Hi Elaine, The values in the table you mentioned seem to correspond to side-chain accessibility only, if I compare them to those for Gly-X-Gly peptide as in the classical paper by Miller et al. (1987), 196, 641-656. Their table can also be found in the book by Creighton: Proteins, 2nd edition, p. 142. Best regards,                  Boaz ----- Original Message ----- From: chimera-users-request@cgl.ucsf.edu Date: Tuesday, December 14, 2010 21:11 Subject: Chimera-users Digest, Vol 92, Issue 11 To: chimera-users@cgl.ucsf.edu

Send Chimera-users mailing list submissions to chimera-users@cgl.ucsf.edu

To subscribe or unsubscribe via the World Wide Web, visit http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users or, via email, send a message with subject or body 'help' to chimera-users-request@cgl.ucsf.edu

You can reach the person managing the list at chimera-users-owner@cgl.ucsf.edu

When replying, please edit your Subject line so it is more specific than "Re: Contents of Chimera-users digest..."

Today's Topics:

   1. Maximum surface areas for each amino acid (Tom Goddard)   2. Center of segmentation regions (Tom Goddard)    3. Chimera Error (Kshatresh Dutta Dubey)    4. Re: Chimera Error (Elaine Meng)    5. Re: Maximum surface areas for each amino acid (Elaine Meng)    6. 3D-Stereo. (ayassin@wadsworth.org)    7. merging 3D volumes (Marlovits,Thomas)    8. Re: merging 3D volumes (Elaine Meng)

----------------------------------------------------------------- -----

Message: 1 Date: Mon, 13 Dec 2010 18:08:11 -0800 From: Tom Goddard <goddard@sonic.net> Subject: [Chimera-users] Maximum surface areas for each amino acid To: iropson@psu.edu Cc: 'Chimera BB' <chimera-users@cgl.ucsf.edu> Message-ID: <4D06D18B.7040806@sonic.net> Content-Type: text/plain; charset="iso-8859-1"

Hi Ira,

   I don't know of any table of maximal solvent accessible surface areas for each residue type when bounded by glycines.  Maybe someone on the Chimera mailing list will know.

   A Chimera Python script could run through the PDB and accumulate per-residue surface area statistics.  One trouble with that would be that surface calculation fails in Chimera in some percentage of cases (~5%) due to numerical problems.

     Tom

...

Hi Tom,

Love the software. Do you have a table for calculating the maximum available surface area for amino acids eg.(Gly-Xxx-Gly) so that I can get a relative percentage exposed surface area from the calculations? Do you know how to find one in the literature? Has anyone written a program that describes the possible surface exposure for a residue in a particular secondary structure and/or a particular sequence? This maximal value would certainly be different depending on the local sequence and structure. For example, a residue in the middle of a helix would have to be shielded from the solvent by the i+4 and i-4 residues, and the size of those residues would matter.

Thanks, Ira

On 12/10/10 2:41 PM, Tom Goddard wrote:

...

Hi Sumitro,

   I made a Chimera video tutorial showing how to determine which residues are on the surface.

http://www.cgl.ucsf.edu/chimera/videodoc/surfaceresidues/index.html

   Tom