Hi Vinny, Chimera does not calculate this directly, but there are a couple of ways to attack the problem. It also depends on what exactly you mean by accessibility: the square angstroms of solvent-accessible surface area for a residue, or that value normalized by the surface area in a model of the fully exposed state of that type of residue (often in an extended Gly-X-Gly peptide). For the former, just the value of the solvent-exposed surface area of each residue, it is possible to do everything in Chimera without file editing, but there are several steps (also, I recommend Chimera version 1.2121 since there is a bug in step 4 in later versions, which we are now fixing): (1) open the structure of interest (2) delete all waters, ligands, etc. you don't want in the surface area calculation, for example using the command: delete solvent | ligand | ions (3) open the Surface Area/Volume tool (Tools... Surface/Binding Analysis... Surface Area/Volume) use that to compute Accessible Surface (Gerstein) and show the resulting attribute in the Render/ Select by Attribute tool (these are the default settings). This generates the values for the ATOMS, which is shown as a histogram in the Render/Select by Attribute tool. Alas, you still have to add up the values for the atoms to get totals for the residues, which is the next step: (4) Choose Tools... Structure Analysis... Attribute Calculator and in that, Calculate attribute named whatever you want for RESIDUES (not atoms, which is the default setting) and enter the formula: sum (atom.accessibleSurface) Also check the option to "Save calculation results to file." This will write a text file listing the residue totals. The file will contain something like attribute: whatever-name-you-specified match mode: 1-to-1 recipient: residues #0:1.A 156.86 #0:2.A 80.45 #0:3.A 129.9 ... etc. ... The resulting residue attribute is also shown in the Render/Select by Attribute tool as a histogram. (5) Here is the fun part: you can move the sliders around on the histogram, add/subtract sliders, and change slider colors to control how the coloring is mapped to surface area values. Click the Help button on the Render/Select by Attribute dialog to get more details if you wish. For the latter, the normalized value, you'd have to get the values outside of Chimera. In the past, I've used the GETAREA server for this purpose. Here are the steps if you use GETAREA; some file editing is required: (1) upload your structure to the GETAREA server, see http://www.scsb.utmb.edu/getarea/area_man.html click the "submission form" link to get the actual form (2) edit the GETAREA results (pick whatever column of values is of interest; I used "Ratio (%)" which is the normalized value) into a text file with the format used by Chimera's Define Attribute tool. The Define Attribute format is described in: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/ defineattrib.html#attrfile (This is the same format written out in step (4) above.) Most of the lines in the file are tab-separated columns where the first column specifies the residue and the second gives the value that should be assigned to that residue. (3) choose Tools... Structure Analysis... Define Attribute and open the file you made (4) use Render/Select by Attribute to color residues according to your new attribute (see (5) above for more info) I hope this helps, 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 On Oct 12, 2005, at 6:58 AM, Vincent Lynch wrote:
To Whom It May Concern,
I am new to Chimera (and molecular modeling in general) and cant figure out if I can color by residue accessibility to solvent and see the raw value of solvent accessibility.
Thanks Vinny
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