<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="">Okay, well, you would need to send me the file for me to figure out why this happens. You can either send it to me directly in email or use Help→Report a Bug in ChimeraX and attach the file.<div class=""><br class=""></div><div class="">--Eric<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Jan 31, 2023, at 9:24 AM, Lenye Dlamini <<a href="mailto:DLMLEN001@myuct.ac.za" class="">DLMLEN001@myuct.ac.za</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="elementToProof" style="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; font-family: Arial, Helvetica, sans-serif; font-size: 11pt; background-color: rgb(255, 255, 255);">Hello Eric,</div><div class="elementToProof" style="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; font-family: Arial, Helvetica, sans-serif; font-size: 11pt; background-color: rgb(255, 255, 255);"><br class=""></div><div class="elementToProof" style="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; font-family: Arial, Helvetica, sans-serif; font-size: 11pt; background-color: rgb(255, 255, 255);">Thanks for your response<br class=""></div><div class="elementToProof" style="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; font-family: Arial, Helvetica, sans-serif; font-size: 11pt; background-color: rgb(255, 255, 255);">Yes I mean models.</div><div class="elementToProof" style="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; font-family: Arial, Helvetica, sans-serif; font-size: 11pt; background-color: rgb(255, 255, 255);">There is an "END" at the end of the file and no "ENDMDL" anywhere on the file.</div><div class="elementToProof" style="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; font-family: Arial, Helvetica, sans-serif; font-size: 11pt; background-color: rgb(255, 255, 255);"><br class=""></div><div class="elementToProof" style="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; font-family: Arial, Helvetica, sans-serif; font-size: 11pt; background-color: rgb(255, 255, 255);"><br class=""></div><div class="elementToProof" style="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; font-family: Arial, Helvetica, sans-serif; font-size: 11pt; background-color: rgb(255, 255, 255);">Kind regards,</div><div class="elementToProof" style="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; font-family: Arial, Helvetica, sans-serif; font-size: 11pt; background-color: rgb(255, 255, 255);">Lenye Dlamini<br class=""></div><div id="appendonsend" 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><hr tabindex="-1" 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; display: inline-block; width: 483.125px;" 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=""></span><div id="divRplyFwdMsg" dir="ltr" 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="Calibri, sans-serif" style="font-size: 11pt;" class=""><b class="">From:</b><span class="Apple-converted-space"> </span>Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu" class="">pett@cgl.ucsf.edu</a>><br class=""><b class="">Sent:</b><span class="Apple-converted-space"> </span>Monday, January 30, 2023 9:50 PM<br class=""><b class="">To:</b><span class="Apple-converted-space"> </span>Lenye Dlamini <<a href="mailto:DLMLEN001@myuct.ac.za" class="">DLMLEN001@myuct.ac.za</a>><br class=""><b class="">Cc:</b><span class="Apple-converted-space"> </span><a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a><span class="Apple-converted-space"> </span><<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>><br class=""><b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [chimerax-users] Multi-chain single macromolecule .pdb file read as two molecules</font><div class=""> </div></div><div class="" 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; word-wrap: break-word; line-break: after-white-space;"><p style="margin-top: 0px; margin-bottom: 0px;" class=""></p><div style="background-color: rgb(255, 235, 156); width: 493px; border: 1pt solid rgb(156, 101, 0); padding: 2pt; font-size: 10pt; line-height: 12pt; font-family: Calibri; text-align: left;" class=""><span style="color: rgb(156, 101, 0);" class="">CAUTION:</span><span class="Apple-converted-space"> </span>This email originated outside the UCT network. Do not click any links or open attachments unless you know and trust the source.</div><br class=""><p style="margin-top: 0px; margin-bottom: 0px;" class=""></p><div class="">Hi Lenye,<div class=""><span class="x_Apple-tab-span" style="white-space: pre;"></span>When you say "molecules", do you actually mean "models",<span class="Apple-converted-space"> </span><i class="">i.e.</i><span class="" style="font-style: normal;"> the file creates multiple models in ChimeraX? Are there MODEL/ENDMDL records in the file? Is there and END record (not ENDMDL record) that's not at the end of the file?</span></div><div class=""><span class="x_Apple-tab-span" style="white-space: pre;"></span>Yes, sending the PDB would be helpful...