[Jmol-developers] [ jmol-Feature Requests-3238524 ] load molecule

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Feature Requests item #3238524, was opened at 2011-03-23 20:42
Message generated for change (Comment added) made by publcif
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https://sourceforge.net/tracker/?func=detail&atid=379136&aid=3238524&group_id=23629

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Category: None
Group: None
Status: Open
Priority: 5
Private: No
Submitted By: Simon Westrip (publcif)
Assigned to: Nobody/Anonymous (nobody)
Summary: load molecule

Initial Comment:
Attached CIF when opened in Jmol 12.1.40 prerelease version does not create a connected molecule for one of the moities - i.e.
the CIF bonds include C9-C9(−x+2, −y+2, −z+1) but this bond (and the symmetry-related site C9) does not seem to be rendered,
though the 'connected' symmetry-related sites appear (thus forming two partial molecules - missing the connecting atom). 
Is there any way round this?

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>Comment By: Simon Westrip (publcif)
Date: 2011-04-11 16:43

Message:
I've had a go at scripting a 'Mercury' view, but without much success.
However, in some respects the Mercury view isnt ideal for these polymeric
organometallics. So I've scripted a 'coordination' view that displays the
ligands in their entirety around the metal sites and cuts off the view
where these ligands bridge to symmetry-related metals. Such a view at least
avoids 'broken' ligands.

Some examples are at http://journals.iucr.org/testing/chemistry/ (follow
the 'Supplementary page' links - 2nd example shows a coordination
polymer).

Again, hope this is of interest.

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Comment By: Bob Hanson (hansonr)
Date: 2011-04-02 17:20

Message:
That's still not it. I see Mercury's load now. Looks like they are ensuring
that all organic parts are continuous and allowing the model to break along
metal bonds. 

I guess there is comfort in seeing that Mercury also gets it wrong in a
different way -- not indicating the alternative locations on some atoms,
and showing two Mg for each S rather than 1.

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Comment By: Simon Westrip (publcif)
Date: 2011-04-02 11:35

Message:
Thanks again for looking at this. I dont know how Mercury approaches this,
but I had a look at PLATON.
The script below seems to emulate the PLATON approach. It doesnt produce
an ideal view, but then
again its perhaps very difficult to say what an 'ideal' view is in such
cases.

Anyway, hope this is of interest.


load "" {444 666 1}
hide none;
select not symop=1555 and connected(symop=1555);
var ss={selected};
select symop=1555;
for (var s=0;s<ss.length;s++)
{
var x= @{ss}[s].symmetry;
x="symop="+x; 
x = x.replace(",",",symop=");
echo @x;
select {selected}, @x;
}
hide not selected;
select none;
unitcell off;
axes off;

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Comment By: Bob Hanson (hansonr)
Date: 2011-03-31 21:05

Message:
I do see that Mercury is able to decipher that and keep the naphthalenes
together. Beats me how they do that. It's certainly a pretty good trick. 

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Comment By: Bob Hanson (hansonr)
Date: 2011-03-31 17:53

Message:
Not in this case. It's a polymeric molecular solid, like diamond, not a set
of molecules. So no matter how you do it, you would have to clip it
somewhere. In this case, Jmol simply delivers the atoms as they are listed
in the CIF file. 

I'm having trouble installing Mercury, or I would check how they handle
this.

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Comment By: Simon Westrip (publcif)
Date: 2011-03-29 11:40

Message:
Thank you for foxing this.

I have a similar problem with the attached CIF (wm2328d.cif) where a
naphthalene ring is 'divided' by symmetry.
Could the 'molecular view' be enhanced to handle such cases?

Cheers

Simon

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Comment By: Bob Hanson (hansonr)
Date: 2011-03-24 02:01

Message:
make that just 12.1.41 -- this molecular load of CIF files is not part of
12.0.

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Comment By: Bob Hanson (hansonr)
Date: 2011-03-24 02:01

Message:
this is a bug, not a feature request. Fixed for Jmol 12.1.41 and 12.0.37

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You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=379136&aid=3238524&group_id=23629