Hello. I found the Avogadro tool and it’s amazingly good, thank you to the developers!
I am using Avogadro to visualize my atomic configurations obtained with LAMMPS and other molecular dynamics tools. I have a noob question: How do I add a simple text box near my crystal, so I can export an eps picture ready for publication?
Thanks and glad it’s helpful. At the moment, Avogadro does not have capabilities to add text boxes, etc.
I’d suggest using Inkscape, etc. to add labels as needed.
Thank you for the suggestion @ghutchis. Unfortunately, the 20 MB eps file generated by Avogadro takes forever to open in Inkscape on my i7-6500U…
The most frequently met causes for such a large .eps are: a) there are really many of atoms in the picture, b) the .eps includes the complete definition of those atoms and bonds behind other objects, thus invisible (equally known as the painter’s problem), or c) the .eps is used as a container for bitmap data.
If it has to be this very visual representation, the import into Inkscape (or other programs) as a .pdf instead of a .(e)ps may be an option; by volume, it is a less large file. ps2pdf (e.g., in Linux) or epspdf (for Windows, from CTAN) are examples to offer such a conversion.
An alternative may be to use e.g., molekel for the image generation. In addition to .png snap shoots, .eps and .pdf may be exported as true vector images. I.e., you may remove and alter the background in Inkscape because it is in a different layer than the molecules which consists of polygons, remove guide lines seen in the preview, etc.
For this, the small Windows XP 32-bit engine often is sufficient (download approx. 80 MB) which, e.g. in Linux Xubuntu 18.04 LTS, is supported well by wine. But the program is cross-platform and the source code public.
(Sadly, the current settings of the discussion interface do not allow to upload an example .pdf, or .zip.)
No, but you can post links to e.g., Google Drive, Dropbox, etc.
Since we can’t easily scan attachments like PDF or ZIP for security / viruses, we won’t be allowing general attachments, whereas services like Google Drive, Dropbox, etc. usually do.
@ghutchis Thank you very much for the prompt reply. Yes, I have a lot of atoms, and this representation is important. I ended up converting the obtained eps into png with a large resolution, then edited with GIMP, then converted back into eps (as this is required by the journal). I hope that such important option as a text box will be added to the code soon, because it’s the only obstacle for me to use Avogadro for everything.