[Chimera-users] Connolly surface and Triangulation

Elaine Meng meng at cgl.ucsf.edu
Mon Sep 25 14:02:23 PDT 2006

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  

>> 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
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