color surface based on NMR Order parameters
Hello,
I like the 'surface color ' feature in Chimera. I think, right now, the surface can be colored by radius, height, volume data and so on..
Is it also possible to color the surface based upon the NMR order parameters or intensity ratios (it will be an Excel file containing just two columns: residue numbers and the respective parameter values)? Or this can be done in some other way?
Thanks in advance,
Regards, Lalit Deshmukh, University of Connecticut Storrs, CT 06269
Hi Lalit, Very similar to the reply I just sent to Wei: you can create a custom attribute or property and assign the values to atoms or residues. Then you can color the structure (including atoms, ribbons, surfaces) by those values.
To create a custom attribute, you create a simple text file and then read it in using the Define Attribute tool (in menu under Tools... Structure Analysis) or the command "defattr". The attribute file format is described here, and some example files are linked:
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html#attrfile http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/defattr.html
Then you can do the coloring with the Render by Attribute tool (under Tools... Structure Analysis): http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#render
Besides colors, the values can be shown with sphere sizes or "worms". You can also show the values as labels, as mentioned in the reply to Wei: http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-June/005249.html
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 7, 2010, at 2:11 PM, lalit.deshmukh@huskymail.uconn.edu wrote:
Hello,
I like the 'surface color ' feature in Chimera. I think, right now, the surface can be colored by radius, height, volume data and so on..
Is it also possible to color the surface based upon the NMR order parameters or intensity ratios (it will be an Excel file containing just two columns: residue numbers and the respective parameter values)? Or this can be done in some other way?
Thanks in advance,
Regards, Lalit Deshmukh, University of Connecticut Storrs, CT 06269
Hi, I forgot to mention to both of you that there is also a Chimera tutorial that is all about attributes:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/attributes.html
and another that explains how to make a figure showing attribute (B-factor) values with color:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/bfactor.html
Besides the "Render by Attribute" tool with graphical interface, you can also use the "rangecolor" command to show attribute values with color: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html
Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
Hello, Reading the posts and the tutorials, I have understood how to make ribbons transparent, but with a single color. I would like to make a rainbow-colored ribbon look transparent. How do I do it? Thanks a lot Stefano
Hi Stefano, Sorry, unlike surfaces, there is no option to keep the ribbon the same color(s) except make it transparent. There is only the capability of making specific transparent colors and then using them on the ribbon, and it sounds like you already know how to do that. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 7, 2011, at 1:27 PM, Stefano Luciano Ciurli wrote:
Hello, Reading the posts and the tutorials, I have understood how to make ribbons transparent, but with a single color. I would like to make a rainbow-colored ribbon look transparent. How do I do it? Thanks a lot Stefano
One trick is that if you define colors with transparency in them (by using the colordef command) then you can use them in the rainbow command to get a rainbow with transparency.
--Eric
On Sep 7, 2011, at 1:55 PM, Elaine Meng wrote:
Hi Stefano, Sorry, unlike surfaces, there is no option to keep the ribbon the same color(s) except make it transparent. There is only the capability of making specific transparent colors and then using them on the ribbon, and it sounds like you already know how to do that. Best, Elaine
Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 7, 2011, at 1:27 PM, Stefano Luciano Ciurli wrote:
Hello, Reading the posts and the tutorials, I have understood how to make ribbons transparent, but with a single color. I would like to make a rainbow-colored ribbon look transparent. How do I do it? Thanks a lot Stefano
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
So it's not too bad then, for example, commands:
colordef tblue 0 0 1 .2 colordef tcyan 0 1 1 .2 colordef tgreen 0 1 0 .2 colordef tyellow 1 1 0 .2 colordef tred 1 0 0 .2 rainbow residue tblue,tcyan,tgreen,tyellow,tred
However, Chimera transparency rendering has some problems. When I do this on a protein ribbon, in some places the stuff behind the ribbon shows through (as it should), but in some other places, it does not.
Also unlike surfaces, there is no single-layer transparency option that would avoid this problem.
