[Jmol-users] Fwd: Returned mail: see transcript for details
Hello, I became interested in the more advanced export features provided by jmol, allowing a generation of interactive 3D pdf data. As the present wiki pages of jmol describe, this could be achieved by 1) export of the present scenery as an IDTF file, then 2) a conversion the IDTF converter in the *.U3D format that finally may be embedded, for example, with movie15.sty package in LaTeX. By doing so, I experienced some odd things concerning the molecular structure being displayed. Some of the atoms are represented as sticks ; some atom/atom groups are represented as spheres, but partially lack connection with the main molecule. So far, I was not aware if the representation (stick-only vs. ball-stick-model) may be altered for single atoms/groups of atoms ; but am even more concerned by the fact of atoms becoming isolated. For this test I used the following enviroment/software: -- Windows XP, service pack 3 -- java verision 1.6.0_07 -- jmol as provided in the repository jmol-11.9.23-binary -- pdfLaTeX with movie15 package -- IDTF Converter.exe for Windows, as pointed by the wiki page pf jmol and it would be possible to share some of the data (initial *.cif file used, generated outputs by jmol/IDTF converter, the pdf-embedded u3d-data). Indeed, I would be interested to know to whom of the developers I eventually could send these files. With regards, Norwid Behrnd --- --- --- Norwid-Rasmus Behrnd, Ph.D. Group E. J. Sorensen Department of Chemistry, Frick Lab phone (609) 258 8160 Washington Rd., Princeton, NJ 08544, U.S.A. www.princeton.edu/~ejsgroup ) -- The Planet: dedicated and managed hosting, cloud storage, colocation Stay online with enterprise data centers and the best network in the business Choose flexible plans and management services without long-term contracts Personal 24x7 support from experience hosting pros just a phone call away. http://p.sf.net/sfu/theplanet-com ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Fwd: Returned mail: see transcript for details
Hello, Norwid We have had little experience with production of PDF files, so your experience will be very helpful. The output should display atoms and bonds as they are rendered in Jmol when you invoke the export. It is certainly possible to have some atoms as ball & stick, others as stick-only, etc, but only if you decide so. I will gladly have a look at your files to see if I can give some help. I am however not sure if I am able to visualize idtf files, and certainly I have no experience in generating pdf files. It is important that you specify if you have done any manipulations of the model in Jmol before doing the export )or you just left the default ball&stick). If so, please save a state script to file and attach it together with the CIF file. Have you had problems with other model files? Finally, any instructions about how you have used the conversion software (pdfLaTeX, movie15, IDTF Converter) will be useful by other users. You are welcome to add some info in the Wiki. -- The Planet: dedicated and managed hosting, cloud storage, colocation Stay online with enterprise data centers and the best network in the business Choose flexible plans and management services without long-term contracts Personal 24x7 support from experience hosting pros just a phone call away. http://p.sf.net/sfu/theplanet-com ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] How can i show the total molecule tegether in JMOL? Thanks.
Hello, everyone, I got a result of molecules coordinates from simulation. When i shown it by JMOL, i found part of molecule is in the left side of x axis in the box; and the other part is in the right side of x axis in the box. This is cause by the period bound condition in the simulation. How can i show the total molecule tegether in JMOL? Thanks. Houyang -- The Planet: dedicated and managed hosting, cloud storage, colocation Stay online with enterprise data centers and the best network in the business Choose flexible plans and management services without long-term contracts Personal 24x7 support from experience hosting pros just a phone call away. http://p.sf.net/sfu/theplanet-com___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] How can i show the total molecule tegether in JMOL? Thanks.
What sort of file is it?
You need to load the file with symmetry and unit cell and load more than one
unit cell. Something like:
load "caffeine.xyz" {1 1 1} spacegroup "P1" unitcell "10.0 10.0 10.0 90 90
90"
However this does not work with all file types. But that can be fixed...
Bob
On Mon, Feb 1, 2010 at 2:45 PM, houyang chen wrote:
> Hello, everyone,
>
> I got a result of molecules coordinates from simulation.
> When i shown it by JMOL, i found part of molecule is in the left side of x
> axis in the box; and the other part
> is in the right side of x axis in the box.
> This is cause by the period bound condition in the simulation.
> How can i show the total molecule tegether in JMOL?
>
> Thanks.
>
> Houyang
>
>
> --
> The Planet: dedicated and managed hosting, cloud storage, colocation
> Stay online with enterprise data centers and the best network in the
> business
> Choose flexible plans and management services without long-term contracts
> Personal 24x7 support from experience hosting pros just a phone call away.
> http://p.sf.net/sfu/theplanet-com
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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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