Avogadro Customization [SOLVED]

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Avogadro Customization [SOLVED]

Postby albert on Fri Feb 26, 2010 12:37 pm

I've installed the molecular visualization tool, Avogadro (0.9.7) and want to customize the labeling of individual atoms, however, when the settings, under label, is changed to "custom", nothing happens.
This is an extraordinary animation tool. It would be nice to find out how to change this setting. Or even the basics of the label file.
Last edited by albert on Wed May 19, 2010 1:13 pm, edited 1 time in total.
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Re: Avogadro Customization

Postby remoulder on Fri Feb 26, 2010 7:10 pm

Google or the apps homepage if it exists, is probably your best bet.
[Edit] your original post and add [SOLVED] once your question is resolved.

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Re: Avogadro Customization

Postby albert on Sat Feb 27, 2010 1:03 am

remoulder wrote:Google or the apps homepage if it exists, is probably your best bet.

Thank you for your suggestion.
Avogadro homepage is a wiki at http://avogadro.openmolecules.net/wiki/Main_Page . I am slowly making my way through its pages ... but so far I have been unable to find out why the custom label doesn't function.
I've also asked at the mailing list, avogadro-discuss @ lists.sourceforge.net, but haven't heard anything yet.
It also helps that I don't understand how to deal with the label file: is it a .so file; if yes, then how to deal with it? This may be it:
/usr/lib/avogadro/engines/labelengine.so
How do I open it? Do I need some supernatural programming abilities to deal with this file?
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Re: Avogadro Customization

Postby remoulder on Sat Feb 27, 2010 5:52 am

albert wrote:/usr/lib/avogadro/engines/labelengine.so


Sorry don't know anything about this particular application, but anything in /usr/lib is part of the application executable and probably shouldn't be touched. The .so file is a library, similar to a Windows .dll
[Edit] your original post and add [SOLVED] once your question is resolved.

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Re: Avogadro Customization

Postby albert on Sat Feb 27, 2010 10:35 am

Thanks. I won't touch those files.
I found some xml example files in the usr/share/doc but if these are modified then it screws up the results.
I guess I wait for them to fix it.
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Re: Avogadro Customization

Postby vortex59 on Sat Feb 27, 2010 11:44 am

Hello! You could try avogadro 1.0.0 from debichem repositories http://ppa.launchpad.net/debichem/ppa/ubuntu/ karmic main
I'm using it (you don't have to setup repositories, just download the deb files and dependencies which are in the same place) with no problem in Linux Mint x86_64.
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Re: Avogadro Customization

Postby albert on Sat Feb 27, 2010 11:56 am

Thanks. I downloaded it but perhaps you can tell me how I would install it. It's now sitting in my downloads folder.
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Re: Avogadro Customization

Postby albert on Sat Feb 27, 2010 12:15 pm

Im at http://ppa.launchpad.net/debichem/ppa/u ... /avogadro/ and I installed the 1.0.0 data file at the top of the list and downloaded the application .. help!! now A doesn't open
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Re: Avogadro Customization

Postby vortex59 on Sat Feb 27, 2010 1:55 pm

In the Mint distribution there is a utility gdebi which install everithing that has the *.deb extension. Usually is necessary only click on the deb file in file browser. This would tell you if some files are missing. Did you downloaded also libavogadro files?
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Re: Avogadro Customization

Postby remoulder on Sat Feb 27, 2010 1:56 pm

Thanks for stepping in vortex59.

albert, it's probably easier if you add the PPA to your sources, then you can install via synaptic and get updates when they're posted. To do this open Software Sources, go to the Other Software tab, click Add and enter ppa:debichem/ppa, click Add source, then Close. You'll be asked to reload so say yes. When finished open mintupdate and you should find there's an update to the version you have already installed.
[Edit] your original post and add [SOLVED] once your question is resolved.

