<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Happy to help!<div class=""><br class=""></div><div class="">—Eric<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Dec 6, 2019, at 12:03 PM, Palani, Kirubakaran <<a href="mailto:Kirubakaran.Palani@fccc.edu" class="">Kirubakaran.Palani@fccc.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="WordSection1" style="page: WordSection1; caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Hi Eric,<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">That looks pretty much what I needed. Thanks for the prompt response also for the point making about the atom type changes.<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Best regards,<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Kiruba<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="border-style: solid none none; border-top-width: 1pt; border-top-color: rgb(181, 196, 223); padding: 3pt 0in 0in;" class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><b class=""><span style="font-size: 12pt;" class="">From:<span class="Apple-converted-space"> </span></span></b><span style="font-size: 12pt;" class="">Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">pett@cgl.ucsf.edu</a>><br class=""><b class="">Reply-To:<span class="Apple-converted-space"> </span></b>"<a href="mailto:chimera-users@cgl.ucsf.edu" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">chimera-users@cgl.ucsf.edu</a><span class="Apple-converted-space"> </span>BB" <<a href="mailto:chimera-users@cgl.ucsf.edu" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">chimera-users@cgl.ucsf.edu</a>><br class=""><b class="">Date:<span class="Apple-converted-space"> </span></b>Friday, December 6, 2019 at 2:28 PM<br class=""><b class="">To:<span class="Apple-converted-space"> </span></b>"Palani, Kirubakaran" <<a href="mailto:Kirubakaran.Palani@fccc.edu" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">Kirubakaran.Palani@fccc.edu</a>><br class=""><b class="">Cc:<span class="Apple-converted-space"> </span></b>"<a href="mailto:chimera-users@cgl.ucsf.edu" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">chimera-users@cgl.ucsf.edu</a>" <<a href="mailto:chimera-users@cgl.ucsf.edu" style="color: rgb(149, 79, 114); text-decoration: underline;" class="">chimera-users@cgl.ucsf.edu</a>><br class=""><b class="">Subject:<span class="Apple-converted-space"> </span></b>Re: [Chimera-users] pseudobond problem while writing mol2 format<o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 10pt; font-family: Verdana, sans-serif; color: red;" class="">EXTERNAL MESSAGE. DO NOT open attachments or click links from unknown senders or unknown emails.</span><o:p class=""></o:p></div><div class="MsoNormal" align="center" style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; text-align: center;"><hr size="0" width="100%" align="center" class=""></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Hi Kiruba,<span class="Apple-converted-space"> </span><o:p class=""></o:p></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">For each of those pseudobonds, there is a hidden “real” bond. To have the Mol2 file treat the segments as disconnected, the hidden bonds have to be deleted. I have attached a simple Python script that does that. So you would open your PDB file, run the script (simply opening the .py file will run it) and then save your Mol2.<o:p class=""></o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Keep in mind that deleting those hidden bonds will change the corresponding atom types. So for instance the backbone nitrogens will be given the Mol2 type N.4 (appropriate for N-terminal) rather than N.am (appropriate for amide).<o:p class=""></o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">—Eric<o:p class=""></o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div class=""><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 9pt; font-family: Helvetica;" class=""><br class=""><br class=""><span class="apple-tab-span"><o:p class=""></o:p></span></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 9pt; font-family: Helvetica;" class="">Eric Pettersen<o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 9pt; font-family: Helvetica;" class="">UCSF Computer Graphics Lab<o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 9pt; font-family: Helvetica;" class=""><o:p class=""> </o:p></span></div></div></div></div></div></div><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><hr style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><font face="Verdana" color="Red" size="2" style="font-style: normal; font-variant-caps: 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; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><br class="">This electronic message is intended to be for the use of the named recipient, and may contain information that is confidential or privileged. 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