Re: [Chimera-users] question about surface properties in Chimera
Hi Katie, The hydrophobicity coloring in the presets menu is simply using the Kyte-Doolittle amino acid hydrophobicity values. That is, all the surface patches belonging to a given amino acid residue type will have the same color, and the colors range from blue for the most hydrophilic through white to orange-red for the most hydrophobic. If you open Render By Attribute (under Tools... Structure Analysis) and set it to show the attribute of "residues" named "kdHydrophobicity" you can apply a different coloring scheme to these same values. Or, if you want, you can write out a file that lists the residues in the protein and the associated values (in that tool's menu, use File... Save Attributes). That will include all the residues, though, not just the ones on the surface. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#...> However, as mentioned, it is merely a lookup based on the residue type. There is a table of Kyte-Doolittle hydrophobicity values here, and instructions for using different scales of amino acid hydrophobicity, if you would like: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hydrophob.html> We encourage Chimera questions to be sent to chimera-users@cgl.ucsf.edu (Cc'd) unless the message includes private data. 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 Jul 4, 2012, at 7:40 AM, Katherine Klymko wrote:
Dear Dr. Meng, Hello--I am a theoretical chemistry student at Columbia University and I am interested in the hydrophobicity maps of proteins that Chimera generates: I know that this can be used to visualize the hydrophobicity of the surface, but does it also generate a file that I can use that lists the positions of the surface atoms or amino acids with their hydrophobic value? I am interested in quantitatively comparing the hydrophobic surface organization in a large number of proteins.
I apologize if you are the wrong person to ask but when searching for solutions on line, you seemed to be the person that a lot of people went to for help. Thank you, Katie Klymko
Thank you for the help. I have another question: Is it possible to write a file with a list of the amino acids on the surface, and possibly their locations relative to the center of mass of the protein? Thank you, Katie On Wed, Jul 4, 2012 at 12:53 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Katie, The hydrophobicity coloring in the presets menu is simply using the Kyte-Doolittle amino acid hydrophobicity values. That is, all the surface patches belonging to a given amino acid residue type will have the same color, and the colors range from blue for the most hydrophilic through white to orange-red for the most hydrophobic.
If you open Render By Attribute (under Tools... Structure Analysis) and set it to show the attribute of "residues" named "kdHydrophobicity" you can apply a different coloring scheme to these same values. Or, if you want, you can write out a file that lists the residues in the protein and the associated values (in that tool's menu, use File... Save Attributes). That will include all the residues, though, not just the ones on the surface. < http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#...
However, as mentioned, it is merely a lookup based on the residue type. There is a table of Kyte-Doolittle hydrophobicity values here, and instructions for using different scales of amino acid hydrophobicity, if you would like: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hydrophob.html>
We encourage Chimera questions to be sent to chimera-users@cgl.ucsf.edu(Cc'd) unless the message includes private data. 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 Jul 4, 2012, at 7:40 AM, Katherine Klymko wrote:
Dear Dr. Meng, Hello--I am a theoretical chemistry student at Columbia University and I am interested in the hydrophobicity maps of proteins that Chimera generates: I know that this can be used to visualize the hydrophobicity of the surface, but does it also generate a file that I can use that lists the positions of the surface atoms or amino acids with their hydrophobic value? I am interested in quantitatively comparing the hydrophobic surface organization in a large number of proteins.
I apologize if you are the wrong person to ask but when searching for solutions on line, you seemed to be the person that a lot of people went to for help. Thank you, Katie
Hi Katie, For identifying surface residues, please see this previous post: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-May/003903.html> For residue locations relative to the center of mass, you could first calculate a centroid using the Axes/Planes/Centroids tool (under Tools... Structure Analysis) or equivalently, the command "define," and then use the "distance" command to measure distances between the centroid and each residue. For example, for commands something like: define centroid mass true name c1 protein dist c1 :1.a@ca dist c1 :2.a@ca [etc.] <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/define.html#centroid> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/distance.html> The distances would be reported in the Reply Log (under Favorites in the menu) and you can save Reply Log contents to a file. You would probably want to make a command file of the distance commands (too tedious to type them individually!). 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 Jul 5, 2012, at 9:49 AM, Katherine Klymko wrote:
Thank you for the help. I have another question: Is it possible to write a file with a list of the amino acids on the surface, and possibly their locations relative to the center of mass of the protein? Thank you, Katie
participants (2)
-
Elaine Meng -
Katherine Klymko