide the isosurfaces such as by clicking the "eye" icon in the Volume Viewer panel, and then carry on with using the coloring command as mentioned above. Of course, you need to open the protein structure and then display the protein's molecular surface first, e.g. with the "surface" command, Actions menu, or Molecule Display icon. http://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.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 May 5, 2020, at 7:14 PM, Yi Shi yi.shi@pitt.edu wrote:
Dear Elaine,
Hope this finds you, your family and colleagues safe and well.
We have a question about Chimera X software that you and your colleagues developed. Do you know how to show the electrostatic potential using Chimera X? Do we need some external software to do this?
BTW, the software that you developed was amazing that we really enjoy it. And thanks a million for using our Nup84 hybrid structure for the cover of your paper in Protein Science. Absolutely beautiful work!
Thanks in advance. Yi
Yi Shi Ph.D. Assistant Professor Department of Cell Biology Program for Integrative Systems Biology Pitt/ CMU Program in Computational Biology University of Pittsburgh School of Medicine BST3 9049 3500 5th Avenue Pittsburgh PA 15213 412-383-3242 (office) 412-383-3243 (lab) www.shi-lab.org
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Thanks again! Yi
On Wed, May 6, 2020 at 1:52 PM Elaine Meng meng@cgl.ucsf.edu wrote:
I forgot to mention that coloring the surface by electrostatic potential is also covered in a ChimeraX tutorial here:
< http://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html#esp
If you open this tutorial in the ChimeraX browser, such as with command:
open http://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html#esp
... then clicking the links will execute the commands in ChimeraX!
Elaine
On May 5, 2020, at 7:50 PM, Yi Shi wally.yis@gmail.com wrote:
Awesome, thanks!!! Yi
On Tue, May 5, 2020 at 10:45 PM Elaine Meng meng@cgl.ucsf.edu wrote: Dear Yi Shi, The structure is nice work, and worth showing off! We are fine so
far... I hope you are well too.
To color a surface by electrostatic potential in ChimeraX, currently you
need to use a separate program to generate the electrostatic potential map, for example the APBS web server or the DelPhi web server mentioned/linked to the Chimera tutorial here:
<
http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/surfprop.html#esp...
After you generate the map (e.g. a .dx file, .phi file, or .cube file) http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#volume
... then you can open it in ChimeraX and use it for coloring the protein
molecular surface with the ChimeraX "color electrostatic" command:
http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#map
If you open a .cube file it will automatically show as isosurfaces.
However, you can hide the isosurfaces such as by clicking the "eye" icon in the Volume Viewer panel, and then carry on with using the coloring command as mentioned above. Of course, you need to open the protein structure and then display the protein's molecular surface first, e.g. with the "surface" command, Actions menu, or Molecule Display icon.
http://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.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 May 5, 2020, at 7:14 PM, Yi Shi yi.shi@pitt.edu wrote:
Dear Elaine,
Hope this finds you, your family and colleagues safe and well.
We have a question about Chimera X software that you and your
colleagues developed. Do you know how to show the electrostatic potential using Chimera X? Do we need some external software to do this?
BTW, the software that you developed was amazing that we really enjoy
it. And thanks a million for using our Nup84 hybrid structure for the cover of your paper in Protein Science. Absolutely beautiful work!
Thanks in advance. Yi
Yi Shi Ph.D. Assistant Professor Department of Cell Biology Program for Integrative Systems Biology Pitt/ CMU Program in Computational Biology University of Pittsburgh School of Medicine BST3 9049 3500 5th Avenue Pittsburgh PA 15213 412-383-3242 (office) 412-383-3243 (lab) www.shi-lab.org
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (2)
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Elaine Meng -
Yi Shi