Dear List, I've spent more time with the excellent online help, and I think I've got the atom selection figured out for my purposes.
Chagrined, Matt On 7/5/12 12:36 PM, "Kubasik, Matt" <[email protected]> wrote: >Dear list, > >I am seeking guidance on getproperty (and possibly correct atom >expressions) within JmolData.jar. Will >x=getproperty(³atominfo[nnn].xxx²} work in JmolData.jar? > >I would like to use JmolData.jar to process Gaussian output files >containing vibrational vectors of atoms in different vibrational modes. > >The following sequence works fine in Jmol.jar (invoked via terminal¹s >command-line, e.g." java -jar $Jmol -on $freqfile -s $script"), but it >prints an empty string in JmolData.jar: > >framenumber=258 >frame @framenumber >c_index=16 >cvibvector=getproperty("atomInfo["+c_index+"].vibVector") >show cvibvector > >Is it that ³frame² does not work in JmolData.jar? Do I need a rigorous >atom expression (for the 16th atom of the 258th frame) for JmolData.jar? > >As a work-around, the following syntax for getproperty places the >vibvector for EVERY 16th atom of EVERY frame in an array in JmolData.jar: > >c_index=16 >allcvibes=getproperty("atominfo.vibVector",{atomno=c_index}) > >Is there a better way to specify a particular atom of a particular >frame/model in JmolData.jar? > >Matt Kubasik >Department of Chemistry and Biochemistry >Fairfield University > >PS Getproperty "modelinfo" seems to work equally well in either Jmol.jar >or JmolData.jar. E.g., the following works the same in both: >freq=getproperty("modelinfo.models["+framenum+"].modelProperties.Frequency >"); > > >Details: >Jmol Version: 12.3.31 2012-06-16 00:04 >java.vendor: Apple Inc. >java.version: 1.6.0_31 >os.name: Mac OS X >Access: ALL >memory: 11.3/85.0 > > >-------------------------------------------------------------------------- >---- >Live Security Virtual Conference >Exclusive live event will cover all the ways today's security and >threat landscape has changed and how IT managers can respond. Discussions >will include endpoint security, mobile security and the latest in malware >threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >_______________________________________________ >Jmol-users mailing list >[email protected] >https://lists.sourceforge.net/lists/listinfo/jmol-users ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
