Re: [Chimera-users] SAS values for single atoms and residues
Hi Dave, It is not clear to me what you did to list values in the Reply Log. After you display surface to create those surface area attributes, then start "Render by Attribute" (for example, from under Tools... Depiction) and in that dialog, choose "File... Save Attributes." In the resulting file-save dialog you can specify not only which attribute you want to save, but there is a checkbox "Restrict save to current selection" that you will want to activate before saving the file. For example, you could select all the LYS and then this would be used to write a file listing the areaSAS of each of those residues. Alternatively you could select all the :lys@nz and then write the areas of the selected atoms. 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 Oct 6, 2009, at 9:23 AM, David Chenoweth wrote:
Hi Elaine,
I'm trying to calculate the solvent accessible surface area for several lysine residues in a protein to evaluate which are most likely to be free on the surface for functionalization. My thought was to just calculate the SAS area and rank order them. When I select just the primary amine of all the lysine residues and go to the reply log I get several numbers in a row under SAS and I'm not sure which are correct. These numbers don't seem to change if I select different residues so I'm not sure how to get the SAS values just for my lysine amines.
Thanks, Dave
Thanks Elaine! Your a life saver. Cheers, Dave On Oct 6, 2009, at 12:24 PM, Elaine Meng wrote:
Hi Dave, It is not clear to me what you did to list values in the Reply Log.
After you display surface to create those surface area attributes, then start "Render by Attribute" (for example, from under Tools... Depiction) and in that dialog, choose "File... Save Attributes." In the resulting file-save dialog you can specify not only which attribute you want to save, but there is a checkbox "Restrict save to current selection" that you will want to activate before saving the file.
For example, you could select all the LYS and then this would be used to write a file listing the areaSAS of each of those residues. Alternatively you could select all the :lys@nz and then write the areas of the selected atoms.
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 Oct 6, 2009, at 9:23 AM, David Chenoweth wrote:
Hi Elaine,
I'm trying to calculate the solvent accessible surface area for several lysine residues in a protein to evaluate which are most likely to be free on the surface for functionalization. My thought was to just calculate the SAS area and rank order them. When I select just the primary amine of all the lysine residues and go to the reply log I get several numbers in a row under SAS and I'm not sure which are correct. These numbers don't seem to change if I select different residues so I'm not sure how to get the SAS values just for my lysine amines.
Thanks, Dave
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participants (2)
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David Chenoweth -
Elaine Meng