SASA calculation per residue
Hello Chimera developers, I'm trying to calculate sasa scores for a list of individual residues in chimera and cant quite get it. Ive tried commands and the define attribute menu. The command ive been using is 0.23:23/areaSAS I've used similar things but I don't know what Im missing. Thanks for any help. Cheers, Andrew MacRae UCSC
Hi Andrew, Your command attempt mystifies me, but I’ll go on the rest of what you said… Just show a molecular surface (e.g. with command “surface”) and then save a file with the list of residue SASA values. You would save that file using the Render by Attribute tool (in menu under Tools… Structure Analysis); in that dialog’s menu choose File… Save Attributes. In the attribute-saving dialog you have to specify which attribute you want: “areaSAS” of “residues” (there is also the same attribute name for individual attoms) Attribute-saving is described here, in the bottom section of the page: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html...> There is an option to restrict the save to the current selection, if you don’t want the list for all residues. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 22, 2018, at 12:01 PM, Andrew Macrae <amacrae@ucsc.edu> wrote:
Hello Chimera developers,
I'm trying to calculate sasa scores for a list of individual residues in chimera and cant quite get it. Ive tried commands and the define attribute menu. The command ive been using is
0.23:23/areaSAS
I've used similar things but I don't know what Im missing. Thanks for any help.
Cheers, Andrew MacRae UCSC
Thanks, that clears it up On Fri, Jun 22, 2018 at 1:09 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Andrew, Your command attempt mystifies me, but I’ll go on the rest of what you said…
Just show a molecular surface (e.g. with command “surface”) and then save a file with the list of residue SASA values. You would save that file using the Render by Attribute tool (in menu under Tools… Structure Analysis); in that dialog’s menu choose File… Save Attributes. In the attribute-saving dialog you have to specify which attribute you want: “areaSAS” of “residues” (there is also the same attribute name for individual attoms)
Attribute-saving is described here, in the bottom section of the page: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/ render.html#saving>
There is an option to restrict the save to the current selection, if you don’t want the list for all residues. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 22, 2018, at 12:01 PM, Andrew Macrae <amacrae@ucsc.edu> wrote:
Hello Chimera developers,
I'm trying to calculate sasa scores for a list of individual residues in chimera and cant quite get it. Ive tried commands and the define attribute menu. The command ive been using is
0.23:23/areaSAS
I've used similar things but I don't know what Im missing. Thanks for any help.
Cheers, Andrew MacRae UCSC
participants (2)
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Andrew Macrae -
Elaine Meng