Re: [Chimera-users] polar and nonpolar surface area
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
Hi Susy, Besides the video that Omar suggested,
I recommend you to follow this short tutorial. http://www.cgl.ucsf.edu/chimera/videodoc/surfaceresidues/index.html Best, Omar
... see also this previous post “identifying surface residues”:
http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-May/003903.html
It describes the same process as shown in the video, as well as possible commands. First you always have to show the molecular surface. You can just show it for the whole molecule.
Then, the process is very similar to identify surface atoms instead of whole residues. In the Select by Attribute dialog, you would just select by attribute of “atoms” instead of “residues”. You can write a list of selected atoms or residues with menu: Actions… Write List, or you can use the selection in some other command, for example: color red sel
Or if you wanted to use commands to select by area instead of the dialog, that previous post showed an example for residues:
select :/areaSES>30
To use it instead for atoms, could be something like
select @/areaSES>4.0 or select @/areaSAS>3.0
… where you would have to decide the minimum value of surface area that you want to use, and whether it should be SAS (solvent-accessible surface) or SES (solvent-excluded surface).
You can even limit the selection by element or by residue type, for example:
select @/areaSAS>3 & ~C (select atoms by area and not-carbon)
select @/areaSAS>3 & :asp,glu,his,lys,arg (select atoms by area and that are also in the named residue types)
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 23, 2019, at 3:35 PM, Susy López susannalopez18@gmail.com wrote:
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.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
Dear Dr. Elaine Meng
Thank you, thank you very much!!!. I'm very grateful. Finally I could, it helped me a lot.
Dear Omar
Really, thank you (:
King regards, Susy
El mar., 24 sept. 2019 a las 11:16, Elaine Meng (meng@cgl.ucsf.edu) escribió:
Hi Susy, Besides the video that Omar suggested,
I recommend you to follow this short tutorial. http://www.cgl.ucsf.edu/chimera/videodoc/surfaceresidues/index.html Best, Omar
... see also this previous post “identifying surface residues”:
http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-May/003903.html
It describes the same process as shown in the video, as well as possible commands. First you always have to show the molecular surface. You can just show it for the whole molecule.
Then, the process is very similar to identify surface atoms instead of whole residues. In the Select by Attribute dialog, you would just select by attribute of “atoms” instead of “residues”. You can write a list of selected atoms or residues with menu: Actions… Write List, or you can use the selection in some other command, for example: color red sel
Or if you wanted to use commands to select by area instead of the dialog, that previous post showed an example for residues:
select :/areaSES>30
To use it instead for atoms, could be something like
select @/areaSES>4.0 or select @/areaSAS>3.0
… where you would have to decide the minimum value of surface area that you want to use, and whether it should be SAS (solvent-accessible surface) or SES (solvent-excluded surface).
You can even limit the selection by element or by residue type, for example:
select @/areaSAS>3 & ~C (select atoms by area and not-carbon)
select @/areaSAS>3 & :asp,glu,his,lys,arg (select atoms by area and that are also in the named residue types)
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 23, 2019, at 3:35 PM, Susy López susannalopez18@gmail.com
wrote:
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.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
participants (2)
-
Elaine Meng -
Susy López