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@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@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@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@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@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
