How do i draw ions and polymers?

General Discussion
1

is there a way to denote ions in a molecule or by themselves? is there a way
to denote charges on atoms?

also, how do i draw a polymer? is there a way to draw the traditional
(monomer)n notation or to display several monomers as a chain? i tried
playing with the unit cell option and i am able to create a chain or even a
surface covered with carbon copy repeats of a monomer, BUT there is no way
for me to connect them so they look like a polymer.

Thank you,
bobby

2

On Fri, Jun 25, 2010 at 4:26 AM, Claudiu Bucur h2sammo@gmail.com wrote:

is there a way to denote ions in a molecule or by themselves? is there a way
to denote charges on atoms?

Charges can be changed using View > Properties > Atom Properties…
This gives an editable table including formal and partial changes

also, how do i draw a polymer? is there a way to draw the traditional
(monomer)n notation or to display several monomers as a chain? i tried
playing with the unit cell option and i am able to create a chain or even a
surface covered with carbon copy repeats of a monomer, BUT there is no way
for me to connect them so they look like a polymer.

I don’t think this is currently supported.

Thank you,
bobby

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3

what is the purpose of the unit cell?

Claudiu Bucur, PhD
USDA-NCAUR
850-566-1562

http://www.linkedin.com/in/claudiubucur

On Fri, Jun 25, 2010 at 4:47 AM, Tim Vandermeersch <
tim.vandermeersch@gmail.com> wrote:

On Fri, Jun 25, 2010 at 4:26 AM, Claudiu Bucur h2sammo@gmail.com wrote:

is there a way to denote ions in a molecule or by themselves? is there a
way
to denote charges on atoms?

Charges can be changed using View > Properties > Atom Properties…
This gives an editable table including formal and partial changes

also, how do i draw a polymer? is there a way to draw the traditional
(monomer)n notation or to display several monomers as a chain? i tried
playing with the unit cell option and i am able to create a chain or
even a
surface covered with carbon copy repeats of a monomer, BUT there is no
way
for me to connect them so they look like a polymer.

I don’t think this is currently supported.

Thank you,
bobby

ThinkGeek and WIRED’s GeekDad team up for the Ultimate
GeekDad Father’s Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit. See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo

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4

what is the purpose of the unit cell?

The purpose of the unit cell is to draw crystalline materials. This does include polymers, but what Tim was saying is that at the moment, Avogadro does not have code to draw bonds across unit cell boundaries. (Consider that in most inorganic crystals, bonding is not shown. We’ve tried to stick to the 20% of the features that people use 80% of the time, and slowly add more features like you describe.)

You can use the unit cell feature to create “supercells” (i.e., magnify a few monomers into a large polymer. This will create new bonds as needed between monomers.

Hope that helps,
-Geoff

5

Thank you for response. In a previous post however, I have been told
linking monomers across unit cells is not supported yet. I have played
with thus but have been able to link identical monomers from cell to
cell. If this is possible please give me a few hints on how to do it.
I would think there are a lot of scientists willing to draw polymers
and related other than DNA or peptide chains which seems to be very
well supported thus far :).

Claudiu B. Bucur, PhD
(850) 566-1562

Sent from my iPhone

On Jun 28, 2010, at 11:06 AM, Geoffrey Hutchison <geoff.hutchison@gmail.com

wrote:

what is the purpose of the unit cell?

The purpose of the unit cell is to draw crystalline materials. This
does include polymers, but what Tim was saying is that at the
moment, Avogadro does not have code to draw bonds across unit cell
boundaries. (Consider that in most inorganic crystals, bonding is
not shown. We’ve tried to stick to the 20% of the features that
people use 80% of the time, and slowly add more features like you
describe.)

You can use the unit cell feature to create “supercells” (i.e.,
magnify a few monomers into a large polymer. This will create new
bonds as needed between monomers.

Hope that helps,
-Geoff

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