[Chimera-users] Chimera-users Digest, Vol 77, Issue 26
vamsi krishna
vamsi at nus.edu.sg
Wed Sep 30 03:33:51 PDT 2009
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
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> 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 at cgl.ucsf.edu>
> To: Thiruvarangan Ramaraj <thiruvaranganr at yahoo.com>
> Cc: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Solvent Accessible Surface Area
> Message-ID: <E24233F9-9564-4824-8D82-6D9506261ACB at 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 at yahoo.com>
> To: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Solvent Accessible Surface Area
> Message-ID: <842106.2825.qm at 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 at cgl.ucsf.edu> wrote:
>
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Subject: Re: Solvent Accessible Surface Area
> To: "Thiruvarangan Ramaraj" <thiruvaranganr at yahoo.com>
> Cc: "chimera-users at cgl.ucsf.edu BB" <chimera-users at 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
>
>
>
>
>
>
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>
> ------------------------------
>
> Message: 3
> Date: Mon, 28 Sep 2009 16:00:08 -0700 (PDT)
> From: Greg Couch <gregc at cgl.ucsf.edu>
> To: Thiruvarangan Ramaraj <thiruvaranganr at yahoo.com>
> Cc: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Solvent Accessible Surface Area
> Message-ID: <Pine.OSF.4.63.0909281534380.1997062 at guanine.cgl.ucsf.edu>
> Content-Type: TEXT/Plain; charset=US-ASCII; format=flowed
>
> On Mon, 28 Sep 2009, Thiruvarangan Ramaraj wrote:
>
>
>> 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
>>
>
> The first thing to try is a chimera daily build. The daily builds make
> fewer assumptions about what Linux provides. However, there is still a
> good chance that chimera will crash in Fedora 11 -- because Fedora 11's
> OpenGL support is based on the latest and greatest Mesa code and as the
> Mesa website says "Those especially concerned about stability may want to
> wait for the follow-on 7.6.1 bug-fix release.".
>
> Currently, we have found that the default NVidia driver does not work, but
> that the driver from NVidia does. The opposite is true for ATI drivers,
> the default driver works, but the one from ATI fails. The default Intel
> driver is mostly okay (e.g,. when doing area selections, the selection box
> can appear in a different application's window!).
>
> So good luck, and please tell me how it goes,
>
> Greg
>
>
> ------------------------------
>
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> End of Chimera-users Digest, Vol 77, Issue 26
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