<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="">Hi Alaa,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Well, the major stumbling block is that the minimization parametrization process cannot handle a proline directly connected to a non-standard amino acid (such as AIB). A secondary problem is that the parameterization of a single AIB differs from that for consecutive AIBs, which confuses the minimization machinery. If you execute these commands (Favorites→Command Line) after opening your structure:</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>setattr r type AXB :11-12,14-15</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>swapaa ALA :13</div><div class=""><br class=""></div><div class="">...then minimization "works". Of course, it isn't really the same structure anymore since the the proline was changed to an alanine.</div><div class=""><br class=""></div><div class=""><div class="">--Eric</div><div class=""><br class=""></div><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></div><div class=""><br class=""></div><div class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Feb 3, 2023, at 12:58 PM, Alaa Nahhas via Chimera-users <<a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="rtl" 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=""><div class="gmail_default" dir="ltr" style="font-size: large; color: rgb(56, 118, 29);">Please find the attached pdb file for the peptide. I just need the minimized step.</div><div class="gmail_default" dir="ltr" style="font-size: large; color: rgb(56, 118, 29);">Thanks</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=""><div class="gmail_quote" 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;"><div dir="rtl" class="gmail_attr">في الجمعة، 3 فبراير 2023 في 11:50 م تمت كتابة ما يلي بواسطة Alaa Nahhas <<a href="mailto:anahhas@kau.edu.sa" class="">anahhas@kau.edu.sa</a>>:<br class=""></div><blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-style: solid; border-left-color: rgb(204, 204, 204); padding-left: 1ex;"><div dir="rtl" class=""><div class="gmail_default" dir="ltr" style="font-size: large; color: rgb(56, 118, 29);">It does work with other peptides that contain Aib. Can I send to you the pdb file to check it.</div><div class="gmail_default" dir="ltr" style="font-size: large; color: rgb(56, 118, 29);">Thanks,</div></div><br class=""><div class="gmail_quote"><div dir="rtl" class="gmail_attr">في الجمعة، 3 فبراير 2023 في 11:47 م تمت كتابة ما يلي بواسطة Dr. Kevin M Jude <<a href="mailto:kjude@stanford.edu" target="_blank" class="">kjude@stanford.edu</a>>:<br class=""></div><blockquote class="gmail_quote" style="margin: 0px 0px 0px 0.8ex; border-left-width: 1px; border-left-style: solid; border-left-color: rgb(204, 204, 204); padding-left: 1ex;"><div class=""><div lang="EN-US" class=""><div class=""><p class="MsoNormal"><span style="font-size: 11pt;" class="">It looks like your peptide contains the nonstandard amino acid alpha-aminoisobutyric acid (AIB), and chimera doesn’t have a dictionary for it.<u class=""></u><u class=""></u></span></p><p class="MsoNormal"><span style="font-size: 11pt;" class=""><u class=""></u> <u class=""></u></span></p><div style="border-style: solid none none; border-top-width: 1pt; border-top-color: rgb(181, 196, 223); padding: 3pt 0cm 0cm;" class=""><p class="MsoNormal" style="margin-bottom: 12pt;"><b class=""><span style="font-size: 12pt;" class="">From:<span class="Apple-converted-space"> </span></span></b><span style="font-size: 12pt;" class="">Chimera-users <<a href="mailto:chimera-users-bounces@cgl.ucsf.edu" target="_blank" class="">chimera-users-bounces@cgl.ucsf.edu</a>> on behalf of Alaa Nahhas via Chimera-users <<a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank" class="">chimera-users@cgl.ucsf.edu</a>><br class=""><b class="">Date:<span class="Apple-converted-space"> </span></b>Friday, February 3, 2023 at 12:38 PM<br class=""><b class="">To:<span class="Apple-converted-space"> </span></b>chimera-users <<a href="mailto:chimera-users@cgl.ucsf.edu" target="_blank" class="">chimera-users@cgl.ucsf.edu</a>><br class=""><b class="">Subject:<span class="Apple-converted-space"> </span></b>Re: [Chimera-users] minimization error<u class=""></u><u class=""></u></span></p></div><div class=""><div class=""><p class="MsoNormal"><span style="font-size: 18pt; color: rgb(56, 118, 29);" class="">Dear Elaine,<u class=""></u><u class=""></u></span></p></div><div class=""><p class="MsoNormal"><span style="font-size: 18pt; color: rgb(56, 118, 29);" class="">The version is updated. I don't know why this message appears?<u class=""></u><u class=""></u></span></p></div><div class=""><p class="MsoNormal"><span style="font-size: 18pt; color: rgb(56, 118, 29);" class="">Thanks,<u class=""></u><u class=""></u></span></p></div><div class=""><p class="MsoNormal"><span style="font-size: 18pt; color: rgb(56, 118, 29);" class="">Alaa<u class=""></u><u class=""></u></span></p></div><div class=""><p class="MsoNormal"><span style="font-size: 18pt; color: rgb(56, 118, 29);" class=""><u class=""></u> <u class=""></u></span></p></div></div><p class="MsoNormal"><span style="font-size: 11pt;" class=""><u class=""></u> <u class=""></u></span></p><div class=""><div class=""><p class="MsoNormal" dir="RTL" style="text-align: right; direction: rtl; unicode-bidi: embed;"><span dir="RTL" class=""></span><span dir="RTL" class=""></span><span lang="AR-SA" style="font-size: 11pt;" class=""><span dir="RTL" class=""></span><span dir="RTL" class=""></span>في الجمعة، 3 فبراير 2023 في 11:07 م تمت كتابة ما يلي بواسطة </span><span dir="LTR" style="font-size: 11pt;" class="">Elaine Meng</span><span dir="RTL" class=""></span><span dir="RTL" class=""></span><span lang="AR-SA" style="font-size: 11pt;" class=""><span dir="RTL" class=""></span><span dir="RTL" class=""></span> <<a href="mailto:meng@cgl.ucsf.edu" target="_blank" class=""><span lang="EN-US" dir="LTR" class="">meng@cgl.ucsf.edu</span></a>>:</span><span dir="LTR" style="font-size: 11pt;" class=""><u class=""></u><u class=""></u></span></p></div><blockquote style="border-style: none none none solid; border-left-width: 1pt; border-left-color: rgb(204, 204, 204); padding: 0cm 0cm 0cm 6pt; margin-left: 4.8pt; margin-right: 0cm;" class=""><div class=""><p class="MsoNormal"><span style="font-size: 11pt;" class="">Dear Alaa, <span lang="AR-SA" dir="RTL" class=""><u class=""></u><u class=""></u></span></span></p><div class=""><p class="MsoNormal"><span style="font-size: 11pt;" class="">Forwarding your question. However, when you get a Chimera error and you think it may be a bug, instead of using e-mail it is usually more helpful to use the Chimera menu: Help... Report a Bug. Also make sure you are using a recent version of Chimera. If you haven't updated in a while, you should try the newest release, then if you still get the error, you could report it.<u class=""></u><u class=""></u></span></p></div><div class=""><p class="MsoNormal"><span style="font-size: 11pt;" class="">Best,<u class=""></u><u class=""></u></span></p></div><div class=""><p class="MsoNormal"><span style="font-size: 11pt;" class="">Elaine<u class=""></u><u class=""></u></span></p></div><div class=""><p class="MsoNormal"><span style="font-size: 11pt;" class=""><u class=""></u> <u class=""></u></span></p><div class=""><blockquote style="margin-top: 5pt; margin-bottom: 5pt;" class=""><div class=""><p class="MsoNormal"><span style="font-size: 11pt;" class="">Begin forwarded message:<u class=""></u><u class=""></u></span></p></div><p class="MsoNormal"><span style="font-size: 11pt;" class=""><u class=""></u> <u class=""></u></span></p><div class=""><p class="MsoNormal"><b class=""><span style="font-size: 11pt; font-family: "Helvetica Neue";" class="">From:<span class="Apple-converted-space"> </span></span></b><span style="font-size: 11pt; font-family: "Helvetica Neue";" class="">Alaa Nahhas <<a href="mailto:anahhas@kau.edu.sa" target="_blank" class="">anahhas@kau.edu.sa</a>></span><span style="font-size: 11pt;" class=""><u class=""></u><u class=""></u></span></p></div><div class=""><p class="MsoNormal"><b class=""><span style="font-size: 11pt; font-family: "Helvetica Neue";" class="">Date:<span class="Apple-converted-space"> </span></span></b><span style="font-size: 11pt; font-family: "Helvetica Neue";" class="">February 3, 2023 at 12:00:13 PM PST</span><span style="font-size: 11pt;" class=""><u class=""></u><u class=""></u></span></p></div><div class=""><p class="MsoNormal"><span style="font-size: 11pt;" class=""><u class=""></u> <u class=""></u></span></p></div><div class=""><div class=""><div class=""><p class="MsoNormal"><span style="font-size: 18pt; color: rgb(56, 118, 29);" class="">Dear Chimera team,<u class=""></u><u class=""></u></span></p></div><div class=""><p class="MsoNormal"><span style="font-size: 18pt; color: rgb(56, 118, 29);" class="">I have a peptide and when I minimize its structure, I got the attached message. How can I solve it.<u class=""></u><u class=""></u></span></p></div><div class=""><p class="MsoNormal"><span style="font-size: 18pt; color: rgb(56, 118, 29);" class="">Thanks,<u class=""></u><u class=""></u></span></p></div><div class=""><p class="MsoNormal"><span style="font-size: 18pt; color: rgb(56, 118, 29);" class="">Alaa<u class=""></u><u class=""></u></span></p></div></div><p class="MsoNormal"><span style="font-size: 11pt;" class=""><u class=""></u> <u class=""></u></span></p><div class=""><p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial, sans-serif; color: gray;" class="">Disclaimer: The information contained in this message is intended for the addressee only and may contain classified information. If you are not the addressee, please delete this message and notify the sender; you should not copy or distribute this message or disclose its contents to anyone. Any views or opinions expressed in this message are those of the individual(s) and not necessarily of the university. No reliance may be placed on this message without written confirmation from an authorized representative of its contents. No guarantee is implied that this message or any attachment is virus free or has not been intercepted and amended. </span><span style="font-size: 11pt;" class=""><u class=""></u><u class=""></u></span></p></div><div class=""><p class="MsoNormal"><span style="font-size: 11pt;" class=""><u class=""></u> <u class=""></u></span></p></div><div class=""><p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial, sans-serif; color: gray;" class="">إخلاء مسؤليه: ان جميع المعلومات المتضمنة في هذه الرسالة تخص المستلم، وربما تتضمن معلومات سرية، واذا لم تكن انت المستلم فالرجاء الغاء الرسالة واشعار المرسل، كما يمنع نسخ او توزيع هذه الرسالة او افشاء محتوياتها لاخرين. ويجدر بالعلم ان جميع الآراء ووجهات النظر الواردة في هذه الرسالة تعتبر شخصية وليست بالضرورة منسوبة للجامعة. كما لايمكن ان يعتمد على هذه الرسالة ما لم تحصل على موافقة خطية من المسئول عن محتوياتها. كما لايوجد ضمان بان هذه الرسالة أو مرفقاتها خالية من الفيروسات أو انها لم يتم اعتراضها وتعديلها</span><span style="font-size: 11pt;" class=""><u class=""></u><u class=""></u></span></p></div><div class=""><p class="MsoNormal"><span style="font-size: 11pt;" class=""><u class=""></u> <u class=""></u></span></p></div></div></blockquote><p class="MsoNormal"><span style="font-size: 11pt;" class=""><span id="cid:1861909892f8478f6f91"><Screen Shot 2023-02-03 at 12.03.46 PM.png></span><u class=""></u><u class=""></u></span></p></div><p class="MsoNormal"><span style="font-size: 11pt;" class=""><u class=""></u> <u class=""></u></span></p></div></div></blockquote></div><p class="MsoNormal"><span style="font-size: 11pt;" class=""><u class=""></u> <u class=""></u></span></p><div class=""><p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial, sans-serif; color: gray;" class="">Disclaimer: The information contained in this message is intended for the addressee only and may contain classified information. If you are not the addressee, please delete this message and notify the sender; you should not copy or distribute this message or disclose its contents to anyone. Any views or opinions expressed in this message are those of the individual(s) and not necessarily of the university. No reliance may be placed on this message without written confirmation from an authorized representative of its