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Re: Avogadro Customization

Postby vortex59 on Sat Feb 27, 2010 2:04 pm

You also need openbabel (translate different chemistry file types) installed and eigen2 (for some molecular mechanics optimizations I presume) both program and libraries. It's possible also to compile the program but you need more time and installations.
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Re: Avogadro Customization

Postby albert on Sat Feb 27, 2010 4:49 pm

remoulder wrote:Thanks for stepping in vortex59.

albert, it's probably easier if you add the PPA to your sources, then you can install via synaptic and get updates when they're posted. To do this open Software Sources, go to the Other Software tab, click Add and enter ppa:debichem/ppa, click Add source, then Close. You'll be asked to reload so say yes. When finished open mintupdate and you should find there's an update to the version you have already installed.


Ok. Done. Updated.
Thank you.

But I am still unable to use the custom data function on the label setting. That is, I would like to label individual atoms with custom data.
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Re: Avogadro Customization

Postby albert on Sat Feb 27, 2010 4:51 pm

vortex59 wrote:You also need openbabel (translate different chemistry file types) installed and eigen2 (for some molecular mechanics optimizations I presume) both program and libraries. It's possible also to compile the program but you need more time and installations.


Thnak you for your suggestion. I have installed as above, however, I am still unable to implement the custom label settings. I am hoping that I am not missing something in the procedure and thus wasting everyones time! My intention is to label each atom with custom text.
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Re: Avogadro Customization

Postby albert on Sat Feb 27, 2010 5:32 pm

I went to the label settings just now and selected the 'custom data' for atom labels; then went to the properties menu under the view menu and opened the atom properties table: I changed the element name to some custom text but then the 'Type' column autofilled to an X and then the 'Element' field followed and changed to an 'Xx', which displayed on the animation. So I guess that the element cannot be custom filled with anything other than a bona fide element name, such as H or C. But how to adjust this to allow custom names?
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Re: Avogadro Customization

Postby vortex59 on Sun Feb 28, 2010 7:29 am

Hi Albert!

I think the "Custom" field in "Label settings" in not yet useable. If you have programming skills you may look in the source files /avogadro-1.0.0/libavogadro/src/engines/ where there are three files labelengine.h, labelengine.cpp and labelsettingswidget.ui. I presume that if one can modify these files one may also activate in a way the Custom Label settings. But this also presume the recompilation of the sources. Maybe it's a better choice to try a dialog with the authors (http://avogadro.openmolecules.net/wiki/Main_Page).

Mihai
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Re: Avogadro Customization

Postby albert on Sun Feb 28, 2010 8:01 am

vortex59 wrote:Hi Albert!

I think the "Custom" field in "Label settings" in not yet useable. If you have programming skills you may look in the source files /avogadro-1.0.0/libavogadro/src/engines/ where there are three files labelengine.h, labelengine.cpp and labelsettingswidget.ui. I presume that if one can modify these files one may also activate in a way the Custom Label settings. But this also presume the recompilation of the sources. Maybe it's a better choice to try a dialog with the authors (http://avogadro.openmolecules.net/wiki/Main_Page).

Mihai


Once again, thank you for your help. I have followed your instructions and am awaiting the results.
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Re: Avogadro Customization

Postby albert on Wed May 19, 2010 1:12 pm

albert wrote:I've installed the molecular visualization tool, Avogadro (0.9.7) and want to customize the labeling of individual atoms, however, when the settings, under label, is changed to "custom", nothing happens.
This is an extraordinary animation tool. It would be nice to find out how to change this setting. Or even the basics of the label file.


This was recently implemented in the latest version, thanks to the diligent Avogadro developers.

In fact, the labeling menu is very comprehensive now.

Thanks Avogadro Dev team! :D
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Re: Avogadro Customization [SOLVED]

Postby remoulder on Wed May 19, 2010 1:47 pm

Glad you got everything working in the end. If there was anything special you had to do, perhaps you could write a tutorial in the Howto section to help any other users wanting to use this app?
[Edit] your original post and add [SOLVED] once your question is resolved.

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