Hi there! I hope you're doing well. I am trying to calculate the solvent exposed surface area for each amino acid in a protein, and from the tutorial it says that once I create a surface it should automatically generate a text file with the areaSAS information, but I have no clue where to find that file. Where does it get saved? Thanks, Jordan
Hi Jordan, Showing a molecular surface automatically creates surface-area attributes of residues and atoms (areaSES and areaSAS), as described here: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfac...> These values are NOT automatically saved to a file, however. To save an attribute to a file you need to use the Render by Attribute tool. Use main menu: Tools... Depiction... Render by Attribute, and then from the menu of that tool, File... Save Attributes. See "Saving Attributes" section at the bottom of this page: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.htm...> In the attribute-saving dialog, choose the level "residues" and attribute name "areaSAS" or "areaSES" depending on which you want. There is a diagram explaining the difference between SAS and SES in the surface help page, the first link in this message. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 14, 2020, at 10:41 PM, Jordan Alexis Gewing-Mullins <JGewingM9030@scrippscollege.edu> wrote:
Hi there! I hope you're doing well. I am trying to calculate the solvent exposed surface area for each amino acid in a protein, and from the tutorial it says that once I create a surface it should automatically generate a text file with the areaSAS information, but I have no clue where to find that file. Where does it get saved? Thanks, Jordan
Thanks so much! Got it to work. -Jordan ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Sunday, November 15, 2020 9:12 AM To: Jordan Alexis Gewing-Mullins <JGewingM9030@scrippscollege.edu> Cc: chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] solvent exposed surface area Hi Jordan, Showing a molecular surface automatically creates surface-area attributes of residues and atoms (areaSES and areaSAS), as described here: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfac...> These values are NOT automatically saved to a file, however. To save an attribute to a file you need to use the Render by Attribute tool. Use main menu: Tools... Depiction... Render by Attribute, and then from the menu of that tool, File... Save Attributes. See "Saving Attributes" section at the bottom of this page: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.htm...> In the attribute-saving dialog, choose the level "residues" and attribute name "areaSAS" or "areaSES" depending on which you want. There is a diagram explaining the difference between SAS and SES in the surface help page, the first link in this message. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 14, 2020, at 10:41 PM, Jordan Alexis Gewing-Mullins <JGewingM9030@scrippscollege.edu> wrote:
Hi there! I hope you're doing well. I am trying to calculate the solvent exposed surface area for each amino acid in a protein, and from the tutorial it says that once I create a surface it should automatically generate a text file with the areaSAS information, but I have no clue where to find that file. Where does it get saved? Thanks, Jordan
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Elaine Meng -
Jordan Alexis Gewing-Mullins