[Chimera-users] broken lines

Elaine Meng meng at cgl.ucsf.edu
Sun May 29 10:46:42 PDT 2016

Hi Shazia,
The lines are where the PDB file does not have atomic coordinates.  It is very common (in many PDB files), where the coordinates could not be determined from the experiment, generally because of disorder and weak density.  You can see the red boxes on the sequence for where the atomic coordinates are missing, and when you put the mouse over one of those red boxes, “no corresponding structure residue” is shown at the bottom of the sequence window.

So it doesn’t matter what program you use to show the file, it will still not have structure there.  Chimera shows the lines so that you know the chain is really connected, but you could hide the lines if you wanted, e.g. with command “~longbond”.

You could try to model the missing residues using Modeller, sequence window menu: Structure… Modeller (loops/refinement), but it would just be a model.  The structure data is simply not available from the experiment, even though the residues are in the sequence.  Modeling missing segments:

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On May 29, 2016, at 1:41 AM, shazia sabir <s.syed005 at gmail.com> wrote:

> Hi dear All,
> Why chimera is showing broken lines (region encircled in red at one area). What can we predict from structure. I attached sequence of structure that shows amino acid is there(gey region in sequence).
> Regards,
> shazia. 
> <broken-lines.tif><Sequence.tif>

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