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Trouble with hooks in chemfig
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up vote
4
down vote
favorite
I am trying to construct this EDTA molecule coordinated to a metal:
and this is what I have so far:
With this code:
chemfig
O=[2,,]C
(-[3,2,,1]CH_2-[1,,1]N
(-[7,,,2]H_2C-[0,,]C
(=[7,,]O)
(-[1,,]O^-))
(-[4,,,2]H_2C-[2,,2,2]H_2C-[0,,]N
(-[1,,,2]H_2C-[0,,2]C
(=[1,,]O)
(-[7,,]O^-))
(-[3,,,2]H_2C-[1,2,2]C
(=[2,,]O)
(-[7,,]O^-))))
(-[1,,]O^-)
What I can't figure out how to do is include the metal in the center. I know I have to use hooks somehow but I don't know where to start. Would I have to start over and begin the figure at the metal?
Bonus question: how do I change the color of the bonds to the metal?
chemfig
asked 2 hours ago
Antidisestablishmentarianism
806
add a comment |Â
up vote
4
down vote
favorite
I am trying to construct this EDTA molecule coordinated to a metal:
and this is what I have so far:
With this code:
chemfig
O=[2,,]C
(-[3,2,,1]CH_2-[1,,1]N
(-[7,,,2]H_2C-[0,,]C
(=[7,,]O)
(-[1,,]O^-))
(-[4,,,2]H_2C-[2,,2,2]H_2C-[0,,]N
(-[1,,,2]H_2C-[0,,2]C
(=[1,,]O)
(-[7,,]O^-))
(-[3,,,2]H_2C-[1,2,2]C
(=[2,,]O)
(-[7,,]O^-))))
(-[1,,]O^-)
What I can't figure out how to do is include the metal in the center. I know I have to use hooks somehow but I don't know where to start. Would I have to start over and begin the figure at the metal?
Bonus question: how do I change the color of the bonds to the metal?
chemfig
asked 2 hours ago
Antidisestablishmentarianism
806
add a comment |Â
up vote
4
down vote
favorite
up vote
4
down vote
favorite
I am trying to construct this EDTA molecule coordinated to a metal:
and this is what I have so far:
With this code:
chemfig
O=[2,,]C
(-[3,2,,1]CH_2-[1,,1]N
(-[7,,,2]H_2C-[0,,]C
(=[7,,]O)
(-[1,,]O^-))
(-[4,,,2]H_2C-[2,,2,2]H_2C-[0,,]N
(-[1,,,2]H_2C-[0,,2]C
(=[1,,]O)
(-[7,,]O^-))
(-[3,,,2]H_2C-[1,2,2]C
(=[2,,]O)
(-[7,,]O^-))))
(-[1,,]O^-)
What I can't figure out how to do is include the metal in the center. I know I have to use hooks somehow but I don't know where to start. Would I have to start over and begin the figure at the metal?
Bonus question: how do I change the color of the bonds to the metal?
chemfig
asked 2 hours ago
Antidisestablishmentarianism
806
I am trying to construct this EDTA molecule coordinated to a metal:
and this is what I have so far:
With this code:
chemfig
O=[2,,]C
(-[3,2,,1]CH_2-[1,,1]N
(-[7,,,2]H_2C-[0,,]C
(=[7,,]O)
(-[1,,]O^-))
(-[4,,,2]H_2C-[2,,2,2]H_2C-[0,,]N
(-[1,,,2]H_2C-[0,,2]C
(=[1,,]O)
(-[7,,]O^-))
(-[3,,,2]H_2C-[1,2,2]C
(=[2,,]O)
(-[7,,]O^-))))
(-[1,,]O^-)
What I can't figure out how to do is include the metal in the center. I know I have to use hooks somehow but I don't know where to start. Would I have to start over and begin the figure at the metal?
