Re: [Jmol-users] multiple structures in cif files
That's the proper behavior. I'm pretty sure they would load that way anyway,
if they were separate files. The 0 0 0 point is being used, of course, as
the same point in each case. So you will have to center those yourself. Say
I wanted to center model 1.2 on model 1.1. I would issue this:
select {1.2}; translateSelected @{ {1.1}.xyz - {1.2}.xyz }
Don't expect the unit cells to be adjusted, however.
Bob
On Wed, May 18, 2011 at 7:51 AM, Pshemak Maslak wrote:
> I have attempted to combine cif files of graphite, diamond and c60
> into one file. The new file shows all three models (separately) as
> desired. However, each model is displayed off center, and is off
> rotation center when manipulated with a mouse,
>
> Is it possible to do the above (combining files without any additional
> action) to get the desired display with center of rotation within the
> models preserved?
>
> Any suggestions would be appreciated,
>
> PM
>
>
> --
> What Every C/C++ and Fortran developer Should Know!
> Read this article and learn how Intel has extended the reach of its
> next-generation tools to help Windows* and Linux* C/C++ and Fortran
> developers boost performance applications - including clusters.
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> Jmol-users mailing list
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>
--
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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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Read this article and learn how Intel has extended the reach of its
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developers boost performance applications - including clusters.
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Re: [Jmol-users] MSIE9 and Mouse Wheel
On 05/18/2011 04:01 PM, Otis Rothenberger wrote: > Hi Rolf, > > I see the behavior that you describe in MSIE 9, Firefox (latest version), > and Chrome (latest version) under Windows 7. I do not see the same behavior > in this scrollable page: > > http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm > > This suggests either a Jmol version problem or a problem in your page. I > see that you have a number of on mouse event trappings on the page. Is it > possible that the applet container inherited something unintended? > The difference seems to be Jmol-version related. With a freshly updated Firefox 4 on WinXP I see the same behaviour with Jmol 11.6.8 but not with 12.0.43 (http://www.imb-jena.de/cgi-bin/3d_mapping.pl?CODE=1deh&JMOLVERSION=12.0.43). Firefox 4.0.1 on OpenSuse 11.4 doesnt' show this behaviour at all, regardless of the Jmol version. The mouse event trappings don't seem to be responsible, because they are only present in the Jena3D viewer for PDB entries that have SCOP, CATH or Pfam mappings. But the behavior is the same on pages without these mappings (http://www.imb-jena.de/cgi-bin/3d_mapping.pl?CODE=1bna). Unfortunately there are some adjustments and extensive compatibility checks necessary until we can upgrade Jena3D to Jmol 12.0.43. Regards, Rolf -- What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] MSIE9 and Mouse Wheel
Hi Rolf, I see the behavior that you describe in MSIE 9, Firefox (latest version), and Chrome (latest version) under Windows 7. I do not see the same behavior in this scrollable page: http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm This suggests either a Jmol version problem or a problem in your page. I see that you have a number of on mouse event trappings on the page. Is it possible that the applet container inherited something unintended? Otis -- Otis Rothenberger Department of Chemistry Illinois State University Normal, IL 61790-4160 http://chemagic.org From: "Rolf Huehne" Sent: Wednesday, May 18, 2011 9:02 AM To: jmol-users@lists.sourceforge.net Subject: [Jmol-users] MSIE9 and Mouse Wheel Dear all, I noticed on my Windows 7 system that Internet Explorer 9 (MSIE9) 'steals' the mouse wheel information from Jmol (version 11.6.8) if the page is scrollable (e.g.: http://www.imb-jena.de/cgi-bin/3d_mapping.pl?CODE=1deh). In all other browsers (which I tested before) zooming with the mouse wheel worked in Jmol, at least after I clicked into the applet once. But with MSIE9 zooming with the mouse wheel only works after the scrollbar has reached the end. This results in a very awkward behaviour. Do others also observe this phenomenon or might this be a specific problem on my system? Regards, Rolf -- What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] multiple structures in cif files
I have attempted to combine cif files of graphite, diamond and c60 into one file. The new file shows all three models (separately) as desired. However, each model is displayed off center, and is off rotation center when manipulated with a mouse, Is it possible to do the above (combining files without any additional action) to get the desired display with center of rotation within the models preserved? Any suggestions would be appreciated, PM -- What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] MSIE9 and Mouse Wheel
Dear all, I noticed on my Windows 7 system that Internet Explorer 9 (MSIE9) 'steals' the mouse wheel information from Jmol (version 11.6.8) if the page is scrollable (e.g.: http://www.imb-jena.de/cgi-bin/3d_mapping.pl?CODE=1deh). In all other browsers (which I tested before) zooming with the mouse wheel worked in Jmol, at least after I clicked into the applet once. But with MSIE9 zooming with the mouse wheel only works after the scrollbar has reached the end. This results in a very awkward behaviour. Do others also observe this phenomenon or might this be a specific problem on my system? Regards, Rolf -- What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] coloring of isosurface is not saved
The range should be saved; the colorScheme is not, though. You just apply that when you reload the file: isosurface "example.jvxl" colorScheme "rwb" 2011/5/18 Angel Herráez > I am creating a molecular isosurface colored by MEP > > isosurface molecular color range -2.2 0.0 colorScheme "rwb" map mep; > > Then I save it to disk. When I load it, the coloring scheme is lost. > > In the jvxl file content I can see the original command, but it is > not being applied. > I can only fix it by applying an additional coloring command: > > isosurface file "example.jvxl"; > isosurface color range -2.2 0.0 colorScheme "rwb"; > > I would expect that the coloring is retained in the jvxl file. Is > that not feasible? > > > > > -- > What Every C/C++ and Fortran developer Should Know! > Read this article and learn how Intel has extended the reach of its > next-generation tools to help Windows* and Linux* C/C++ and Fortran > developers boost performance applications - including clusters. > http://p.sf.net/sfu/intel-dev2devmay > ___ > 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 -- What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] coloring of isosurface is not saved
I am creating a molecular isosurface colored by MEP isosurface molecular color range -2.2 0.0 colorScheme "rwb" map mep; Then I save it to disk. When I load it, the coloring scheme is lost. In the jvxl file content I can see the original command, but it is not being applied. I can only fix it by applying an additional coloring command: isosurface file "example.jvxl"; isosurface color range -2.2 0.0 colorScheme "rwb"; I would expect that the coloring is retained in the jvxl file. Is that not feasible? -- What Every C/C++ and Fortran developer Should Know! Read this article and learn how Intel has extended the reach of its next-generation tools to help Windows* and Linux* C/C++ and Fortran developers boost performance applications - including clusters. http://p.sf.net/sfu/intel-dev2devmay ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
