coloring a clipped surface cap by property
Hi Noam, Glad you like ChimeraX!
(A) The way to color a clipped surface cap by the molecular liphilicity potential (MLP) or Coulombic electrostatic potential (ESP) is covered in this tutorial section:
https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html#cap-example
(B) The way to color a clipped surface cap by an atomic or residue attribute is to:
1) color the underlying atoms by the atom or residue attribute (with command "color byattribute" or the Render by Attribute tool)
2) use command "color zone" on the surface cap model to make it match the atoms. You may need to use the disclosure triangles in the Models panel to figure out the model number of the surface cap model.
Example: color zone #1.1.1 near #1 distance 3
https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#zone
Since "N" heads are better than one, we generally recommend sending questions to chimerax-users@cgl.ucsf.edu (CC'd here) unless you are including data or figures that should remain private.
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 10, 2023, at 7:40 AM, Noam Prywes noam.prywes@gmail.com wrote:
Dr. Meng,
I'm a postdoc at berkeley and I'm trying to make a figure where I slice a surface structure and color the clipped surface based on an attribute that I defined (example from a paper attached). I can get clipped surfaces to display the electrostatic potential but not my defined attribute (that I fed in using a .defattr file with a number for each residue). I also can't get the surface to color by lipophilicity.
Do I need to make a .defattr file that colors by atom instead?
Thanks for your help and the amazing service that is chimeraX.
Best wishes, Noam
Thank you, that worked incredibly!
I know that I'm being greedy at this point but do you know if there's some way to smooth out the borders between the patches? They're a little fuzzy, which is ok but I'm just curious if there happens to be an easy fix.
Thanks! Noam
[image: activeSiteSlice.png]
On Wed, May 10, 2023 at 9:28 AM Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Noam, Glad you like ChimeraX!
(A) The way to color a clipped surface cap by the molecular liphilicity potential (MLP) or Coulombic electrostatic potential (ESP) is covered in this tutorial section:
< https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html#ca...
(B) The way to color a clipped surface cap by an atomic or residue attribute is to:
- color the underlying atoms by the atom or residue attribute (with
command "color byattribute" or the Render by Attribute tool)
- use command "color zone" on the surface cap model to make it match the
atoms. You may need to use the disclosure triangles in the Models panel to figure out the model number of the surface cap model.
Example: color zone #1.1.1 near #1 distance 3
https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#zone
Since "N" heads are better than one, we generally recommend sending questions to chimerax-users@cgl.ucsf.edu (CC'd here) unless you are including data or figures that should remain private.
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 10, 2023, at 7:40 AM, Noam Prywes noam.prywes@gmail.com wrote:
Dr. Meng,
I'm a postdoc at berkeley and I'm trying to make a figure where I slice
a surface structure and color the clipped surface based on an attribute that I defined (example from a paper attached). I can get clipped surfaces to display the electrostatic potential but not my defined attribute (that I fed in using a .defattr file with a number for each residue). I also can't get the surface to color by lipophilicity.
Do I need to make a .defattr file that colors by atom instead?
Thanks for your help and the amazing service that is chimeraX.
Best wishes, Noam
Hi Noam, Progress! For smoother boundaries between atom sectors, see the "surface cap" command with "subdivision" option to divide the surface cap into more tiny triangles.
https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html#cap
Example:
surface cap subdivision 5
Note if you give a very high value of subdivision it might slow things down, since there are so many triangles in the scene.
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 10, 2023, at 11:59 AM, Noam Prywes via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Thank you, that worked incredibly!
I know that I'm being greedy at this point but do you know if there's some way to smooth out the borders between the patches? They're a little fuzzy, which is ok but I'm just curious if there happens to be an easy fix.
Thanks! Noam
<activeSiteSlice.png>
On Wed, May 10, 2023 at 9:28 AM Elaine Meng meng@cgl.ucsf.edu wrote: Hi Noam, Glad you like ChimeraX!
(A) The way to color a clipped surface cap by the molecular liphilicity potential (MLP) or Coulombic electrostatic potential (ESP) is covered in this tutorial section:
https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html#cap-example
(B) The way to color a clipped surface cap by an atomic or residue attribute is to:
color the underlying atoms by the atom or residue attribute (with command "color byattribute" or the Render by Attribute tool)
use command "color zone" on the surface cap model to make it match the atoms. You may need to use the disclosure triangles in the Models panel to figure out the model number of the surface cap model.
