[Chimera-users] Undisplay pseudo bonds (missing segments) in pipes-and-planks representation?

Elaine Meng meng at cgl.ucsf.edu
Fri Jul 3 08:25:48 PDT 2015

Hi Oliver,
Pipes-and-planks should be smarter about the missing segments, but with its current behavior, a workaround is to edit the input PDB by putting a TER card between the ATOM records of the peptides flanking the gap.

Yes, we have discussed at length the need for integrated cylinders in Chimera2!
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jul 3, 2015, at 7:19 AM, Oliver Clarke <olibclarke at gmail.com> wrote:

> Hi all, just wondering if there is an option I am missing to undisplay pseudobonds when using pipes-and-planks? 
> At present chimera seems to represent missing segments in pipes-and-planks as a continuation of the chain rather than a break, which is a little confusing, e.g. check the following pair of snapshots (chain break in green section corresponds to missing 10aa loop):
> https://www.dropbox.com/s/cbwar1i197kt3ep/Screenshot%202015-07-03%2010.09.54.png?dl=0
> https://www.dropbox.com/s/we058qjv3ibwjmn/Screenshot%202015-07-03%2010.10.07.png?dl=0
> Also in general it would be nice if cylindrical representations of helices were more integrated into chimera, perhaps with their own style adjustments (e.g. allowing for curved cylinders), as for large structures they provide much less visual clutter, but I guess that is probably something for Chimera 2.
> Cheers, Oliver.

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