[Chimera-users] solvent exposed charged resides
meng at cgl.ucsf.edu
Wed May 4 15:20:02 PDT 2011
Welcome to Chimera! Don't worry, I'm not a programmer either. There is a video tutorial that covers some of what I describe below,
I can't tell from your description what might be going wrong, but yes the basic procedure would be to show a surface (which you could then hide, the important part is showing it at some point), and then choose residues of the desired types that have surface area greater than some cutoff.
For example, open PDB 2gbp, show surface with Actions... Surface... show (or command "surface"). As soon as you create the surface, atoms and residues will be assigned attributes named areaSES and areaSAS containing their solvent-excluded and solvent-accessible surface areas. The solvent-excluded surface is what Chimera displays, but both are calculated, as discussed here:
These values will include surface area from interior bubbles. If you don't want interior bubbles to be included, next enter the command:
setattr s allComponents false
Then, so you will be able to see what you are selecting, hide the surface and show all atoms, for example with commands:
Then, experiment with different cutoffs of surface area to classify a residue as solvent-exposed or not. Don't worry about the residue type for now. You could do this interactively using Select by Attribute (menu: Select... By Attribute Value, set level to "residues" instead of "atoms" and attribute to "areaSAS" or "areaSES" as preferred), or with commands such as:
I'd probably use something like 40 or 50, but it depends on your goal, so go with whatever cutoff you find selects the residues you expect. Then you can unselect residues that are not of the desired type, for example with command:
(unselect residues that are NOT the ones named). The names/numbers of the remaining selected residues can be written out to a file with "Actions... Write List" in the menu, or the command "writesel".
Render by Attribute or command "rangecolor" would be used if you wanted to show the surface area values with colors.
If you wanted to write out the area values along with the residues, you would use "File... Save Attributes" from the menu of the dialog of Render/Select by Attribute. There is an option to save only the values for the current selection.
I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
On May 4, 2011, at 10:44 AM, George Feldman wrote:
> Hello Chimera community,
> I am rather new to Chimera, but in general familiar with PyMol. I switched to Chimera for the added functionality and general "free-ness," and so far I like it, but I'm having difficulty getting started. What I really need to do is identify the solvent exposed (SAS) residues that are charged. In particular I would like to identify exposed lysines, arginines, glutamic acids, and aspartic acids. All I need to do is identify and count them, is there a way to do this without slowly going over the entire molecular surface? Please bear in mind that I am capable of typing in commands, but I am no programmer. If it is too complex, I will simply, and sadly, have to do it manually. My fear with the manual approach is that I will miss something or miss-classify it. Your advise and help is greatly appreciated.
> PS. I've tried to do Render by Attribute -> areaSAS, but that doesn't seem to be working for me even after I tell it to calculate the surface. I'm not sure what I'm doing wrong if this is the approach that I am supposed to be taking.
> Best regards,
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