Hi, Not sure if this went the first time, so sending it again: ----------------------------------------------------------------------------------------------- I have been using Chimera to generate the Connolly surface for several different proteins and saving the surface information in X3D format. I was wondering what algorithms are used in the Connolly surface generation. Is it the same approach that Michael Connolly had come up with in his 1983 paper on Analytical Molecular Surface Calculation, or is it a variation of that algorithm? Also, when the surface information is saved by Chimera in X3D, it breaks the surface into triangular faces. I noticed that the coordinates of the points comprising the triangles are completely different from the atomic coordinates. I am interested in learning more about how the triangulation is created. If you could direct me to a link or paper that would help me better understand the algorithms involved in these two processes, that would be great! Thanks. Sincerely, Nihshanka
Hi Nihshanka, Messages to this list might not appear immediately if the moderator has to approve them. Currently, molecular surfaces in Chimera are calculated by the MSMS package, as mentioned in this man page: http://www.cgl.ucsf.edu/chimera/1.2199/docs/UsersGuide/ representation.html#surfaces There is some description of surfaces there, but if you want more details you could get the reference cited therein and/or follow the "MSMS package" link to that software's home page. I believe the algorithm includes some heuristics to make it faster. Regardless of the algorithm, a molecular surface would never contain a point that is at the same position as an atom, because the atom will generally have a nonzero radius - the surface touches the surface of the atom, not its center. I hope this helps, Elaine On Sep 23, 2006, at 2:39 PM, Nihshanka Debroy wrote:
Hi, Not sure if this went the first time, so sending it again:
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I have been using Chimera to generate the Connolly surface for several different proteins and saving the surface information in X3D format. I was wondering what algorithms are used in the Connolly surface generation. Is it the same approach that Michael Connolly had come up with in his 1983 paper on Analytical Molecular Surface Calculation, or is it a variation of that algorithm? Also, when the surface information is saved by Chimera in X3D, it breaks the surface into triangular faces. I noticed that the coordinates of the points comprising the triangles are completely different from the atomic coordinates. I am interested in learning more about how the triangulation is created. If you could direct me to a link or paper that would help me better understand the algorithms involved in these two processes, that would be great!
Thanks. Sincerely, Nihshanka _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
Hi Nihshanka, It just occurred to me that maybe you meant the surface overall was in a different place than your original structure. Exporting a scene uses the transformed coordinates - if you moved the structure around, the coordinates would be different from the original coordinates of the structure. You might want to use the command "reset" right before exporting so that the coordinates will match, OR save the PDB file in the same transformed coordinate system in which the scene was exported (i.e. without moving things around in between the two saving operations). Best, Elaine
Hi, Not sure if this went the first time, so sending it again:
--------------------------------------------------------------------- --------------------------
I have been using Chimera to generate the Connolly surface for several different proteins and saving the surface information in X3D format. I was wondering what algorithms are used in the Connolly surface generation. Is it the same approach that Michael Connolly had come up with in his 1983 paper on Analytical Molecular Surface Calculation, or is it a variation of that algorithm? Also, when the surface information is saved by Chimera in X3D, it breaks the surface into triangular faces. I noticed that the coordinates of the points comprising the triangles are completely different from the atomic coordinates. I am interested in learning more about how the triangulation is created. If you could direct me to a link or paper that would help me better understand the algorithms involved in these two processes, that would be great!
Thanks. Sincerely, Nihshanka
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
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Elaine Meng -
Nihshanka Debroy