<div dir="ltr"><p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:15.6933px;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:14pt;line-height:19.9733px">Dear all</span></p><p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:15.6933px;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:14pt;line-height:19.9733px"> </span></p><p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:15.6933px;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:14pt;line-height:19.9733px">This does not answer my question. Maybe, I don't explain it properly.</span></p><p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:15.6933px;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:14pt;line-height:19.9733px">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).</span></p><p class="MsoNormal" style="margin:0cm 0cm 8pt;text-align:justify;line-height:15.6933px;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:14pt;line-height:19.9733px"> </span></p><p class="MsoNormal" style="margin:0cm 0cm 8pt;text-align:justify;line-height:15.6933px;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:14pt;line-height:19.9733px">I will try to explain my question with an example.</span></p><p class="MsoNormal" style="margin:0cm 0cm 8pt;text-align:justify;line-height:15.6933px;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:14pt;line-height:19.9733px">First,</span></p><p class="MsoNormal" style="margin:0cm 0cm 0.0001pt;line-height:15.6933px;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:14pt;line-height:19.9733px;color:rgb(31,78,121)">Commands:</span></p><p class="MsoNormal" style="margin:0cm 0cm 0.0001pt;line-height:15.6933px;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:14pt;line-height:19.9733px;color:rgb(31,78,121)">open 121p</span></p><p class="MsoNormal" style="margin:0cm 0cm 0.0001pt;line-height:15.6933px;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:14pt;line-height:19.9733px;color:rgb(31,78,121)">select :62</span></p><p class="MsoNormal" style="margin:0cm 0cm 0.0001pt;line-height:15.6933px;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:14pt;line-height:19.9733px;color:rgb(31,78,121)">show sel</span></p><p class="MsoNormal" style="margin:0cm 0cm 0.0001pt;line-height:15.6933px;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:14pt;line-height:19.9733px;color:rgb(31,78,121)">Select>residue>all nonstandard</span></p><p class="MsoNormal" style="margin:0cm 0cm 0.0001pt;line-height:15.6933px;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:14pt;line-height:19.9733px;color:rgb(31,78,121)">Actions>Atoms/Bonds>delete</span></p><p class="MsoNormal" style="margin:0cm 0cm 0.0001pt;line-height:15.6933px;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:14pt;line-height:19.9733px;color:rgb(31,78,121)">select :62@OE1</span></p><p class="MsoNormal" style="margin:0cm 0cm 0.0001pt;line-height:15.6933px;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:14pt;line-height:19.9733px;color:rgb(31,78,121)">surface sel</span></p><p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:15.6933px;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:14pt;line-height:19.9733px;color:rgb(31,78,121)"> </span></p><div><img src="cid:ii_k0wzocq70" alt="image.png" width="451" height="301"><br></div><p class="MsoNormal" style="margin:0cm 0cm 8pt;text-align:justify;line-height:15.6933px;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:14pt;line-height:19.9733px"><br></span></p><p class="MsoNormal" style="margin:0cm 0cm 8pt;text-align:justify;line-height:15.6933px;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:14pt;line-height:19.9733px">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.</span></p><p class="MsoNormal" style="margin:0cm 0cm 8pt;text-align:justify;line-height:15.6933px;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:14pt;line-height:19.9733px">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).</span></p><p class="MsoNormal" style="margin:0cm 0cm 8pt;text-align:justify;line-height:15.6933px;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:14pt;line-height:19.9733px"> </span></p><p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:15.6933px;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:14pt;line-height:19.9733px">Thank you (:</span></p><p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:15.6933px;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:14pt;line-height:19.9733px"> </span></p><p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:15.6933px;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:14pt;line-height:19.9733px">kind regards,</span></p><p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:15.6933px;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:14pt;line-height:19.9733px">Susanna</span></p><p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:15.6933px;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:14pt;line-height:19.9733px"> </span></p></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">El lun., 23 sept. 2019 a las 17:33, Susy López (<<a href="mailto:susannalopez18@gmail.com">susannalopez18@gmail.com</a>>) escribió:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:14pt;line-height:107%">Dear all</span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:14pt;line-height:107%"> </span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:14pt;line-height:107%">This does
not answer my question. Maybe, I don't explain it properly.</span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:14pt;line-height:107%">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).</span></p>
