<div dir="ltr"><font face="arial, sans-serif">Hi Elaine,</font><div><font face="arial, sans-serif"><br></font></div><div><font face="arial, sans-serif">The methods you suggested for calculating SASA for residues saved me so much time. Thank you once again for it.</font></div><div><font face="arial, sans-serif">But I have noticed an ambiguity.</font></div><div><font face="arial, sans-serif">When I calculate the SASA for the same residue using chimera and chimeraX, I am getting different values.</font></div><div><font face="arial, sans-serif">For ex: in the PDB file 1TY4, the SASA value for residue 174.a is 2.55 when calculated using chimera and it is 292.44 when calculated using chimeraX. The same is true for other amino acids in other PDB files as well.</font></div><div><font face="arial, sans-serif">Why is there such a difference?</font></div><div><font face="arial, sans-serif">On which of the two software should I rely on?</font></div><div>Also, what is the unit of SASA calculated by these two softwares?</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Nov 17, 2022 at 10:42 AM Prathvi Singh <<a href="mailto:prathvi@iitk.ac.in">prathvi@iitk.ac.in</a>> wrote:<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">Thank you so much Elaine!!</div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Nov 14, 2022 at 9:42 PM Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" target="_blank">meng@cgl.ucsf.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi Prathvi,<br>
Yes, either one. <br>
<br>
In Chimera, they are automatically calculated when you show a molecular surface. It creates an attribute named areaSAS, as explained here:<br>
<<a href="https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces" rel="noreferrer" target="_blank">https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces</a>><br>
<br>
See also this previous chimera-user post on using Chimera to get a list of residue SASA values<br>
<<a href="http://www.cgl.ucsf.edu/pipermail/chimera-users/2018-June/014729.html" rel="noreferrer" target="_blank">http://www.cgl.ucsf.edu/pipermail/chimera-users/2018-June/014729.html</a>><br>
<br>
(If you use this page <<a href="https://www.rbvi.ucsf.edu/chimera/docs/feedback.html" rel="noreferrer" target="_blank">https://www.rbvi.ucsf.edu/chimera/docs/feedback.html</a>> to search chimera-users by "sasa", that was the top hit)<br>
<br>
In ChimeraX, you would use the command "measure sasa" <br>
<<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#sasa" rel="noreferrer" target="_blank">https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#sasa</a>><br>
... then save attribute "area" to file<br>
<<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#attributes" rel="noreferrer" target="_blank">https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#attributes</a>><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 Nov 14, 2022, at 6:29 AM, Prathvi Singh via Chimera-users <<a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank">chimera-users@cgl.ucsf.edu</a>> wrote:<br>
> <br>
> Hi Elaine,<br>
> Can I use chimera or chimeraX to know the solvent accessible surface area (SASA) for selected residues?<br>
<br>
</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr"><div dir="ltr"><div><div dir="ltr">Prathvi Singh,<div>Research Fellow,<br><div>Department of Biological Sciences & Bioengineering,</div><div>Indian Institute of Technology, Kanpur-208016</div></div></div></div></div></div>
</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr">Prathvi Singh,<div>Research Fellow,<br><div>Department of Biological Sciences & Bioengineering,</div><div>Indian Institute of Technology, Kanpur-208016</div></div></div></div></div></div>