<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 Eddie,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Since some hexadecimal numbers are indistinguishable from decimal numbers despite representing very different values, ChimeraX does not support hexadecimal numbering for atoms past 99,999. It supports Hybrid-36 numbering (which Greg mentioned) and "Amber" numbering, both of which are described briefly in the documentation of the serialNumbering keyword in the PDB section of the <a href="https://www.cgl.ucsf.edu/chimerax/docs/user/commands/save.html#pdb" class="">save command</a>. You would have to use one of those numberings. Alternatively you could change all the > 99,999 numbers to 99999 and I think that will work, though ChimeraX will complain bitterly about duplicate atom serial numbers.</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><br class=""><blockquote type="cite" class=""><div class="">On Oct 4, 2022, at 2:14 PM, Dr. Eddie via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div 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=""><div class="">Thank you! It seems the error occurs at the 100000 atom. The numbers there start to be hexidecimal. It starts to see the numbers in base 10 and hexidecimal numbers as the same so it counts them as duplicates (like 18700 in decimal and 18700 = 100096 (decimal)). Is there some conversion I need to do?</div><div class="">Thanks!</div><div class="">Eddie<br class=""></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="ltr" class="gmail_attr">On Tue, Oct 4, 2022 at 4:01 PM Greg Couch <<a href="mailto:gregc@cgl.ucsf.edu" class="">gregc@cgl.ucsf.edu</a>> wrote:<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;">Sorry, that was only one of the problems. As you can see from the log,<span class="Apple-converted-space"> </span><br class="">when you open your file in ChimeraX, there are many bad PDB records. <span class="Apple-converted-space"> </span><br class="">See<span class="Apple-converted-space"> </span><br class=""><a href="https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro.html" rel="noreferrer" target="_blank" class="">https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro.html</a><span class="Apple-converted-space"> </span><br class="">for details about the format, or the full PDB format documentation at<span class="Apple-converted-space"> </span><br class=""><a href="https://www.wwpdb.org/documentation/file-format" rel="noreferrer" target="_blank" class="">https://www.wwpdb.org/documentation/file-format</a>. There are also lots of<span class="Apple-converted-space"> </span><br class="">duplicate atom serial numbers that confuse things.<br class=""><br class=""> <span class="Apple-converted-space"> </span>-- Greg<br class=""><br class="">On 10/4/22 13:52, Greg Couch via ChimeraX-users wrote:<br class="">> The coordinates are in the wrong columns for your HETATM residues.<span class="Apple-converted-space"> </span><br class="">> Remove the spaces after HETATM.<br class="">><br class="">> -- Greg<br class="">><br class="">> On 10/4/22 13:19, Dr. Eddie via ChimeraX-users wrote:<br class="">>> Hi all,<br class="">>> I've got a pdb and I can't seem to get ChimeraX to recognize the<span class="Apple-converted-space"> </span><br class="">>> ligand (resname STR) at the end of the pdb. I've modified the ATOM to<span class="Apple-converted-space"> </span><br class="">>> be HETATM but it still does not show up. I hide solvent and the<span class="Apple-converted-space"> </span><br class="">>> lipids and I know where it should be (from seeing it in vmd) but only<span class="Apple-converted-space"> </span><br class="">>> a void is there. Any ideas what is wrong with the pdb?<br class="">>> Thanks,<br class="">>> Eddie<br class="">>><br class="">>> _______________________________________________<br class="">>> ChimeraX-users mailing list<br class="">>><span class="Apple-converted-space"> </span><a href="mailto:ChimeraX-users@cgl.ucsf.edu" target="_blank" class="">ChimeraX-users@cgl.ucsf.edu</a><br class="">>> Manage subscription:<br class="">>><span class="Apple-converted-space"> </span><a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" rel="noreferrer" target="_blank" class="">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a><br class="">> _______________________________________________<br class="">> ChimeraX-users mailing list<br class="">><span class="Apple-converted-space"> </span><a href="mailto:ChimeraX-users@cgl.ucsf.edu" target="_blank" class="">ChimeraX-users@cgl.ucsf.edu</a><br class="">> Manage subscription:<br class="">><span class="Apple-converted-space"> </span><a href="https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" rel="noreferrer" target="_blank" class="">https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a><br class="">><br class=""></blockquote></div><br clear="all" 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 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="">--<span class="Apple-converted-space"> </span></span><br style="caret-color: rgb(0, 0, 0); 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