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cryos / avogadro

Avogadro 1 is not under active development, the repository was archived in September 2021. Development of Avogadro 2 is being done at https://github.com/openchemistry/avogadrolibs. Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.
http://avogadro.cc/
GNU General Public License v2.0
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Minor bug for terminal serine peptides #551

Open cryos opened 14 years ago

cryos commented 14 years ago

When I use the peptide builder to build peptides with a C-terminal serine and save then as a pdb file, the residues names of the entire peptide go to UNK instead of the right names (... - ... - SER). I've built all dipeptide combinations and it happened in all of the ones with a terminal Ser.

Contact: pim.frederix@strath.ac.uk OS: Mac OS X 10.6.4

Reported by: *anonymous

cryos commented 14 years ago

Ile-Ser pdb file

Original comment by: nobody

cryos commented 14 years ago

I suspect OpenBabel bug here

Original comment by: @annulen

cryos commented 13 years ago

I agree. I'll add this to the OB test set and see if I can find the bug. Thanks pim!

Original comment by: @ghutchis

cryos commented 12 years ago

This should now be fixed fully in a new patch, which avoids calling OBChainsParser unless absolutely necessary. http://review.source.kitware.com/#/t/819

Original comment by: @ghutchis

cryos commented 12 years ago

Great, but how can I find and apply this patch? I have to make 400 structures with terminal serines, so I'd prefer to have this fixed before I start. Sorry for the trouble.

Original comment by: prinsf

cryos commented 12 years ago

Sorry, try one of the nightly unstable builds: http://avogadro.openmolecules.net/nightly/mac/unstable/

This has the patch "baked in" already -- it's compiled on my desktop every night.

Hope that helps, -Geoff

Original comment by: @ghutchis

cryos commented 12 years ago

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Original comment by: nobody

cryos commented 12 years ago

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Original comment by: nobody

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Original comment by: nobody