<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Jun 19, 2008, at 10:08 AM, Kamal Al Nasr wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><div>Dear Sir/Madam,</div> <div> </div> <div>I am using Chimera viewer..and it is a great viewer ever...</div></div></blockquote><div><br></div>Thanks! I'm glad you like it.</div><div><br><blockquote type="cite"><div style="font-family:times new roman, new york, times, serif;font-size:12pt"> <div> <span class="Apple-style-span" style="-webkit-text-stroke-width: -1; ">I kindly have a question... how could you know (from PDB file) the coorect bonding between atoms? I mean that how could you know that this atom is connected with CA not N nor C.....do u have all these bonds stored already in a database? or you use atom positions to determine that?</span></div></div></blockquote><br></div><div>For standard amino and nucleic acids, Chimera has templates containing the correct connectivity. For non-standard residues it bases the connectivity on inter-atomic distances, with a few added heuristics (e.g. hydrogens can only have one bond).</div><div><br></div><div>The templates are accessible in the Python layer with the chimera.restmplFindResidue() function. You can look in the Rotamers extension for examples of its use. The distance-based connectivity function is also available for an entire molecule as chimera.connectMolecule(). It takes the molecule as its only argument and adds bonds to it.</div><div><br></div><div>--Eric</div><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "><br class="Apple-interchange-newline"> Eric Pettersen</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> UCSF Computer Graphics Lab</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> <a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></div></div><br><div></div></body></html>