# Homopolymers build

**URL:** <https://discuss.avogadro.cc/t/homopolymers-build/4150>\
**Category:** Support\
**Created:** [January 4, 2023, 1:41pm UTC](https://discuss.avogadro.cc/t/homopolymers-build/4150 "2023-01-04T13:41:08Z")\
**Posts on this page:** 1\
**Showing post:** 2

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**Author:** ![Thomas](https://discuss.avogadro.cc/user_avatar/discuss.avogadro.cc/thomas/32/3403_2.png) [@Thomas](https://discuss.avogadro.cc/u/Thomas)\
**Post date:** [January 4, 2023, 8:22pm UTC](https://discuss.avogadro.cc/t/homopolymers-build/4150/2 "2023-01-04T20:22:10Z")

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There is [entry 20719176](https://pubchem.ncbi.nlm.nih.gov/compound/epsilon-Polylysine) of [PubChem](https://pubchem.ncbi.nlm.nih.gov/), an open access database provided by the National Institute of Health/NIH. Go to [section 1.2](https://pubchem.ncbi.nlm.nih.gov/compound/epsilon-Polylysine#section=3D-Conformer)

 ![section_01](https://discuss.avogadro.cc/uploads/default/original/2X/5/50e941d8a01eeb27fa02421a646d36cc0b153443.png)

and click in the top right corner (marked above): one option allows you to save a `.sdf` file locally you eventually may read e.g., with Avogadro.

With a running instance of Avogadro, choose `Ctrl + O` (or in the GUI of Avogadro, File → Open) to read this file just saved. Avogadro will ask you how to process this input; in the intermediate interface, choose `Avogadro: MDL` as file reader, and confirm by `Enter`. On occasion, you have to tap once (left mouse button) on Avogadro’s canvas to complete the display of the newly accessed model.

If not already selected (typically left hand side of the GUI), you may choose the representation of a ball-stick models:

 ![display_types](https://discuss.avogadro.cc/uploads/default/original/2X/8/8c94a46cad63a19fa2626196f8b7771c04bb6d03.png)

(In case you got a model which still is flat-2D, you have to run a quick, computationally affordable geometry optimization. There are two way to launch this: either by pressing `Ctrl + Alt + O` simultaneously as a shortcut, or – using the GUI – by mouse clicking on Extensions → OpenBabel → Optimize Geometry to yield one plausible conformer. Usually, the geometry assigned by NIH however is retained, and this extra step is not necessary.) And this should offer you the model of a monomer of ε-polylysine:

 ![complete](https://discuss.avogadro.cc/uploads/default/original/2X/f/f42b7471ce1ee9a698dc18f6fba90d173434bada.png)

edit: correction of the import of 2D/3D data.

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_[View the full topic](https://discuss.avogadro.cc/t/homopolymers-build/4150)._