Then mmCIF is perfect for you. Just create one loop like I showed, along
with those two necessary header lines. Done.
On Fri, Jan 30, 2015 at 8:04 AM, Rolf Huehne <rhue...@fli-leibniz.de> wrote:
> On 01/29/2015 10:21 PM, Robert Hanson wrote:
> > My point was that you can easily create a CIF with Perl or anything else
> > that Jmol will parse *for the information in the ATOM/HETATM/CONECT
> lines*,
> > which is what it sounded like you were saying. You did not refer to
> > specific REMARK records. Some of those are more involved.
> >
> > Basically you just add a couple of single-character columns to keep
> values
> > separate, define your _loop keys, and you are done.
> >
> You were right with this. And if mmCIF currently is the only choice and
> the behaviour with CML is as intended and not a bug I can adapt to this
> and use mmCIF.
>
> > What do you really want to do - exactly? Which records do you need?
> >
> I want to import network data (connection information and node type
> information) and then translate this within Jmol into hetero atom and
> bond information, determine suitable coordinates for the atoms, and
> build model data that Jmol can then load from a variable and that Jmol
> can save and that Jmol (and maybe also other programs) can reload.
> Essential for this would be to be able to specify the following atom
> properties:
> 1) atom number
> 2) atom name
> 3) residue name
> 4) model number
> 5) chain id
> 6) atom coordinates
>
> In the future maybe also the 'residue number' might be useful. But
> currently all residues will only have a single atom. So it wouldn't
> provide any extra information that the 'atom number' not already provides.
>
> > Is this your real question?
> >
> > *I am looking for a replacement for the mmCIF format that offers all of
> the
> > information that Jmol can read from mmCIF files, but isn't mmCIF.*
> No. Within Jmol I don't need any extra information. (see above)
>
> Regards,
> Rolf
> --
>
> Rolf Huehne
> Postdoc
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/
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