[Chimera-users] pyroglutamate distorted in 3PFJ

[Elaine Meng]

Hi Craig,
This is an artifact from the ribbon smoothing, where by default (only when ribbon is shown) the apparent positions of peptide backbone atoms are adjusted to fall along the smoothed ribbon path. The real positions are used for any measurements.  The real positions are apparent if you just hide ribbon for that residue, e.g. with command:

~ribbon :1

(or ribbon and atoms can be shown simultaneously after you use command "ribbackbone").  The issue is described in more depth here:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbonstyle.html#offset>

Another possibility is to use a different method with less smoothing to calculate the ribbon path, e.g. command:

ribspline cardinal
...or...
ribspline cardinal smooth strand

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 Jan 16, 2014, at 2:27 PM, Craig Dana wrote:

> I'm looking at the N-terminal pyroglutamate residue in PDB: 3PFJ. It is clearly distorted, but when I open the same PDB file in VMD, the pyroglutamate is not distorted.