Re: [Chimera-users] Chimera-users Digest, Vol 77, Issue 26
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:
- Re: Solvent Accessible Surface Area (Elaine Meng)
- Re: Solvent Accessible Surface Area (Thiruvarangan Ramaraj)
- 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
Dear Vamsi, I do not think there is a definite answer. This is a somewhat philosophical rather than technical question... it depends what you are going to do with the resulting list of residues. You could try different values and see whether the resulting set of residues agrees with your intuition.
If I remember correctly, there are some alanine scanning papers that indicate even residues that are in contact are not always important for binding energy. These were experiments done on protein-protein systems, however. Perhaps there are some published papers that discuss these issues for substrates -- if anybody has an opinion on this topic or can suggest references, please speak up!
However, if you have a protein-ligand complex structure, why not just use the "Find Contacts/Clashes" tool instead of dealing with solvent- accessible surface areas? That is what I would use.
"Find Contacts/Clashes" documentation: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash...
Also, the "distances, H-bonds, contacts" section of this tutorial includes an example of finding residues that interact with a ligand: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ squalene.html>
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
On Sep 30, 2009, at 3:33 AM, vamsi krishna wrote:
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
participants (2)
-
Elaine Meng
-
vamsi krishna