[Chimera-users] pyroglutamate distorted in 3PFJ

Craig Dana craigmdana at gmail.com
Fri Jan 17 10:16:49 PST 2014

Much better - that's the ring shape I recognize.  That was very helpful!

I appreciate it.


On Fri, Jan 17, 2014 at 10:09 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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.
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