Example: color zone #1.1.1 near #1 distance 3
https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#zone
Since "N" heads are better than one, we generally recommend sending questions to chimerax-users@cgl.ucsf.edu (CC'd here) unless you are including data or figures that should remain private.
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 10, 2023, at 7:40 AM, Noam Prywes noam.prywes@gmail.com wrote:
Dr. Meng,
I'm a postdoc at berkeley and I'm trying to make a figure where I slice a surface structure and color the clipped surface based on an attribute that I defined (example from a paper attached). I can get clipped surfaces to display the electrostatic potential but not my defined attribute (that I fed in using a .defattr file with a number for each residue). I also can't get the surface to color by lipophilicity.
Do I need to make a .defattr file that colors by atom instead?
Thanks for your help and the amazing service that is chimeraX.
Best wishes, Noam
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
For smooth edges on the cap coloring you can instead use the color zone command option "sharpEdges true" which will make the coloring on the cap exactly match the nearest atom by retriangulating the cap surface so triangle edges are at those boundaries between atoms
color zone #1.2 near #1 sharpEdges true
https://www.cgl.ucsf.edu/chimerax/docs/user/commands/color.html#zone
Tom
On May 10, 2023, at 12:31 PM, Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Noam, Progress! For smoother boundaries between atom sectors, see the "surface cap" command with "subdivision" option to divide the surface cap into more tiny triangles.
https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html#cap
Example:
surface cap subdivision 5
Note if you give a very high value of subdivision it might slow things down, since there are so many triangles in the scene.
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 10, 2023, at 11:59 AM, Noam Prywes via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Thank you, that worked incredibly!
I know that I'm being greedy at this point but do you know if there's some way to smooth out the borders between the patches? They're a little fuzzy, which is ok but I'm just curious if there happens to be an easy fix.
Thanks! Noam
<activeSiteSlice.png>
On Wed, May 10, 2023 at 9:28 AM Elaine Meng meng@cgl.ucsf.edu wrote: Hi Noam, Glad you like ChimeraX!
(A) The way to color a clipped surface cap by the molecular liphilicity potential (MLP) or Coulombic electrostatic potential (ESP) is covered in this tutorial section:
https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html#cap-example
(B) The way to color a clipped surface cap by an atomic or residue attribute is to:
color the underlying atoms by the atom or residue attribute (with command "color byattribute" or the Render by Attribute tool)
use command "color zone" on the surface cap model to make it match the atoms. You may need to use the disclosure triangles in the Models panel to figure out the model number of the surface cap model.
Example: color zone #1.1.1 near #1 distance 3
https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#zone
Since "N" heads are better than one, we generally recommend sending questions to chimerax-users@cgl.ucsf.edu (CC'd here) unless you are including data or figures that should remain private.
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 10, 2023, at 7:40 AM, Noam Prywes noam.prywes@gmail.com wrote:
Dr. Meng,
I'm a postdoc at berkeley and I'm trying to make a figure where I slice a surface structure and color the clipped surface based on an attribute that I defined (example from a paper attached). I can get clipped surfaces to display the electrostatic potential but not my defined attribute (that I fed in using a .defattr file with a number for each residue). I also can't get the surface to color by lipophilicity.
Do I need to make a .defattr file that colors by atom instead?
Thanks for your help and the amazing service that is chimeraX.
Best wishes, Noam
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
This worked perfectly, thanks so much!
[image: Screenshot 2023-05-10 at 2.42.44 PM.png]
On Wed, May 10, 2023 at 12:31 PM Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Noam, Progress! For smoother boundaries between atom sectors, see the "surface cap" command with "subdivision" option to divide the surface cap into more tiny triangles.
https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html#cap
Example:
surface cap subdivision 5
Note if you give a very high value of subdivision it might slow things down, since there are so many triangles in the scene.
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 10, 2023, at 11:59 AM, Noam Prywes via ChimeraX-users <
chimerax-users@cgl.ucsf.edu> wrote:
Thank you, that worked incredibly!
I know that I'm being greedy at this point but do you know if there's
some way to smooth out the borders between the patches? They're a little fuzzy, which is ok but I'm just curious if there happens to be an easy fix.