<p class="MsoNormal" style="text-align:justify;margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:14pt;line-height:107%"> </span></p>
<p class="MsoNormal" style="text-align:justify;margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:14pt;line-height:107%">I will try to explain my question with an example.</span></p>
<p class="MsoNormal" style="text-align:justify;margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:14pt;line-height:107%">First,</span></p>
<p class="MsoNormal" style="margin:0cm 0cm 0.0001pt;line-height:107%;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:14pt;line-height:107%;color:rgb(31,78,121)">Commands:</span></p>
<p class="MsoNormal" style="margin:0cm 0cm 0.0001pt;line-height:107%;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:14pt;line-height:107%;color:rgb(31,78,121)">open 121p </span></p>
<p class="MsoNormal" style="margin:0cm 0cm 0.0001pt;line-height:107%;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:14pt;line-height:107%;color:rgb(31,78,121)">select :62</span></p>
<p class="MsoNormal" style="margin:0cm 0cm 0.0001pt;line-height:107%;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:14pt;line-height:107%;color:rgb(31,78,121)">show sel</span></p>
<p class="MsoNormal" style="margin:0cm 0cm 0.0001pt;line-height:107%;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:14pt;line-height:107%;color:rgb(31,78,121)">Select>residue>all nonstandard</span></p>
<p class="MsoNormal" style="margin:0cm 0cm 0.0001pt;line-height:107%;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:14pt;line-height:107%;color:rgb(31,78,121)">Actions>Atoms/Bonds>delete</span></p>
<p class="MsoNormal" style="margin:0cm 0cm 0.0001pt;line-height:107%;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:14pt;line-height:107%;color:rgb(31,78,121)">select :62@OE1</span></p>
<p class="MsoNormal" style="margin:0cm 0cm 0.0001pt;line-height:107%;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:14pt;line-height:107%;color:rgb(31,78,121)">surface sel</span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:14pt;line-height:107%;color:rgb(31,78,121)"> </span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:Calibri,sans-serif"><img width="451" height="301"><span style="font-size:14pt;line-height:107%"></span></p>
<p class="MsoNormal" style="text-align:justify;margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:14pt;line-height:107%">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.</span></p>
<p class="MsoNormal" style="text-align:justify;margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:14pt;line-height:107%">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).</span></p>
<p class="MsoNormal" style="text-align:justify;margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:14pt;line-height:107%"> </span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:14pt;line-height:107%">Thank you (:</span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:14pt;line-height:107%"> </span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:14pt;line-height:107%">kind regards,</span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:14pt;line-height:107%">Susanna</span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:14pt;line-height:107%"> </span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:14pt;line-height:107%"> </span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:14pt;line-height:107%"> </span></p>
<p class="MsoNormal" style="margin:0cm 0cm 8pt;line-height:107%;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:14pt;line-height:107%"> </span></p></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">El lun., 23 sept. 2019 a las 11:54, Elaine Meng (<<a href="mailto:meng@cgl.ucsf.edu" target="_blank">meng@cgl.ucsf.edu</a>>) escribió:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Dear Susanna,<br>
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! :-)<br>
<br>
Please see this recent response, and links therein:<br>
<<a href="http://plato.cgl.ucsf.edu/pipermail/chimera-users/2019-September/016160.html" rel="noreferrer" target="_blank">http://plato.cgl.ucsf.edu/pipermail/chimera-users/2019-September/016160.html</a>><br>
<br>
…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…”<br>
<<a href="http://plato.cgl.ucsf.edu/pipermail/chimera-users/2019-September/016140.html" rel="noreferrer" target="_blank">http://plato.cgl.ucsf.edu/pipermail/chimera-users/2019-September/016140.html</a>><br>
<br>
…or a web server you could try instead of Chimera:<br>
<<a href="http://plato.cgl.ucsf.edu/pipermail/chimera-users/2019-September/016141.html" rel="noreferrer" target="_blank">http://plato.cgl.ucsf.edu/pipermail/chimera-users/2019-September/016141.html</a>><br>
<br>
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<br>
<br>
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.<br>
<br>
I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D.<br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
> On Sep 21, 2019, at 3:12 PM, Susy López <<a href="mailto:susannalopez18@gmail.com" target="_blank">susannalopez18@gmail.com</a>> wrote:<br>
> <br>
> Dear all<br>
> I am starting to use Chimera as a master's student and I have some difficulties.<br>
> <br>
> 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.<br>
> <br>
> My second question is:<br>
> <br>
> 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?<br>
> <br>
> I would be grateful if someone could help me, thank you.<br>
> <br>
> Best regards,<br>
> <br>
> <br>
> Susanna<br>
<br>
</blockquote></div>
</blockquote></div>