Calculating ASA for side chain
Respected Admin
I would like to know if there is any way to modify the calculation of Accessible Surface Area (ASA) to calculate only the ASA for the side chain or a particular group of atoms in chimera. If not possible could someone guide me to some other tool. I will be obliged if someone sort this problem for me
Regards Saad Raza
Dear Saad, There is no need to modify: even though only the total is reported in the Reply Log, the surface area values for each atom and residue are also calculated and stored as attributes, and you can add up the values for any set of atoms that you like.
When you show a molecular surface, "Analytical solvent-excluded and solvent-accessible surface areas per atom and residue are assigned as attributes named areaSES and areaSAS, respectively." http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html#attribdef
You can sum the atomic values over any set of atoms of interest using the Attribute Calculator tool: http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/calculator/calculator.html
For example, after showing the surface (you can hide it so you can see the atoms if they are displayed): (A) select the atoms of interest, e.g. command: select :35.A & without CA/C1' ... would select side chain atoms of residue 35 chain A, not including CA atom (use "with" instead of "without" to include CA atom) (B) use Attribute Calculator (in menu under Tools... Structure Analysis) to calculate a new attribute of *residues* named whatever you want, e.g. sidechainSAS, with formula: sum(atom.areaSAS) ...and also use the option to "Restrict formula domain to current selection" and "Open Render/Select by Attribute"
The Render/Select by Attribute tool will show the result, the sum of areaSAS over the selected atoms. Since this would define a new residue attribute with a different value for each residue, you could select the side chains of many sidechains at once (e.g. command: select protein & without CA/C1') and this process would give a separate total for each residue. To find out the values of your new residue attribute, you could write them out as a list using Render/Select by Attribute's menu: File... Save Attributes, or show them with labels, see main Chimera menu: Actions... Label... residue... custom, if using my example name, with Residue label: %(sidechainSAS).2f
The list I wrote for my test structure looked like this:
attribute: sidechainSAS recipient: residues :1.A 130.75730800628662 :2.A 76.83372020721436 :3.A 131.37474918365479 :4.A 119.24635934829712 :5.A 24.345003843307495 :6.A 74.95613121986389 (... etc. ...)
See also the discussion on calculating normalized surface areas (however, the normalizing values are only available for SES, not SAS): http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfnorm.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
P.S. Recently some of my emails have been going out twice, and I don't know why. Apologies, and I hope the problem will not continue!
On Jun 26, 2014, at 11:32 PM, saadraza@bs.qau.edu.pk wrote:
Respected Admin I would like to know if there is any way to modify the calculation of Accessible Surface Area (ASA) to calculate only the ASA for the side chain or a particular group of atoms in chimera. If not possible could someone guide me to some other tool. I will be obliged if someone sort this problem for me Regards Saad Raza
One more point: if you want to calculate the sum over a set of atoms that includes more than one residue, use Attribute Calculator to create a new attribute for "molecules" instead of "residues" -- then you will just get one value for the whole structure, but restricted to the selected atoms if you turned on that option.
Elaine
On Jun 27, 2014, at 9:46 AM, Elaine Meng wrote:
Dear Saad, There is no need to modify: even though only the total is reported in the Reply Log, the surface area values for each atom and residue are also calculated and stored as attributes, and you can add up the values for any set of atoms that you like.
When you show a molecular surface, "Analytical solvent-excluded and solvent-accessible surface areas per atom and residue are assigned as attributes named areaSES and areaSAS, respectively." http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html#attribdef
You can sum the atomic values over any set of atoms of interest using the Attribute Calculator tool: http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/calculator/calculator.html
For example, after showing the surface (you can hide it so you can see the atoms if they are displayed): (A) select the atoms of interest, e.g. command: select :35.A & without CA/C1' ... would select side chain atoms of residue 35 chain A, not including CA atom (use "with" instead of "without" to include CA atom) (B) use Attribute Calculator (in menu under Tools... Structure Analysis) to calculate a new attribute of *residues* named whatever you want, e.g. sidechainSAS, with formula: sum(atom.areaSAS) ...and also use the option to "Restrict formula domain to current selection" and "Open Render/Select by Attribute"
The Render/Select by Attribute tool will show the result, the sum of areaSAS over the selected atoms. Since this would define a new residue attribute with a different value for each residue, you could select the side chains of many sidechains at once (e.g. command: select protein & without CA/C1') and this process would give a separate total for each residue. To find out the values of your new residue attribute, you could write them out as a list using Render/Select by Attribute's menu: File... Save Attributes, or show them with labels, see main Chimera menu: Actions... Label... residue... custom, if using my example name, with Residue label: %(sidechainSAS).2f
The list I wrote for my test structure looked like this:
attribute: sidechainSAS recipient: residues :1.A 130.75730800628662 :2.A 76.83372020721436 :3.A 131.37474918365479 :4.A 119.24635934829712 :5.A 24.345003843307495 :6.A 74.95613121986389 (... etc. ...)
