[Chimera-users] polar and nonpolar surface area

[Susy López]

Dear all



This does not answer my question. Maybe, I don't explain it properly.

I would just like to know if there is any command in Chimera, which allows
me to identify the atoms that are part of the total solvent accessible
surface area (SAS).



I will try to explain my question with an example.

First,

Commands:

open 121p

select :62

show sel

Select>residue>all nonstandard

Actions>Atoms/Bonds>delete

select :62 at OE1

surface sel


[image: image.png]


As shown in the image, I have identified an atom that forms the surface
accessible to the solvent. However, to identify the total atoms of that
protein I have to select atom by atom, which implies a lot of time and more
if I have several proteins.

So, I would like to know, if it´s possible to obtain a command that allows
me to select all the atoms at the same time, specifying the atoms that are
part of the total solvent accessible surface area(SAS).



Thank you (:



kind regards,

Susanna



El lun., 23 sept. 2019 a las 17:33, Susy López (<susannalopez18 at gmail.com>)
escribió:

> Dear all
>
>
>
> This does not answer my question. Maybe, I don't explain it properly.
>
> I would just like to know if there is any command in Chimera, which allows
> me to identify the atoms that are part of the total solvent accessible
> surface area (SAS).
>
>
>
> I will try to explain my question with an example.
>
> First,
>
> Commands:
>
> open 121p
>
> select :62
>
> show sel
>
> Select>residue>all nonstandard
>
> Actions>Atoms/Bonds>delete
>
> select :62 at OE1
>
> surface sel
>
>
>
> As shown in the image, I have identified an atom that forms the surface
> accessible to the solvent. However, to identify the total atoms of that
> protein I have to select atom by atom, which implies a lot of time and more
> if I have several proteins.
>
> So, I would like to know, if it´s possible to obtain a command that allows
> me to select all the atoms at the same time, specifying the atoms that are
> part of the total solvent accessible surface area(SAS).
>
>
>
> Thank you (:
>
>
>
> kind regards,
>
> Susanna
>
>
>
>
>
>
>
>
>
> El lun., 23 sept. 2019 a las 11:54, Elaine Meng (<meng at cgl.ucsf.edu>)
> escribió:
>
>> Dear Susanna,
>> This sounds like the same question others have been asking recently…
>> maybe a class assignment.  If so, you can tell the others in the class so
>> that they don’t have to ask here again!  :-)
>>
>> Please see this recent response, and links therein:
>> <
>> http://plato.cgl.ucsf.edu/pipermail/chimera-users/2019-September/016160.html
>> >
>>
>> …including the following, which has with more details starting at the
>> fifth paragraph, “However, you can get the total surface area given some
>> range of hydrophobicity values…”
>> <
>> http://plato.cgl.ucsf.edu/pipermail/chimera-users/2019-September/016140.html
>> >
>>
>> …or a web server you could try instead of Chimera:
>> <
>> http://plato.cgl.ucsf.edu/pipermail/chimera-users/2019-September/016141.html
>> >
>>
>> These answers suggest selecting polar and nonpolar residues, giving a few
>> different options for deciding which ones are polar and nonpolar, and then
>> just adding up the surface area from the selection.  Maybe by “customize”
>> you meant deciding for yourself which is polar and nonpolar?  You can just
>> select a list of whatever residue types you want, e.g. command:  select
>> :asp,glu,his,lys,arg
>>
>> You don’t have to worry about selecting only the atoms on the surface,
>> because if they are not on the surface they will just add zero area to the
>> total and the result will be the same.  Selecting a residue selects all the
>> atoms in that residue.
>>
>> I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>>
>> > On Sep 21, 2019, at 3:12 PM, Susy López <susannalopez18 at gmail.com>
>> wrote:
>> >
>> > Dear all
>> > I am starting to use Chimera as a master's student and I have some
>> difficulties.
>> >
>> > I know how to select the amino acids that are part of the surface of my
>> protein. However, I don't know how to select the atoms of the surface.
>> Specifically, the atoms accessible to the solvent.
>> >
>> > My second question is:
>> >
>> > I would like to know how polar amino acids (arginine, asparagine,
>> aspartic acid, cysteine, etc.) and non-polar amino acids (alanine, glycine,
>> isoleucine, leucine, etc.) can appear. Is there any configuration that
>> allows me to identify polar and non-polar amino acids for edit them? Is it
>> possible to customize those amino acids when I select them?
>> >
>> > I would be grateful if someone could help me, thank you.
>> >
>> > Best regards,
>> >
>> >
>> > Susanna
>>
>>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20190923/d06adbb4/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 80740 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20190923/d06adbb4/attachment.png>