Dear all, I am using chimera to calculate solvent accessibility of residues , may i ask you what cutoff is appropriate to identify surface residues significant for substrate binding . Thank you vamsi chimera-users-request@cgl.ucsf.edu wrote:

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

To subscribe or unsubscribe via the World Wide Web, visit http://www.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. Re: Solvent Accessible Surface Area (Elaine Meng) 2. Re: Solvent Accessible Surface Area (Thiruvarangan Ramaraj) 3. Re: Solvent Accessible Surface Area (Greg Couch)

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

Message: 1 Date: Mon, 28 Sep 2009 12:14:48 -0700 From: Elaine Meng <meng@cgl.ucsf.edu> To: Thiruvarangan Ramaraj <thiruvaranganr@yahoo.com> Cc: "chimera-users@cgl.ucsf.edu BB" <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Solvent Accessible Surface Area Message-ID: <E24233F9-9564-4824-8D82-6D9506261ACB@cgl.ucsf.edu> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes

On Sep 28, 2009, at 10:46 AM, Thiruvarangan Ramaraj wrote:

...

Hi Elaine, I am using Chimera for identifying the surface residues.

I select areaSAS > 0.05 square angstroms, is this same as saying areaSAS > 5%, I am getting confused with the numbers 5% and 0.05 sq angstroms have these been switched some how or are they curiously the same in the following statement?

I just need some help in understanding. Thank You Sincerely -Thiru Ramaraj

Hi Thiru, In Chimera there is no percentage (%) measurement, it is only the area value in square angstroms. Some other programs give % exposed for a residue, which is a ratio of the area of that residue in your structure to the area of the same type of residue in some theoretical unfolded state. See for example the GetArea server, which gives "Ratio(%)": <http://curie.utmb.edu/area_man.html>

However, what Chimera reports is just the surface area of the atom or residue in your structure. To choose surface residues, I'd probably use a bigger cutoff, say

select :/areaSAS>10

but it depends on what you are going to do with the results. You can try different values and see what looks reasonable. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco

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

Message: 2 Date: Mon, 28 Sep 2009 13:49:00 -0700 (PDT) From: Thiruvarangan Ramaraj <thiruvaranganr@yahoo.com> To: "chimera-users@cgl.ucsf.edu BB" <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] Solvent Accessible Surface Area Message-ID: <842106.2825.qm@web53905.mail.re2.yahoo.com> Content-Type: text/plain; charset="iso-8859-1"

Thanks,? Elaine for the information.

Also I am having problems with installing Chimera on Linux Fedora 11(32 bit version). I am able to download it and install it. When I start chimera it comes up and then crashes immediately, the only message it gives is Segmentation Fault.

Is there anyway I could resolve this problem.

Thank You

-Thiru Ramaraj

--- On Mon, 9/28/09, Elaine Meng <meng@cgl.ucsf.edu> wrote:

From: Elaine Meng <meng@cgl.ucsf.edu> Subject: Re: Solvent Accessible Surface Area To: "Thiruvarangan Ramaraj" <thiruvaranganr@yahoo.com> Cc: "chimera-users@cgl.ucsf.edu BB" <chimera-users@cgl.ucsf.edu> Date: Monday, September 28, 2009, 1:14 PM

On Sep 28, 2009, at 10:46 AM, Thiruvarangan Ramaraj wrote:

...

Hi Elaine, I am using Chimera for identifying the surface residues.

I select areaSAS > 0.05 square angstroms, is this same as saying areaSAS > 5%, I am getting confused with the numbers? 5% and 0.05 sq angstroms have these been switched some how or are they curiously the same in the following statement?

I just need some help in understanding. Thank You Sincerely -Thiru Ramaraj

Hi Thiru, In Chimera there is no percentage (%) measurement, it is only the area value in square angstroms.? Some other programs give % exposed for a residue, which is a ratio of the area of that residue in your structure to the area of the same type of residue in some theoretical unfolded state.? See for example the GetArea server, which gives "Ratio(%)": <http://curie.utmb.edu/area_man.html>

However, what Chimera reports is just the surface area of the atom or residue in your structure.? To choose surface residues, I'd probably use a bigger cutoff, say

select :/areaSAS>10

but it depends on what you are going to do with the results.? You can try different values and see what looks reasonable. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco