<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Tommy,<div class=""><br class=""></div><div class=""> Sure those things can be easily be done. I'd encourage you to use ChimeraX instead of the old Chimera program. Also best to email questions to the Chimera mailing list (<a href="mailto:chimera-users@cgl.ucsf.edu" class="">chimera-users@cgl.ucsf.edu</a>) or ChimeraX mailing list (<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>).</div><div class=""><br class=""></div><div class=""> To delete a domain of a protein in ChimeraX that is say residues 151 to 375 of chain B</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>delete /B:151-375</div><div class=""><br class=""></div><div class="">The command syntax would be different in Chimera. To add short linkers is more difficult and I will leave that question to Elaine to advise on the mailing list -- I am not the most knowledgable about how to do that.</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Apr 26, 2022, at 4:45 PM, Tommy Tong <<a href="mailto:ttong@SDBRI.ORG" class="">ttong@SDBRI.ORG</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta charset="UTF-8" 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: 400; 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; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Dear Thomas,<o:p class=""></o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Good afternoon. How are you? My name is Tommy from San Diego Biomedical Research Institute, CA. I am new to Chimera software and my level of usage has been at the basic level, eg selecting chains and to color label the specific region on the protein.<o:p class=""></o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">May I ask if there is a way to selectively deleting a specific domain on a protein from a pdb file? I want to show graphically how the structure of the molecule will look like without the domain(s). In addition, is it possible to add short amino acid sequence, such as short linkers (eg GSGS) after a domain has been deleted from the protein structure?<o:p class=""></o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">I am currently using UCSF Chimera version 1.16.<o:p class=""></o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Your help and advice are greatly appreciated.<o:p class=""></o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Thank you for your time.<o:p class=""></o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Sincerely,<o:p class=""></o:p></div><div style="margin: 0in; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Tommy<span class="Apple-converted-space"> </span></div></div></div></blockquote></div><br class=""></div></body></html>