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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:16.0pt;font-family:"Times New Roman","serif"'>Dear all,<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:16.0pt;font-family:"Times New Roman","serif"'>I have one question about the Molecular Representations.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:16.0pt;font-family:"Times New Roman","serif"'>In chimera, molecule can be represented by ball and sphere. Sphere is with the VDW radius for atoms and stick bonds. What about the ball? What is the ball size? <o:p></o:p></span></p><p class=MsoNormal><span style='font-size:16.0pt;font-family:"Times New Roman","serif"'>I tried to measure the distance between two molecules. I used command line of “measure distance #1 #2”. It shows closest distance between two sets of atoms. When I made surface map for the same two molecules, I used the same command, it showed different number. I understand it is the distance of VDW. But what is the distance between atoms if I used PDB file instead of surface map? Which one is more reliable?<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:16.0pt;font-family:"Times New Roman","serif"'>Thanks,<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:16.0pt;font-family:"Times New Roman","serif"'>Jian<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt'><o:p> </o:p></span></p></div></body></html>