[Chimera-users] Pdb saved in Chimera not displaying upon opening

[Magdalena Riad]

Hi Elaine,

That was indeed the problem. Thanks a lot!

Cheers,
Magdalena

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________________________________
Från: Elaine Meng <meng at cgl.ucsf.edu>
Skickat: Thursday, September 8, 2022 6:04:00 PM
Till: Magdalena Riad <magdalena.riad at ki.se>
Kopia: chimera-users at cgl.ucsf.edu <chimera-users at cgl.ucsf.edu>
Ämne: Re: [Chimera-users] Pdb saved in Chimera not displaying upon opening

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Hi Magdalena,
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.

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).

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Sep 8, 2022, at 1:53 AM, Magdalena Riad via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
>
> Hi,
>
> 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”.
>
> Do you know how I can solve this issue? Is it a saving issue or a displaying issue?
>
> Thanks,
> Magdalena
>




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