[Chimera-users] Problem on Nucleic Acid Ribbon

Elaine Meng meng at cgl.ucsf.edu
Tue Oct 6 15:10:00 PDT 2015


Good morning (or afternoon for us!),

One issue is that the default ribbon path is smoothed, and the smoothing has the following side effects:

(A) being a bit shorter at the end so the last base is hanging out beyond it
(B) being farther from the real backbone atom positions, so that when a connecting stick is drawn between the backbone and sidechain atoms, it can be obviously too long or short compared to the real bond

It’s discussed further here, 
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbonstyle.html#offset>

…. but the short answer is to fix it, you could use a different ribbon spline that is guaranteed to follow the real backbone atom positions (for nucleic acids, the P atoms).  For example, command:

ribspline cardinal

Then the ribbon will not be as smooth, but the connections to the sidechain atoms will look better.  There are some options to the command for tweaking the result, see:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ribspline.html>

However, I don’t know what is causing the problem of not showing that residue as fill and slab like the others.  I did not have that problem with my test PDB file (1BNA), and I don’t recall seeing the problem with other structures either.  If the structure is not private, you could try using menu: Help… Report a Bug and attaching the file and including a short description and your email address.  It might be not be a bug, but instead something with the atom names in the file or whether that last residue is missing any atoms, but no way to tell without looking at it.  Or if it is private but you don’t mind sharing it with just the Chimera team, you can mail it to just me (meng at cgl.ucsf.edu).

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


> On Oct 6, 2015, at 2:47 AM, Francesco Papi <francesco.papi at unifi.it> wrote:
> 
> Good morning,
> 
> I'm working on a DNA X-ray structure. The problem I have observed is that the terminal nucleotide of the DNA sequence is excluded from the backbone ribbon, in other terms the backbone ribbon is shown and it is ok, but it is made of all the residues except the terminal one, which is linked to the ribbon by a long phosphodiester bond (see the attached image). Moreover, if I put the representation "Show side (sugar/base)", from the option "Nucleotides", to be "fill/slab", the terminal residue still features an "Atom & Bonds" style. The PDB file seems to be ok, as confirmed by a colleague. Do you how to solve this problem?
> 
> Best regards
> 
> Francesco Papi<image.png>



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