[Chimera-users] Weird looking stretch in ribbon presentation

Boaz Shaanan bshaanan at exchange.bgu.ac.il
Sat Mar 30 04:06:08 PDT 2013


Thanks Elaine, 

I'll try your suggestions.

  Boaz


Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel

E-mail: bshaanan at bgu.ac.il
Phone: 972-8-647-2220  Skype: boaz.shaanan
Fax:   972-8-647-2992 or 972-8-646-1710





________________________________________
From: Elaine Meng [meng at cgl.ucsf.edu]
Sent: Saturday, March 30, 2013 5:05 AM
To: בעז שאנן
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Weird looking stretch in ribbon presentation

Hi Boaz,
The default ribbon is smoothed (B-spline) and in regions of high curvature, does not overlap the "real" backbone atom positions.  You can use an unsmoothed ribbon if you want.

The issue and possible solutions are explained here:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbonstyle.html#offset>

You can use cardinal spline ribbon that goes through the real backbone atom positions, or a partially smoothed compromise.  For example, commands:

ribspline cardinal
ribspline cardinal smooth strand

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ribspline.html>

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 Mar 29, 2013, at 5:11 PM, Boaz Shaanan wrote:

> Hi ,
> I came across a weird looking stretch when I use ribbons presentation (latest build x86_64, 38529, 27/3/13). Please check it yourself. In the entry 2pan, if you select residues  114-115 (Phe-Gln) and a few residues before and after in any chain (well, I checked C & D, I guess it's the same for all chains) and use ribbons + side-chains presentation the Ca-Cb gets very long compared to backbone+side-chain presentation (the Cb's are in the same place in both presentation, of course). In fact, the ribbon trace is shifted away from the backbone really is, hence the Ca-Cb bond gets excessively long.  It probably has to do with the shape of the turn in this stretch and the way the ribbons are calculated. However as this is an important region for my analysis it drew my attention by its weirdness. Is there no remedy for this?
>   Thanks,
>               Boaz
>



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