Elaine
On Sep 7, 2011, at 2:15 PM, Eric Pettersen wrote:
One trick is that if you define colors with transparency in them (by using the colordef command) then you can use them in the rainbow command to get a rainbow with transparency.
--Eric
On Sep 7, 2011, at 1:55 PM, Elaine Meng wrote:
Hi Stefano, Sorry, unlike surfaces, there is no option to keep the ribbon the same color(s) except make it transparent. There is only the capability of making specific transparent colors and then using them on the ribbon, and it sounds like you already know how to do that. Best, Elaine
Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 7, 2011, at 1:27 PM, Stefano Luciano Ciurli wrote:
Hello, Reading the posts and the tutorials, I have understood how to make ribbons transparent, but with a single color. I would like to make a rainbow-colored ribbon look transparent. How do I do it? Thanks a lot Stefano
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
yes, not too bad. Thanks a lot! Stefano
On Sep 7, 2011, at 11:27 PM, Elaine Meng wrote:
So it's not too bad then, for example, commands:
colordef tblue 0 0 1 .2 colordef tcyan 0 1 1 .2 colordef tgreen 0 1 0 .2 colordef tyellow 1 1 0 .2 colordef tred 1 0 0 .2 rainbow residue tblue,tcyan,tgreen,tyellow,tred
However, Chimera transparency rendering has some problems. When I do this on a protein ribbon, in some places the stuff behind the ribbon shows through (as it should), but in some other places, it does not.
Also unlike surfaces, there is no single-layer transparency option that would avoid this problem.
Elaine
On Sep 7, 2011, at 2:15 PM, Eric Pettersen wrote:
One trick is that if you define colors with transparency in them (by using the colordef command) then you can use them in the rainbow command to get a rainbow with transparency.
--Eric
On Sep 7, 2011, at 1:55 PM, Elaine Meng wrote:
Hi Stefano, Sorry, unlike surfaces, there is no option to keep the ribbon the same color(s) except make it transparent. There is only the capability of making specific transparent colors and then using them on the ribbon, and it sounds like you already know how to do that. Best, Elaine
Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 7, 2011, at 1:27 PM, Stefano Luciano Ciurli wrote:
Hello, Reading the posts and the tutorials, I have understood how to make ribbons transparent, but with a single color. I would like to make a rainbow-colored ribbon look transparent. How do I do it? Thanks a lot Stefano
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
And don't forget the Rainbow Tool (under Depiction). You can change the colors in each color well to be transparent and then create the rainbow.
-- Greg
On 9/7/2011 2:27 PM, Elaine Meng wrote:
So it's not too bad then, for example, commands:
colordef tblue 0 0 1 .2 colordef tcyan 0 1 1 .2 colordef tgreen 0 1 0 .2 colordef tyellow 1 1 0 .2 colordef tred 1 0 0 .2 rainbow residue tblue,tcyan,tgreen,tyellow,tred
However, Chimera transparency rendering has some problems. When I do this on a protein ribbon, in some places the stuff behind the ribbon shows through (as it should), but in some other places, it does not.
Also unlike surfaces, there is no single-layer transparency option that would avoid this problem.
Elaine
On Sep 7, 2011, at 2:15 PM, Eric Pettersen wrote:
One trick is that if you define colors with transparency in them (by using the colordef command) then you can use them in the rainbow command to get a rainbow with transparency.
--Eric
On Sep 7, 2011, at 1:55 PM, Elaine Meng wrote:
Hi Stefano, Sorry, unlike surfaces, there is no option to keep the ribbon the same color(s) except make it transparent. There is only the capability of making specific transparent colors and then using them on the ribbon, and it sounds like you already know how to do that. Best, Elaine
Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 7, 2011, at 1:27 PM, Stefano Luciano Ciurli wrote:
Hello, Reading the posts and the tutorials, I have understood how to make ribbons transparent, but with a single color. I would like to make a rainbow-colored ribbon look transparent. How do I do it? Thanks a lot Stefano
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (5)
-
Elaine Meng -
Eric Pettersen -
Greg Couch -
lalit.deshmukhï¼ huskymail.uconn.edu -
Stefano Luciano Ciurli