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Hi JD,<div><span class="Apple-tab-span" style="white-space:pre"> </span>Unfortunately, Chimera isn't really being as smart here as you are giving it credit for. Many PDB files specify coordination bonds in CONECT records. Chimera identifies those bonds and converts them to pseudobonds (otherwise its atom-typing code, which depends on correct covalent bonding, would get the bonded atoms wrong). So PDB files that do not identify the coordination bonds with CONECT records (e.g. 1lwx) will not have any coordination bonds in Chimera.</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>I'm wondering if what you are hoping to do is along the lines of this previous mail to chimera-users:</div><div><br class="webkit-block-placeholder"></div><div><a href="http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-May/001529.html">http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-May/001529.html</a></div><div><br class="webkit-block-placeholder"></div><div>--Eric</div><div><br><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; "> 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 class="webkit-block-placeholder"></div><div>On Nov 23, 2007, at 9:30 AM, Jean-Didier Maréchal wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Hi Eric,</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Thanks for that. I have been able to get a bit further.<span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">To follow with my problem, I have one question more though. Basically, I</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">would like to know how chimera "Recognizes" metal chelation and</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">coordination bounds.<span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">What I see is that when you open a pdb with a metal ion, the program</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">places correctly "semi bounds" corresponding to coordination</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">interactions. Unfortunately, I work with a series of protein structures</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">where metals do not adopt a typical geometries (ex: 1lwx). First, I</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">would like to be able to improve the number of acceptable metal</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">geometries, but my questions are: how does chimera recognize the right</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">geometry of the metal ions? Is it implemented in a python module? It is</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">a C++ code?<span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">All the best,</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">JD</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div></blockquote></div></div></div><div> <span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><p style="margin: 0.0px 0.0px 0.0px 0.0px"><br></p></span> </div><br></body></html>