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<p class="MsoNormal"><span style="font-family:"Arial",sans-serif">New subscriber here, with a question about whether Chimera currently can measure arc-length (geodesic distance) between atoms on a protein surface (or, for example, generate a Calpha-Calpha distance
matrix of this). <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif">I am (very) interested in measuring/obtaining distances between pairs of Calpha carbons (or pairs of other atoms, I suppose) of different amino acids that are on the surface of a protein. While
the difference between arc-length (geodesic) distance and cartesian/Euclidean distance will be negligible if, for example, the two solvent-exposed Calpha atoms are on the same solvent-exposed face of an alpha-helix, the difference could be significant for
residues on opposite “sides” of the protein. I did see that there are ways in Chimera to get distances between an atom and a molecular surface, or to place markers on the surface & obtain the lengths between these for a distance, but I am VERY interested in
whether one can simply select two atoms and get the arc-length (geodesic) distance or generate an arc-length (geodesic distance) matrix of all surface-exposed Calpha pairs.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif">Several computational methods have been developed for this sort of thing, via graph theoretical or other approximation method, and have been published (Hall et al., Biophysical Chemistry 190-191
[2014] 50-55). However, I have not yet (?) found this to be in any graphics/analysis program. I’m thinking that this could perhaps be useful to someone besides me?
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif">Any assistance would be greatly appreciated. My lab and I are (much) more on the user side than the developer side, so are not currently well-positioned to code it in-lab.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif">Regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif">-MW<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif">(btw, if anyone in the “Chimera Group” wants to know more about why I am interested in this, don’t hesitate to send me an email. This type of distance calculation is related to some experimental
technology/assay development that we are doing.)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif">-----<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif">Michael C. Wiener. Ph.D., Professor<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif">Department of Molecular Physiology and<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif"> Biological Physics<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif">University of Virginia<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif">Charlottesville, VA 22908-0886<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif">434-243-2731 (office); 434-243-2730 (lab)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Arial",sans-serif"><o:p> </o:p></span></p>
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