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Re: [Jmol-users] FW: add new atoms via Cartesian coordinates
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From: Robert H. <ha...@st...> - 2010-11-11 19:59:48
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This assumes you want cartesians -- If you want fractional coordinates, you will need to use a CIF format, I think, and use the LOAD DATA version of the command, perhaps. I have to think about that. I guess you could actually write a DATA command using a Jmol script, converting fractionals to cartesians as you do it. An option anyway.... In any case, both are relatively simple. You can find plenty of examples in the data directory. XYZ is just # atoms comment line Sym1 x1 y1 z1 Sym2 x2 y2 z2 like that, pretty free format. See the examples. Bob On Thu, Nov 11, 2010 at 1:27 PM, pieremanuele canepa <pc...@ke...>wrote: > Can you give me more details about (simple XYZ file format) > so the command will be > > set appendNew false > DATA "model" > (Fe fx fy fz, O fx fy fz, etc. ) > end "model" > > > On Thu, Nov 11, 2010 at 6:40 PM, P.Canepa <pc...@ke...> wrote: > >> >> ------------------------------------------- >> From: Robert Hanson[SMTP:HANSONR@STOLAF.EDU <SMTP%3AHANSONR@STOLAF.EDU>] >> Sent: Thursday, November 11, 2010 6:40:19 PM >> To: jmo...@li... >> Subject: Re: [Jmol-users] add new atoms via Cartesian coordinates >> Auto forwarded by a Rule the simplest way to do it if you have several >> atoms to add is: >> >> >> set appendNew false >> >> and then >> >> DATA "model" >> (simple XYZ file format) >> end "model" >> >> We also have a new (undocumented) command ASSIGN that we use for the model >> kit. >> >> On Thu, Nov 11, 2010 at 10:45 AM, pieremanuele canepa <pc...@ke...>wrote: >> >>> Dear All, >>> >>> Can you show me the Jmol command to add a new atom knowing its >>> fractional or Cartesian coordinates? >>> >>> Thanks a lot, Piero >>> >>> -- >>> *Please consider the environment before printing this e-mail.* >>> ** >>> Pieremanuele Canepa >>> Room 104 >>> Functional Material Group >>> School of Physical Sciences, Ingram Building, >>> University of Kent, Canterbury, Kent, >>> CT2 7NH >>> United Kingdom >>> >>> e-mail: pc...@ke... >>> mobile: +44 (0) 7772-9756456 >>> ----------------------------------------------------------- >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> Centralized Desktop Delivery: Dell and VMware Reference Architecture >>> Simplifying enterprise desktop deployment and management using >>> Dell EqualLogic storage and VMware View: A highly scalable, end-to-end >>> client virtualization framework. Read more! >>> http://p.sf.net/sfu/dell-eql-dev2dev >>> _______________________________________________ >>> Jmol-users mailing list >>> Jmo...@li... >>> 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 >> > > > > -- > *Please consider the environment before printing this e-mail.* > ** > Pieremanuele Canepa > Room 104 > Functional Material Group > School of Physical Sciences, Ingram Building, > University of Kent, Canterbury, Kent, > CT2 7NH > United Kingdom > > e-mail: pc...@ke... > mobile: +44 (0) 7772-9756456 > ----------------------------------------------------------- > > > > ------------------------------------------------------------------------------ > Centralized Desktop Delivery: Dell and VMware Reference Architecture > Simplifying enterprise desktop deployment and management using > Dell EqualLogic storage and VMware View: A highly scalable, end-to-end > client virtualization framework. Read more! > http://p.sf.net/sfu/dell-eql-dev2dev > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > 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 |