On Tue, Jun 13, 2017 at 7:27 AM, Wayne Decatur via Jmol-users <
jmol-users@lists.sourceforge.net> wrote:
> Hi,
> Is `set backboneSteps` removed? I see `set cartoonSteps` now in use at the
> awesome http://jmol.x3dna.org.
>
>
Oooh, thank you, Wayne, for that shout-out. It was fabulously fun putting
that together. Really developed nicely, and I hear that the paper may be
featured on the cover of Nucleic Acids Research (
https://www.ncbi.nlm.nih.gov/pubmed/28472503)
Yes, in the development of that page, I realized that this feature had to
be a cartoon feature, not a backbone feature. Backbone has the oddness that
it only shows up if there are two adjacent residues. Cartoon is different
-- it can appear even if there is only one. This is what was happening. The
release note reads:
bug fix: backboneSteps moved to cartoonSteps
// order of checking for TRUE is:
// cartoonBlocks, cartoonBaseEdges, cartoonSteps, cartoonLadders,
cartoonRibose
JmolVersion="14.11.1" // 2017-04-03
bug fix: set cartoonBlocks; set cartoonBlockHeight x.x
-- needs to be cartoon, not backbone (needs to be single-monomer based)
-- replaces set backboneBlocks; set backboneBlockHeight x.x from 14.11.0
-- for nucleic only
-- overrides set cartoonSteps and cartoonBaseEdges
-- uses DSSR data if present (using calculate structure DSSR or load
=xxxx/dssr)
-- displays a DSSR block for each base based on dssr.nts.frame
-- x.x is height of box in Angstroms (default 0.5)
> In the Jmol documentation, `set backboneSteps` is still shown as part of a
> demo script under '[atom expressions]' at https://chemapps.stolaf.
> edu/jmol/docs/#atomexpressions for 'WITHIN(DSSR,type)'
> '
>
>
I wll get that fixed.
> Is there anyway to use `ribbon` for nucleic acid and have the cartoonSteps
> shown between the ribbon but without other parts of the cartoon being
> visible, i.e., the backbone?
>
I don't think so. I get your point, though, that if it were backbone you
could do that. Do you see that as an important feature?
Bob
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