[Chimera-users] Calculating ASA for side chain

saadraza at bs.qau.edu.pk saadraza at bs.qau.edu.pk
Sun Jun 29 02:52:58 PDT 2014


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 at 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
>>
>
>




More information about the Chimera-users mailing list