Re: [Chimera-users] Solvent Accessible Surface Area
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
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
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
Hi Elaine, Thanks For your help. Just another question, Where are the values for attributes areaSAS and areaSES stored, is there a way to extract these values for the residues and write it to a file. Thank You -Thiru --- 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
Hi Thiru, You can save attribute values to a file from the Render by Attribute tool. Start that tool (under Tools... Depiction, for example), then choose "File.. Save Attributes" from its menu. In the resulting dialog, you can specify which attribute you want to save. General information on attributes: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ defineattrib/defineattrib.html#attribdef> Saving attributes: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/ render.html#saving> I hope this helps, 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 Oct 1, 2009, at 1:39 PM, Thiruvarangan Ramaraj wrote:
Hi Elaine, Thanks For your help. Just another question, Where are the values for attributes areaSAS and areaSES stored, is there a way to extract these values for the residues and write it to a file. Thank You -Thiru
Hi Elaine, Thanks for your reply. I figured out how to save it using the GUI, but I was wondering if there is a command line option to accomplish this. Sorry I should have made my question clear. Thank You. -Thiru --- On Thu, 10/1/09, Elaine Meng <meng@cgl.ucsf.edu> wrote: From: Elaine Meng <meng@cgl.ucsf.edu> Subject: Re: [Chimera-users] Solvent Accessible Surface Area To: "Thiruvarangan Ramaraj" <thiruvaranganr@yahoo.com> Cc: "chimera-users@cgl.ucsf.edu BB" <chimera-users@cgl.ucsf.edu> Date: Thursday, October 1, 2009, 2:57 PM Hi Thiru, You can save attribute values to a file from the Render by Attribute tool. Start that tool (under Tools... Depiction, for example), then choose "File.. Save Attributes" from its menu. In the resulting dialog, you can specify which attribute you want to save. General information on attributes: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html#attribdef> Saving attributes: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#saving> I hope this helps, 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 Oct 1, 2009, at 1:39 PM, Thiruvarangan Ramaraj wrote:
Hi Elaine, Thanks For your help. Just another question, Where are the values for attributes areaSAS and areaSES stored, is there a way to extract these values for the residues and write it to a file. Thank You -Thiru
Hi Thiru, The short answer is no. I have such a command on my to-do list, but it hasn't happened yet. So you would have to resort to Python. So a script like this would write areaSAS and areasSES to a file named ~/ out for example: from chimera import openModels, Molecule import os out = open(os.path.expanduser("~/out", "w")) for m in openModels.list(modelTypes=[Molecule]): for r in m.residues: print>>out, r, r.areaSAS, r.areaSES out.close() You could put that in a file (say ~/getArea.py) and then run it with "open ~/getArea.py". --Eric On Oct 1, 2009, at 2:08 PM, Thiruvarangan Ramaraj wrote:
Hi Elaine,
Thanks for your reply. I figured out how to save it using the GUI, but I was wondering if there is a command line option to accomplish this. Sorry I should have made my question clear.
Thank You.
-Thiru
--- On Thu, 10/1/09, Elaine Meng <meng@cgl.ucsf.edu> wrote:
From: Elaine Meng <meng@cgl.ucsf.edu> Subject: Re: [Chimera-users] Solvent Accessible Surface Area To: "Thiruvarangan Ramaraj" <thiruvaranganr@yahoo.com> Cc: "chimera-users@cgl.ucsf.edu BB" <chimera-users@cgl.ucsf.edu> Date: Thursday, October 1, 2009, 2:57 PM
Hi Thiru, You can save attribute values to a file from the Render by Attribute tool. Start that tool (under Tools... Depiction, for example), then choose "File.. Save Attributes" from its menu. In the resulting dialog, you can specify which attribute you want to save.
General information on attributes: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/define...
Saving attributes: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#...
I hope this helps, 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 Oct 1, 2009, at 1:39 PM, Thiruvarangan Ramaraj wrote:
Hi Elaine, Thanks For your help. Just another question, Where are the values for attributes areaSAS and areaSES stored, is there a way to extract these values for the residues and write it to a file. Thank You -Thiru
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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
participants (4)
-
Elaine Meng -
Eric Pettersen -
Greg Couch -
Thiruvarangan Ramaraj