[Chimera-users] Display errors

Elaine Meng meng at cgl.ucsf.edu
Thu Jun 28 11:47:19 PDT 2018

Hi Ahmad,
To summarize for the others:  this is not a display error but missing secondary structure information.

The reason is that the multiple-model single-PDB format is technically only for multiple coordinate sets of the same set of atoms (like an NMR ensemble), and there is only one set of helix/strand information at the top of the file that is used for each of the models. Chimera includes only the information from the first model when writing the file.

In your case, although the two models look like copies of each other, they actually have some different chain IDs.  In the new single file, your second model is mostly lacking this information.

As I mentioned before, you can simply calculate helix and strand after opening the file:


However (and you might not care about this anyway), the assignments might be slightly different than in the original files.

If you want to keep exactly the original secondary structure assignments , the better way to make a single PDB file is to combine the two models into one model before saving.  You can combine models using the Model Panel (open from Favorites menu): choose both models on the left, then click “copy/combine” on the right, or with the “combine” command, for example:

combine #0,1 model #2 close true

and then save only the new combined model (#2) to a PDB file.
I hope this helps,

> On Jun 28, 2018, at 11:01 AM, Ahmad Khalifa <underoath006 at gmail.com> wrote:
> Thanks a lot Elaine. I would appreciate you taking a look at my structures. Please find it in the attachments. 
> Kind regards. 
> On Thu, Jun 28, 2018 at 12:51 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Ahmad,
> I do not have this problem when I just open two structures and save them as a single PDB.  When I reopen the saved PDB it shows all the secondary structure of both structures.
> When you save make sure you are saving all of the atoms (do not use options “Save displayed atoms only” or “Save selected atoms only”).  Other than that, I don’t have any idea what happened with your file, without seeing that file.  You could send (attach) it to e-mail.  You could send to just me if you don’t want to put it on the list.
> Regards,
> Elaine
> > On Jun 27, 2018, at 5:30 PM, Ahmad Khalifa <underoath006 at gmail.com> wrote:
> > 
> > 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>
> > 
> <A9_padded.pdb><A10_padded.pdb>

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