From owner-chemistry ^%at%^ ccl.net Fri Mar 7 14:36:00 2008 From: "Elaine Meng meng()cgl.ucsf.edu" To: CCL Subject: CCL: calculating and displaying surface residues Message-Id: <-36458-080307132355-23297-Umg5wU1zJc42GSdLUaLaFw]![server.ccl.net> X-Original-From: "Elaine Meng" Date: Fri, 7 Mar 2008 13:23:52 -0500 Sent to CCL by: "Elaine Meng" [meng]=[cgl.ucsf.edu] On Mar 6, 2008, at 7:51 PM, Kalpana Krishnaswami kalpuk*_*gmail.com wrote: Hi We would like to calculate and display exposed hydrophobic surfaces on a protein. We would also like to list the residues on the surface. Are there freeware/ scripts/plugins to pymol/rasmol that would do this? Thanks -- Kalpana Krishnaswami Hi Kalpana, If you want calculations based on the hydrophobicity of each atom, take a look at the GetArea server: http://pauli.utmb.edu/cgi-bin/get_a_form.tcl If you want calculations based on the hydrophobicity of amino acid residues in proteins, you may want to try UCSF Chimera - not a web server, but freely downloadable for noncommercial use (Windows, Mac, Linux, etc.): http://www.cgl.ucsf.edu/chimera/index.html I recommend the recent snapshot: http://www.cgl.ucsf.edu/chimera/download.html#snapshots In Chimera, there are many related possibilities. After opening the structure ("File... Open" for local file or "File... Fetch by ID" to get from PDB) you could (A) color the surface by amino acid hydrophobicity - simply choosing "Presets... interactive 3 (hydrophobicity surface)" from the menu will apply a built-in scheme. Or to specify the color mapping yourself, use the "Render by Attribute" tool (under Tools... Depiction) on the residue attribute named kdHydrophobicity. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/menu.html#menupresets http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html (B) calculate surface area values - first calculate the surface areas for all atoms, then later you can sum over subsets such as the hydrophobic residues. To calculate atomic surface areas, use the "Area/Volume from Web" tool (under Tools... Surface/Binding Analysis) and pick which surface area method and parameters you want. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfvol/surfvol.html After that, to sum over only residues with a certain hydrophobicity, first select them with "Select... by Attribute Value" and then with "Attribute Calculator" (under Tools... Structure Analysis), sum the surface area values of all selected atoms in the whole model. Similarly, to get a list of all surface residues, you could select all atoms with surface area >0 and then use "Actions... Write List" to make a text file listing those residues or "Actions... Write PDB" to save the coordinates of those residues. http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/calculator/calculator.html The Kyte-Doolittle amino acid hydrophobicity is used by default, but you can use different scales. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hydrophob.html I realize there is a learning curve with Chimera, but you can do many powerful things. I can provide more details if you try any of these things but get stuck. Best, Elaine ----- Elaine C. Meng, Ph.D. meng###cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html