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<p>Hex numbers don't work for atom serial numbers. You'll need to
use the hybrid-36 format. That is a base 36 format where the
capital letters are additional digits. See
<a class="moz-txt-link-freetext" href="https://cci.lbl.gov/hybrid_36/">https://cci.lbl.gov/hybrid_36/</a>.</p>
<p>You should also consider switching to the mmCIF format, which
does not have a limit on the number of atoms.<br>
</p>
<p> -- Greg<br>
</p>
<div class="moz-cite-prefix">On 10/4/22 14:14, Dr. Eddie wrote:<br>
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<blockquote type="cite"
cite="mid:CAD8Y7_nLWpUMVrCF_uG+YA7bvmc+X4KwC4pMrKJeD5yx4cV00w@mail.gmail.com">
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<div>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>Thanks!</div>
<div>Eddie<br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Tue, Oct 4, 2022 at 4:01 PM
Greg Couch <<a href="mailto:gregc@cgl.ucsf.edu"
moz-do-not-send="true" class="moz-txt-link-freetext">gregc@cgl.ucsf.edu</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Sorry,
that was only one of the problems. As you can see from the
log, <br>
when you open your file in ChimeraX, there are many bad PDB
records. <br>
See <br>
<a
href="https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro.html"
rel="noreferrer" target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro.html</a>
<br>
for details about the format, or the full PDB format
documentation at <br>
<a href="https://www.wwpdb.org/documentation/file-format"
rel="noreferrer" target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">https://www.wwpdb.org/documentation/file-format</a>.
There are also lots of <br>
duplicate atom serial numbers that confuse things.<br>
<br>
-- Greg<br>
<br>
On 10/4/22 13:52, Greg Couch via ChimeraX-users wrote:<br>
> The coordinates are in the wrong columns for your HETATM
residues. <br>
> Remove the spaces after HETATM.<br>
><br>
> -- Greg<br>
><br>
> On 10/4/22 13:19, Dr. Eddie via ChimeraX-users wrote:<br>
>> Hi all,<br>
>> I've got a pdb and I can't seem to get ChimeraX to
recognize the <br>
>> ligand (resname STR) at the end of the pdb. I've
modified the ATOM to <br>
>> be HETATM but it still does not show up. I hide
solvent and the <br>
>> lipids and I know where it should be (from seeing it
in vmd) but only <br>
>> a void is there. Any ideas what is wrong with the
pdb?<br>
>> Thanks,<br>
>> Eddie<br>
>><br>
>> _______________________________________________<br>
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target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">ChimeraX-users@cgl.ucsf.edu</a><br>
>> Manage subscription:<br>
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rel="noreferrer" target="_blank" moz-do-not-send="true"
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</blockquote>
</div>
<br clear="all">
<br>
-- <br>
<div dir="ltr" class="gmail_signature">Eddie<br>
</div>
</blockquote>
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