Dear Angel Herráez,
I've found the answer really helpful but using magic word "jmolscript:"
as a second line one loose the possibility of multi models in a single
XYZ file feature which is very useful in analysis of phonon vibrations.
And there is no possibility to create supercell with command
load "" {2 2 2}
Anyway I've found there is possible to run script with -s key. So I can
prepare script which extracts the unitcell vectors from XYZ and run JMOL
with -s parameter. Thus this question is partly solved for me.
But the Single window mode is still a question. I'm using OpenBox as a
window manager and manager is not able to merge console and main window,
it "thinks" they are separate programs and rising jmol after it was
minimized restores console but not both main window and console. Running
JSmol in the browser does not seems acceptable also since I need main
menu to change distance units and other settings. Thus it seems the only
way is to put Jmol to separate virtual desktops and loop through them.
Thank you for all the efforts,
Eugene
On 05/29/2016 09:13 PM, Angel Herráez wrote:
> Hello Eugene
>
> You should better use the jmol-users list for this kind of questions. I am
> moving the discussion there.
>
>> I'm performing animating vibrations in crystal files in XYZ format which
>> is simple and well documented. But every time I'm loading the file I
>> should provide unit cell vectors by activating JMOL console in new
>> rising window and running the command like:
>>
>> load "" {1 1 1} UNITCELL
>> [4.2695378,0.0000000,0.0000000,2.1347689,3.6975282,0.0000000,0.0000000,0.0000000,8.0000006]
>>
>> Truly saying that is not very comfortable. Is it possible to ask JMOL
>> automatically run the JMOL command provided in XYZ file. Maybe some
>> specific word in the end of XYZ file like:
> Yes, that is possible. The magic word is "jmolscript:" and in the case of xyz
> files it must go in the second line. For details, please see
> http://wiki.jmol.org/index.php/File_formats/Scripting#Script_inline_within_a_
> molecular_coordinates_file
>
>
>> The other question related to JMOL interface. Is it possible to activate
>> console in the same window there the menu and structure showed (i.e.
>> single window mode). I'm always use console and switch between main
>> window and console makes me crazy :)
> I do not think there is a way to do that. The console uses a separate window,
> but you can resize them so both are visible side by side (and their position
> will be remembered for next time you start Jmol)
> You could set-up a web page that would contain a JSmol panel and a
> command line panel.
>
>
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