</div><div class=""><br class=""></div><div class=""><div class="">--Eric</div><div class=""><br class=""></div><div class=""><span class="x_Apple-tab-span" style="white-space: pre;"></span>Eric Pettersen</div><div class=""><span class="x_Apple-tab-span" style="white-space: pre;"></span>UCSF Computer Graphics Lab</div><div class=""><br class=""></div><div class=""><br class=""><blockquote type="cite" class=""><div class="">On Jan 28, 2023, at 1:27 PM, Lenye Dlamini via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:</div><br class="x_Apple-interchange-newline"><div class=""><div class="x_elementToProof" style="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; text-decoration: none; font-family: Arial, Helvetica, sans-serif; font-size: 11pt; background-color: rgb(255, 255, 255);">Hello,</div><div class="x_elementToProof" style="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; text-decoration: none; font-family: Arial, Helvetica, sans-serif; font-size: 11pt; background-color: rgb(255, 255, 255);"><br class=""></div><div class="x_elementToProof" style="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; text-decoration: none; font-family: Arial, Helvetica, sans-serif; font-size: 11pt; background-color: rgb(255, 255, 255);">I have a homo-oligomeric model that I've refined using phenix and the ISOLDE tool in ChimeraX that's read during deposition as 2 separate molecules, a larger 14mer and a smaller tetramer.<span class="x_Apple-converted-space"> </span><br class=""></div><div class="x_elementToProof" style="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; text-decoration: none; font-family: Arial, Helvetica, sans-serif; font-size: 11pt; background-color: rgb(255, 255, 255);">It's read as one molecule in Coot, Chimera and Pymol but read as two distinct molecules in ChimeraX exactly like the deposition. I found this curious and thought that perhaps you might have some idea of what's wrong with the file.<br class=""></div><div class="x_elementToProof" style="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; text-decoration: none; font-family: Arial, Helvetica, sans-serif; font-size: 11pt; background-color: rgb(255, 255, 255);">There is nothing that appears obviously incorrect to me in the text of the .pdb file, all TER cards follow the chains and all amino acids and their identifiers are in sequence and correct.<br class=""></div><div class="x_elementToProof" style="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; text-decoration: none; font-family: Arial, Helvetica, sans-serif; font-size: 11pt; background-color: rgb(255, 255, 255);"><br class=""></div><div class="x_elementToProof" style="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; text-decoration: none; font-family: Arial, Helvetica, sans-serif; font-size: 11pt; background-color: rgb(255, 255, 255);">I'd appreciate any ideas you may have and I'm happy to send the file to you if you prefer.</div><div class="x_elementToProof" style="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; text-decoration: none; font-family: Arial, Helvetica, sans-serif; font-size: 11pt; background-color: rgb(255, 255, 255);"><br class=""></div><div class="x_elementToProof" style="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; text-decoration: none; font-family: Arial, Helvetica, sans-serif; font-size: 11pt; background-color: rgb(255, 255, 255);">Thank you,</div><div class="x_elementToProof" style="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; text-decoration: none; font-family: Arial, Helvetica, sans-serif; font-size: 11pt; background-color: rgb(255, 255, 255);">Kind regards,</div><div class="x_elementToProof" style="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; text-decoration: none; font-family: Arial, Helvetica, sans-serif; font-size: 11pt; background-color: rgb(255, 255, 255);">Lenye Dlamini<br class=""></div><span class="" style="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; text-decoration: none; float: none; display: inline !important;">Disclaimer - University of Cape Town This email is subject to UCT policies and email disclaimer published on our website at<span class="x_Apple-converted-space"> </span></span><a href="https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fprotect-za.mimecast.com%2Fs%2F_ER2CNxKq0i0N07GXFm8jQk&data=05%7C01%7Cdlmlen001%40myuct.ac.za%7C8b53751ab9e64d137a5408db03631d98%7C92454335564e4ccfb0b024445b8c03f7%7C0%7C0%7C638107496512969304%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=MkUHSJqUiwNM86jM0sVpaCeyTfvZNX%2BmKJ3vvkUxT18%3D&reserved=0" originalsrc="https://protect-za.mimecast.com/s/_ER2CNxKq0i0N07GXFm8jQk" shash="jd8kQCknb8Ej6I8LyZh+Fa6V8CRQ4cYR+ZTQpJta2basLkdjr5DxGl59SFv+Y32PhSSvmjAHKphtjRCiemjuCqsBj3Wmj4ex7f6e11ukGlB+QgPvoe9NChqOEiUeM9+KkqXrZH8mU+8W20Wwr+iizOtP/sGXDS5ZnA3e6R58BkI=" class="" style="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;">http://www.uct.ac.za/main/email-disclaimer</a><span class="" style="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; text-decoration: none; float: none; display: inline !important;"><span class="x_Apple-converted-space"> </span>or obtainable from +27 21 650 9111. 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