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<div>Hi Elaine,</div>
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<div dir="ltr">That was indeed the problem. Thanks a lot!</div>
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<div dir="ltr">Cheers,</div>
<div dir="ltr">Magdalena </div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>Från:</b> Elaine Meng <meng@cgl.ucsf.edu><br>
<b>Skickat:</b> Thursday, September 8, 2022 6:04:00 PM<br>
<b>Till:</b> Magdalena Riad <magdalena.riad@ki.se><br>
<b>Kopia:</b> chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu><br>
<b>Ämne:</b> Re: [Chimera-users] Pdb saved in Chimera not displaying upon opening</font>
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<div class="PlainText">[Du får inte e-post ofta från meng@cgl.ucsf.edu. Läs om varför det här är viktigt på
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Hi Magdalena,<br>
It is not possible to answer with certainty since I don't know exactly what atoms you had displayed when you tried to the save the PDB.<br>
<br>
However, most likely the problem is that you displayed ribbons only. Displaying ribbons is not the same as displaying the atoms (e.g. as sticks or wire). For example, to show atoms, menu: Presets... interactive 2 (all atoms).<br>
<br>
I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D.<br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
<br>
> On Sep 8, 2022, at 1:53 AM, Magdalena Riad via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:<br>
><br>
> Hi,<br>
><br>
> I have opened a pdb structure of a ribosome, hidden parts of it and then saved a new pdb of the displayed atoms through “File->Save pdb” ticking “save displayed atoms only”. When I try to open this saved pdb file, Chimera states “Opened ….pdb”, however, it
does not display. The model panel is empty etc. Checking the pdb file in textedit, it does contain the secondary structure information and all the amino acids but it seems to lack coordinate information, see pictures below of parts of it. I’ve also tried to
save the pdb through “Actions-> write pdb”.<br>
><br>
> Do you know how I can solve this issue? Is it a saving issue or a displaying issue?<br>
><br>
> Thanks,<br>
> Magdalena<br>
><br>
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