It does look to me that the covalent radius for P is quite short. But there
is nothing I can really do about that. These are from other sources. See
spreadsheet files in
https://sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol/_documents/ for
details.
I think if you use
*set bondingVersion 1*
and then load your file, it will look better.
Here are my development notes:
/**
* Default table of bonding radii stored as a short mar ... milliangstrom
* radius
*
* Column 1 (default): Values taken from OpenBabel.
* http://sourceforge.net/p/openbabel
* /code/485/tree/openbabel/trunk/data/element.txt (dated 10/20/2004)
*
* These values are a mix of common ion (Ba2+, Na+) distances and
covalent distances.
* They are the default for autobonding in Jmol.
*
* Column 2: Blue Obelisk Data Repository (2/22/2014)
*
https://github.com/wadejong/bodr/blob/c7917225cad829507bdd4c8c2fe7ebd3d795c021/bodr/elements/elements.xml
* which is from:
*
* Pyykkö, P. and Atsumi, M. (2009),
* Molecular Single-Bond Covalent Radii for Elements 1–118.
* Chem. Eur. J., 15: 186–197. doi: 10.1002/chem.200800987
*
* (See also http://en.wikipedia.org/wiki/Covalent_radius)
*
* These are strictly covalent numbers.
* The user must use "set bondingVersion 1" to set these to be used for
autobonding
*
*/
public final static short[] defaultBondingMars = {
0, 0, // 0 Xx does not bond
230, 320, //1 H 39% larger
930, 460, //2 He 51% smaller
680, 1330, //3 Li 95% larger
350, 1020, //4 Be 191% larger
830, 850, //5 B 2% larger
680, 750, //6 C 10% larger
680, 710, //7 N 4% larger
680, 630, //8 O 8% smaller
640, 640, //9 F 0% larger
1120, 670, //10 Ne 41% smaller
970, 1550, //11 Na 59% larger
1100, 1390, //12 Mg 26% larger
1350, 1260, //13 Al 7% smaller
1200, 1160, //14 Si 4% smaller
* 750, 1110, //15 P 48% larger*
1020, 1030, //16 S 0% larger
On Mon, Jan 30, 2017 at 3:58 PM, Jörg Saßmannshausen <
j.sassmannshau...@ucl.ac.uk> wrote:
> Dear all,
>
> I seem to have a display problem when I am trying to open cartesian (xyz)
> files: quite often the P-C bond is not drawn which means the molecule looks
> wrong.
> If I am using Molden to view the structure it is perfectly ok. Exporting
> the
> structure from Molden as a xyz file and opening that file in jmol causes
> this
> problem. However, if I am exporting it as a mol or mol2 file the same
> structure
> is ok apart from an odd looking pyridine ring (two double bonds or three).
> I usually save the coordinates as a cartesian file as most journals would
> like
> to have the coordinates of the final geometry as cartesians.
>
> I am aware of the connect command so that would be a way out of it but I
> would
> have thought that the standart P-C bonds will be drawn automatically
>
> Is there something I do wrong or why does jmol has this problem?
> I am using Jmol-14.8.0 and one of the latests Oracle java on Debian Wheezy.
>
> Any suggestion?
>
> All the best from London
>
> Jörg
>
> --
> *************************************************************
> Dr. Jörg Saßmannshausen, MRSC
> University College London
> Department of Chemistry
> 20 Gordon Street
> London
> WC1H 0AJ
>
> email: j.sassmannshau...@ucl.ac.uk
> web: http://sassy.formativ.net
>
> Please avoid sending me Word or PowerPoint attachments.
> See http://www.gnu.org/philosophy/no-word-attachments.html
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
> _______________________________________________
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
--
Robert M. Hanson
Larson-Anderson Professor 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
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, SlashDot.org! http://sdm.link/slashdot
_______________________________________________
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
