On Oct 7, 2009, at 4:33 PM, Thiruvarangan Ramaraj wrote:

Thanks Eric, but just to follow up on the surf sel command,

It displays the surface for the selected residues,

does it assign solvent-excluded and solvent-accessible surface areas per atom and residue to attributes named areaSES and areaSAS to the selected residues or to the whole protein?.

after I do "surf sel" I have select:/areaSAS > 50 , looks like it selects for the whole protein. Shouldn't it show only for the selected surface region.

Hi Thiru,
Surfaces are computed for the entirety of the molecule (that the surface covers), not just the residues you display the surface on. So therefore other residues also got areaSAS/SES attributes. To get what you want I think you need:

sel :/areaSAS > 50 & @/surfaceDisplay

--Eric

Thanks

-Thiru

--- On Wed, 10/7/09, Eric Pettersen <pett@cgl.ucsf.edu> wrote:

From: Eric Pettersen <pett@cgl.ucsf.edu>
Subject: Re: Displaying Surface For Selected Residues
To: "Thiruvarangan Ramaraj" <thiruvaranganr@yahoo.com>
Date: Wednesday, October 7, 2009, 5:14 PM

Yes, most commands work on everything if you don't specify what to work on. For instance "color red" colors everything red whereas "color red sel" colors the selection red.

--Eric

On Oct 7, 2009, at 4:09 PM, Thiruvarangan Ramaraj wrote:

Worked fine, Thanks, Eric

-Thiru

--- On Wed, 10/7/09, Eric Pettersen <pett@cgl.ucsf.edu> wrote:

From: Eric Pettersen <pett@cgl.ucsf.edu>
Subject: Re: Displaying Surface For Selected Residues
To: "Thiruvarangan Ramaraj" <thiruvaranganr@yahoo.com>
Date: Wednesday, October 7, 2009, 5:04 PM

"surface sel"

--Eric

On Oct 7, 2009, at 4:03 PM, Thiruvarangan Ramaraj wrote:

Hi Eric,

I have a protein with a few residues selected, and I wanted to show surface only on the selected residues, when I go to Actions - Surface -Show , it shows surface only for the selected residues, but when I use the command surface on the command line it shows the surface for the entire protein. Is there a command line option to show surface only for the selected residues on the protein.

Thanks

Thiru

--- On Thu, 10/1/09, Eric Pettersen <pett@cgl.ucsf.edu> wrote:

From: Eric Pettersen <pett@cgl.ucsf.edu>
Subject: Re: [Chimera-users] Solvent Accessible Surface Area
To: "Thiruvarangan Ramaraj" <thiruvaranganr@yahoo.com>
Cc: "UCSF Chimera Mailing List" <chimera-users@cgl.ucsf.edu>
Date: Thursday, October 1, 2009, 3:38 PM

Oops, spotted a bug in the script. This line:

out = open(os.path.expanduser("~/out", "w"))

should be:

out = open(os.path.expanduser("~/out"), "w")

--Eric