[Chimera-users] Display errors

Ahmad Khalifa underoath006 at gmail.com
Wed Jun 27 17:30:42 PDT 2018

I open the structures in the first image, which have the secondary
structures displayed correctly. I click file save pdb as single file.That's
the process I follow to save the file. How can I fix it?

On Wed, Jun 27, 2018 at 4:54 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Ahmad,
> I don’t what process you used to save the structures in a single file, so
> I don’t know what went wrong.  All I can tell from your images is that in
> the bottom image, some of the copies do not have secondary structure
> assignments, and that is why they show up as thin “coil” ribbon instead of
> the wider helix and strand ribbon.  It might be that something is wrong
> about the format of your single file, or that some of the backbone atoms
> are missing.  If you don’t think there are missing backbone atoms, you
> could try command “ksdssp” to reassign helix and strand, but the
> assignments probably won’t be exactly the same as from the original PDB
> file.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ksdssp.html>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> > On Jun 27, 2018, at 8:24 AM, Ahmad Abdelzaher <underoath006 at gmail.com>
> wrote:
> >
> > Hello,
> >
> > After saving the two side by side structures in a single file, I get the
> weird display errors in the picture shown below. How can I fix that?
> >
> > Regards.
> > <before_saving.png><after_Saving.png>
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