Thanks! Noam
<activeSiteSlice.png>
On Wed, May 10, 2023 at 9:28 AM Elaine Meng meng@cgl.ucsf.edu wrote: Hi Noam, Glad you like ChimeraX!
(A) The way to color a clipped surface cap by the molecular liphilicity
potential (MLP) or Coulombic electrostatic potential (ESP) is covered in this tutorial section:
<
https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html#ca...
(B) The way to color a clipped surface cap by an atomic or residue
attribute is to:
- color the underlying atoms by the atom or residue attribute (with
command "color byattribute" or the Render by Attribute tool)
- use command "color zone" on the surface cap model to make it match
the atoms. You may need to use the disclosure triangles in the Models panel to figure out the model number of the surface cap model.
Example: color zone #1.1.1 near #1 distance 3
https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#zone
Since "N" heads are better than one, we generally recommend sending
questions to chimerax-users@cgl.ucsf.edu (CC'd here) unless you are including data or figures that should remain private.
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 10, 2023, at 7:40 AM, Noam Prywes noam.prywes@gmail.com
wrote:
Dr. Meng,
I'm a postdoc at berkeley and I'm trying to make a figure where I
slice a surface structure and color the clipped surface based on an attribute that I defined (example from a paper attached). I can get clipped surfaces to display the electrostatic potential but not my defined attribute (that I fed in using a .defattr file with a number for each residue). I also can't get the surface to color by lipophilicity.
Do I need to make a .defattr file that colors by atom instead?
Thanks for your help and the amazing service that is chimeraX.
Best wishes, Noam
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
You're welcome!
The alternative method Tom suggested (using "color zone") is probably more effective in making clean boundaries without as many triangles, if that becomes an issue. I just failed to think of it when sending my answer.
Best, Elaine
On May 10, 2023, at 2:46 PM, Noam Prywes noam.prywes@gmail.com wrote:
This worked perfectly, thanks so much!
<Screenshot 2023-05-10 at 2.42.44 PM.png>
On Wed, May 10, 2023 at 12:31 PM Elaine Meng meng@cgl.ucsf.edu wrote: Hi Noam, Progress! For smoother boundaries between atom sectors, see the "surface cap" command with "subdivision" option to divide the surface cap into more tiny triangles.
https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html#cap
Example:
surface cap subdivision 5
Note if you give a very high value of subdivision it might slow things down, since there are so many triangles in the scene.
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 10, 2023, at 11:59 AM, Noam Prywes via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Thank you, that worked incredibly!
I know that I'm being greedy at this point but do you know if there's some way to smooth out the borders between the patches? They're a little fuzzy, which is ok but I'm just curious if there happens to be an easy fix.
Thanks! Noam
<activeSiteSlice.png>
On Wed, May 10, 2023 at 9:28 AM Elaine Meng meng@cgl.ucsf.edu wrote: Hi Noam, Glad you like ChimeraX!
(A) The way to color a clipped surface cap by the molecular liphilicity potential (MLP) or Coulombic electrostatic potential (ESP) is covered in this tutorial section:
https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html#cap-example
(B) The way to color a clipped surface cap by an atomic or residue attribute is to:
color the underlying atoms by the atom or residue attribute (with command "color byattribute" or the Render by Attribute tool)
use command "color zone" on the surface cap model to make it match the atoms. You may need to use the disclosure triangles in the Models panel to figure out the model number of the surface cap model.
Example: color zone #1.1.1 near #1 distance 3
https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#zone
Since "N" heads are better than one, we generally recommend sending questions to chimerax-users@cgl.ucsf.edu (CC'd here) unless you are including data or figures that should remain private.
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 10, 2023, at 7:40 AM, Noam Prywes noam.prywes@gmail.com wrote:
Dr. Meng,
I'm a postdoc at berkeley and I'm trying to make a figure where I slice a surface structure and color the clipped surface based on an attribute that I defined (example from a paper attached). I can get clipped surfaces to display the electrostatic potential but not my defined attribute (that I fed in using a .defattr file with a number for each residue). I also can't get the surface to color by lipophilicity.
Do I need to make a .defattr file that colors by atom instead?
Thanks for your help and the amazing service that is chimeraX.
Best wishes, Noam
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (3)
-
Elaine Meng -
Noam Prywes -
Tom Goddard