See also the discussion on calculating normalized surface areas (however, the normalizing values are only available for SES, not SAS): http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfnorm.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
P.S. Recently some of my emails have been going out twice, and I don't know why. Apologies, and I hope the problem will not continue!
On Jun 26, 2014, at 11:32 PM, saadraza@bs.qau.edu.pk wrote:
Respected Admin I would like to know if there is any way to modify the calculation of Accessible Surface Area (ASA) to calculate only the ASA for the side chain or a particular group of atoms in chimera. If not possible could someone guide me to some other tool. I will be obliged if someone sort this problem for me Regards Saad Raza
Dear Elaine
Thanks for your help, I am really grateful for your help
Regards Saad Raza
One more point: if you want to calculate the sum over a set of atoms that includes more than one residue, use Attribute Calculator to create a new attribute for "molecules" instead of "residues" -- then you will just get one value for the whole structure, but restricted to the selected atoms if you turned on that option.
Elaine
On Jun 27, 2014, at 9:46 AM, Elaine Meng wrote:
Dear Saad, There is no need to modify: even though only the total is reported in the Reply Log, the surface area values for each atom and residue are also calculated and stored as attributes, and you can add up the values for any set of atoms that you like.
When you show a molecular surface, "Analytical solvent-excluded and solvent-accessible surface areas per atom and residue are assigned as attributes named areaSES and areaSAS, respectively." http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html#attribdef
You can sum the atomic values over any set of atoms of interest using the Attribute Calculator tool: http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/calculator/calculator.html
For example, after showing the surface (you can hide it so you can see the atoms if they are displayed): (A) select the atoms of interest, e.g. command: select :35.A & without CA/C1' ... would select side chain atoms of residue 35 chain A, not including CA atom (use "with" instead of "without" to include CA atom) (B) use Attribute Calculator (in menu under Tools... Structure Analysis) to calculate a new attribute of *residues* named whatever you want, e.g. sidechainSAS, with formula: sum(atom.areaSAS) ...and also use the option to "Restrict formula domain to current selection" and "Open Render/Select by Attribute"
The Render/Select by Attribute tool will show the result, the sum of areaSAS over the selected atoms. Since this would define a new residue attribute with a different value for each residue, you could select the side chains of many sidechains at once (e.g. command: select protein & without CA/C1') and this process would give a separate total for each residue. To find out the values of your new residue attribute, you could write them out as a list using Render/Select by Attribute's menu: File... Save Attributes, or show them with labels, see main Chimera menu: Actions... Label... residue... custom, if using my example name, with Residue label: %(sidechainSAS).2f
The list I wrote for my test structure looked like this:
attribute: sidechainSAS recipient: residues :1.A 130.75730800628662 :2.A 76.83372020721436 :3.A 131.37474918365479 :4.A 119.24635934829712 :5.A 24.345003843307495 :6.A 74.95613121986389 (... etc. ...)
See also the discussion on calculating normalized surface areas (however, the normalizing values are only available for SES, not SAS): http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfnorm.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
P.S. Recently some of my emails have been going out twice, and I don't know why. Apologies, and I hope the problem will not continue!
On Jun 26, 2014, at 11:32 PM, saadraza@bs.qau.edu.pk wrote:
Respected Admin I would like to know if there is any way to modify the calculation of Accessible Surface Area (ASA) to calculate only the ASA for the side chain or a particular group of atoms in chimera. If not possible could someone guide me to some other tool. I will be obliged if someone sort this problem for me Regards Saad Raza
participants (2)
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Elaine Meng -
saadraza＠bs.qau.edu.pk