contents. No guarantee is implied that this message or any attachment is virus free or has not been intercepted and amended. </span><span style="font-size: 11pt;" class=""><u class=""></u><u class=""></u></span></p></div><div class=""><p class="MsoNormal"><span style="font-size: 11pt;" class=""><u class=""></u> <u class=""></u></span></p></div><div class=""><p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial, sans-serif; color: gray;" class="">إخلاء مسؤليه: ان جميع المعلومات المتضمنة في هذه الرسالة تخص المستلم، وربما تتضمن معلومات سرية، واذا لم تكن انت المستلم فالرجاء الغاء الرسالة واشعار المرسل، كما يمنع نسخ او توزيع هذه الرسالة او افشاء محتوياتها لاخرين. ويجدر بالعلم ان جميع الآراء ووجهات النظر الواردة في هذه الرسالة تعتبر شخصية وليست بالضرورة منسوبة للجامعة. كما لايمكن ان يعتمد على هذه الرسالة ما لم تحصل على موافقة خطية من المسئول عن محتوياتها. كما لايوجد ضمان بان هذه الرسالة أو مرفقاتها خالية من الفيروسات أو انها لم يتم اعتراضها وتعديلها</span><span style="font-size: 11pt;" class=""><u class=""></u><u class=""></u></span></p></div><div class=""><p class="MsoNormal"><span style="font-size: 11pt;" class=""><u class=""></u> <u class=""></u></span></p></div></div></div></div></blockquote></div></blockquote></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=""><div 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 color="#808080" face="Arial, Helvetica, sans-serif" class="">Disclaimer: The information contained in this message is intended for the addressee only and may contain classified information. If you are not the addressee, please delete this message and notify the sender; you should not copy or distribute this message or disclose its contents to anyone. Any views or opinions expressed in this message are those of the individual(s) and not necessarily of the university. No reliance may be placed on this message without written confirmation from an authorized representative of its contents. No guarantee is implied that this message or any attachment is virus free or has not been intercepted and amended. </font></div><div 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 color="#808080" face="Arial, Helvetica, sans-serif" class=""><br class=""></font></div><div 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 color="#808080" face="Arial, Helvetica, sans-serif" class="">إخلاء مسؤليه: ان جميع المعلومات المتضمنة في هذه الرسالة تخص المستلم، وربما تتضمن معلومات سرية، واذا لم تكن انت المستلم فالرجاء الغاء الرسالة واشعار المرسل، كما يمنع نسخ او توزيع هذه الرسالة او افشاء محتوياتها لاخرين. ويجدر بالعلم ان جميع الآراء ووجهات النظر الواردة في هذه الرسالة تعتبر شخصية وليست بالضرورة منسوبة للجامعة. كما لايمكن ان يعتمد على هذه الرسالة ما لم تحصل على موافقة خطية من المسئول عن محتوياتها. كما لايوجد ضمان بان هذه الرسالة أو مرفقاتها خالية من الفيروسات أو انها لم يتم اعتراضها وتعديلها</font></div><div 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=""><br class=""></div><span id="cid:f_ldp0cr2v1"><pep1.pdb></span><span 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; float: none; display: inline !important;" class="">_______________________________________________</span><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=""><span 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; float: none; display: inline !important;" class="">Chimera-users mailing list:<span class="Apple-converted-space"> </span></span><a href="mailto:Chimera-users@cgl.ucsf.edu" style="font-family: Helvetica; font-size: 12px; 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;" class="">Chimera-users@cgl.ucsf.edu</a><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=""><span 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; float: none; display: inline !important;" class="">Manage subscription:<span class="Apple-converted-space"> </span></span><a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users" style="font-family: Helvetica; font-size: 12px; 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;" class="">https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users</a></div></blockquote></div><br class=""></div></body></html>