Bonus question: how do I change the color of the bonds to the metal?
chemfig
chemfig
asked 2 hours ago
Antidisestablishmentarianism
806
asked 2 hours ago
Antidisestablishmentarianism
806
asked 2 hours ago
Antidisestablishmentarianism
806
asked 2 hours ago
Antidisestablishmentarianism
806
asked 2 hours ago
Antidisestablishmentarianism
806
806
add a comment |Â
add a comment |Â
1 Answer
1
active
oldest
votes
up vote
3
down vote
accepted
Placing the M is rather straightforward: use chemmove, which produces an overlay tikzpicture and then e.g. the calc syntax. What I find more difficult is to reproduce the bond styles. I ended up looking up the definitions and then to repeat what I think they do. (EDIT: Minor fine-tuning, big thanks to AndréC for pushing me.)
documentclassarticle
usepackagechemfig
usetikzlibrarycalc
begindocument
chemfig
O=[2,,]C
(-[3,1.8,,1]CH_2-[1,,1]@N1N
(-[7,,,2]H_2C-[0,,]@C1C
(=[7,,]O)
(-[1,,]@OM1O^-))
(-[4,,,2]H_2C-[2,,2,2]H_2C-[0,,]@N2N
(-[1,,,2]H_2C-[0,,2]@C2C
(=[1,,]O)
(-[7,,]@OM2O^-))
(-[3,1.2,,2]H_2C-[1,2,2]C
(=[2,,]O)
(-[7,,]@OM3O^-))))
(-[1,,]@OM4O^-)
chemmove[brown!70!black]%
node (M) at ($(OM1)!0.5!(N2)$) M;
fill let p1=($(M)-(OM1)$),n1=atan2(y1,x1) in
($(OM1.n1)!1mm!(M)$) coordinate (aux1) (M) --
($ (aux1)!1mm!90:(M) $) -- ($ (aux1)!1mm!-90:(M) $)
-- cycle;
fill let p1=($(M)-(N1)$),n1=atan2(y1,x1) in
($(N1.n1)!1mm!(M)$) coordinate (aux2)
(M) --
($ (aux2)!1mm!90:(M) $) -- ($ (aux2)!1mm!-90:(M) $)
-- cycle;
draw[thick,-,shorten >=1mm] (M) to (OM3.south -
enddocument
answered 38 mins ago
marmot
68.2k475147
The vertical line from one O- to the other is not well centered, it is slightly too far to the left.
– AndréC
33 mins ago
@AndréC One can either have a vertical line or a centered line in the OP's setup. If one makes the C--H_2C lines a bit longer, it is better centered.
– marmot
31 mins ago
Unfortunately I can't get this to work properly. Can this be used in a figure environment?
– Antidisestablishmentarianism
20 mins ago
+1, perfect now!
– AndréC
19 mins ago
1
@Antidisestablishmentarianism You have to compile twice to get the right placement!
– AndréC
18 mins ago
 |Â
show 1 more comment
1 Answer
1
active
oldest
votes
1 Answer
1
active
oldest
votes
active
oldest
votes
active
oldest
votes
up vote
3
down vote
accepted
Placing the M is rather straightforward: use chemmove, which produces an overlay tikzpicture and then e.g. the calc syntax. What I find more difficult is to reproduce the bond styles. I ended up looking up the definitions and then to repeat what I think they do. (EDIT: Minor fine-tuning, big thanks to AndréC for pushing me.)
documentclassarticle
usepackagechemfig
usetikzlibrarycalc
begindocument
chemfig
O=[2,,]C
(-[3,1.8,,1]CH_2-[1,,1]@N1N
(-[7,,,2]H_2C-[0,,]@C1C
(=[7,,]O)
(-[1,,]@OM1O^-))
(-[4,,,2]H_2C-[2,,2,2]H_2C-[0,,]@N2N
(-[1,,,2]H_2C-[0,,2]@C2C
(=[1,,]O)
(-[7,,]@OM2O^-))
(-[3,1.2,,2]H_2C-[1,2,2]C
(=[2,,]O)
(-[7,,]@OM3O^-))))
(-[1,,]@OM4O^-)
chemmove[brown!70!black]%
node (M) at ($(OM1)!0.5!(N2)$) M;
fill let p1=($(M)-(OM1)$),n1=atan2(y1,x1) in
($(OM1.n1)!1mm!(M)$) coordinate (aux1) (M) --
($ (aux1)!1mm!90:(M) $) -- ($ (aux1)!1mm!-90:(M) $)
-- cycle;
fill let p1=($(M)-(N1)$),n1=atan2(y1,x1) in
($(N1.n1)!1mm!(M)$) coordinate (aux2)
(M) --
($ (aux2)!1mm!90:(M) $) -- ($ (aux2)!1mm!-90:(M) $)
-- cycle;
draw[thick,-,shorten >=1mm] (M) to (OM3.south -
enddocument
answered 38 mins ago
marmot
68.2k475147
The vertical line from one O- to the other is not well centered, it is slightly too far to the left.
