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).

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

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