Avogadro2 Rev. 1.98.1

Is there any way to include the INset Peptide function in the Build of the Avogadro2 Rev. 1.98.1 like it is in Avogadro1 Rev. 1.2.0?
This would make it a lot easier when Building Custom peptides when you already have the Fasta that can be copied and inserted into the “Insert Peptide” window versus having to click on each one. Just a thought as you finish the development on Avogadro 2.0.
I also agree that being able to add the Word “Atom” before the x,y,z coordinates would be great, but even better would be adding the peptide/amino acid Fasta name for each amino acid be added to the x,y,z coordinates. Like the protein PDB from the protein data base.

There’s a feature request for this: Peptide builder command · Issue #910 · OpenChemistry/avogadrolibs · GitHub

It’s also on the roadmap although I’m not sure if it will be completed for 1.99. In the meantime, I’d recommend downloading and installing the PyPept plugin (e.g., Extensions ⇒ Download) which will insert FASTA sequences.

Can you be a bit more specific or sketch what you have in mind? I’m not sure I follow either of these points.

This is what I’m referring to, which may be more difficult to do… that is to have the Cartesian Editor display more in line with the PDB format, i.e.,:
ATOM 110 HB2 ASP N 7 42.590 80.542 47.776 1.00 83.87 H

You can submit a feature request … but you can also export as a PDB file.

I’m not sure adding that option is high on my personal To Do list because the PDB format is … weird to say the least (e.g., getting the columns exactly right), and explicitly deprecated by PDB in favor of PDBx / mmCIF and MMTF.

On the other hand, if someone submits a patch, or is willing to help, I’m happy to point them to the appropriate areas of the code to add that support.

Happy Holidays Geoff… and Happy New Year! Thank you for all that you and your team do…
Regarding your comment about being able to Export as a PDB File. I am not able to find this Function in the Export List… Is it under a different function name?

File ⇒ Export ⇒ Molecule… then set the filename to e.g., file.pdb

I’ll be honest that I don’t know how much of the residue / chain / atom name data is exported. (I don’t do much in the way of biomolecule simulation.)

The current “export to PDB” is through Open Babel. Please feel free to open a feature request for native PDB export.

Good morning Geoff…
Thank you for the quick response.
Wishing you and yours a very Happy New Year! Along with good health and prosperity and continued success…