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<p>Hi Eric,<br>
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<p>Thanks for this approach. I found it worked nicely too. I had tried to change the atom type via the user interface but I could not get one that didn't add the extra hydrogen.<br>
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<p>jim<br>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Eric Pettersen <pett@cgl.ucsf.edu><br>
<b>Sent:</b> Wednesday, October 4, 2017 1:42 PM<br>
<b>To:</b> Wikel, Jim<br>
<b>Cc:</b> chimera-users@cgl.ucsf.edu<br>
<b>Subject:</b> Re: [Chimera-users] Create oxime functional group</font>
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<div>Hi Jim,
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>Chimera, perhaps unrealistically, prefers to make the central ring of the fused-ring system aromatic, and therefore puts a single bond between the ring and those nitrogens, which requires
adding a hydrogen to each of them. You can force Chimera to think otherwise by assigning a different atom type to those nitrogens with the following command (Favorites->Command Line):</div>
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<div class="">setattr a idatmType N2 @n2,n3</div>
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<div class="">—Eric</div>
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<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>Eric Pettersen</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>UCSF Computer Graphics Lab</div>
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<div class="">On Oct 4, 2017, at 9:25 AM, Wikel, Jim <<a href="mailto:jimwikel@iu.edu" class="">jimwikel@iu.edu</a>> wrote:</div>
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Hello,<br class="">
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I recently had difficulties with creating a particular structure in Chimera. The SMILES is depicted below. The problem is I have not been able to represent the oxime portion of the molecule. I have tried to reset atomtypes, redrawing the structure, adding
and deleting the atoms, passing it through other drawing programs, reformatting the file to other formats, but to no resolution. Chimera insists on adding a hydrogen to the oxime nitrogen prior to minimization. I am puzzled and suspect I may be doing fundamentally
wrong. Any advice would be helpful.<br class="">
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CC1CC(C)CN(C1)S(=O)(=O)C1=CC=C2C(=C1)C(=NO)C1=CC(=CC=C1C2=NO)S(=O)(=O)N1CC(C)CC(C)C1<br class="">
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Thanks you.<br class="">
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jim<br class="">
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<span class="" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; background-color:rgb(255,255,255); float:none; display:inline!important">_______________________________________________</span><br class="" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; background-color:rgb(255,255,255)">
<span class="" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; background-color:rgb(255,255,255); float:none; display:inline!important">Chimera-users
mailing list:<span class="Apple-converted-space"> </span></span><a href="mailto:Chimera-users@cgl.ucsf.edu" class="" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px; font-style:normal; font-weight:normal; letter-spacing:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px; background-color:rgb(255,255,255)">Chimera-users@cgl.ucsf.edu</a><br class="" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; background-color:rgb(255,255,255)">
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subscription:<span class="Apple-converted-space"> </span></span><a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px; font-style:normal; font-weight:normal; letter-spacing:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px; background-color:rgb(255,255,255)">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br class="" style="font-family:Calibri,Arial,Helvetica,sans-serif; font-size:16px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; background-color:rgb(255,255,255)">
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