– AndréC
33 mins ago
@AndréC One can either have a vertical line or a centered line in the OP's setup. If one makes the C--H_2C lines a bit longer, it is better centered.
– marmot
31 mins ago
Unfortunately I can't get this to work properly. Can this be used in a figure environment?
– Antidisestablishmentarianism
20 mins ago
+1, perfect now!
– AndréC
19 mins ago
1
@Antidisestablishmentarianism You have to compile twice to get the right placement!
– AndréC
18 mins ago
 |Â
show 1 more comment
up vote
3
down vote
accepted
Placing the M is rather straightforward: use chemmove, which produces an overlay tikzpicture and then e.g. the calc syntax. What I find more difficult is to reproduce the bond styles. I ended up looking up the definitions and then to repeat what I think they do. (EDIT: Minor fine-tuning, big thanks to AndréC for pushing me.)
documentclassarticle
usepackagechemfig
usetikzlibrarycalc
begindocument
chemfig
O=[2,,]C
(-[3,1.8,,1]CH_2-[1,,1]@N1N
(-[7,,,2]H_2C-[0,,]@C1C
(=[7,,]O)
(-[1,,]@OM1O^-))
(-[4,,,2]H_2C-[2,,2,2]H_2C-[0,,]@N2N
(-[1,,,2]H_2C-[0,,2]@C2C
(=[1,,]O)
(-[7,,]@OM2O^-))
(-[3,1.2,,2]H_2C-[1,2,2]C
(=[2,,]O)
(-[7,,]@OM3O^-))))
(-[1,,]@OM4O^-)
chemmove[brown!70!black]%
node (M) at ($(OM1)!0.5!(N2)$) M;
fill let p1=($(M)-(OM1)$),n1=atan2(y1,x1) in
($(OM1.n1)!1mm!(M)$) coordinate (aux1) (M) --
($ (aux1)!1mm!90:(M) $) -- ($ (aux1)!1mm!-90:(M) $)
-- cycle;
fill let p1=($(M)-(N1)$),n1=atan2(y1,x1) in
($(N1.n1)!1mm!(M)$) coordinate (aux2)
(M) --
($ (aux2)!1mm!90:(M) $) -- ($ (aux2)!1mm!-90:(M) $)
-- cycle;
draw[thick,-,shorten >=1mm] (M) to (OM3.south -
enddocument
answered 38 mins ago
marmot
68.2k475147
The vertical line from one O- to the other is not well centered, it is slightly too far to the left.
– AndréC
33 mins ago
@AndréC One can either have a vertical line or a centered line in the OP's setup. If one makes the C--H_2C lines a bit longer, it is better centered.
– marmot
31 mins ago
Unfortunately I can't get this to work properly. Can this be used in a figure environment?
– Antidisestablishmentarianism
20 mins ago
+1, perfect now!
– AndréC
19 mins ago
1
@Antidisestablishmentarianism You have to compile twice to get the right placement!
– AndréC
18 mins ago
 |Â
show 1 more comment
up vote
3
down vote
accepted
up vote
3
down vote
accepted
Placing the M is rather straightforward: use chemmove, which produces an overlay tikzpicture and then e.g. the calc syntax. What I find more difficult is to reproduce the bond styles. I ended up looking up the definitions and then to repeat what I think they do. (EDIT: Minor fine-tuning, big thanks to AndréC for pushing me.)
documentclassarticle
usepackagechemfig
usetikzlibrarycalc
begindocument
chemfig
O=[2,,]C
(-[3,1.8,,1]CH_2-[1,,1]@N1N
(-[7,,,2]H_2C-[0,,]@C1C
(=[7,,]O)
(-[1,,]@OM1O^-))
(-[4,,,2]H_2C-[2,,2,2]H_2C-[0,,]@N2N
(-[1,,,2]H_2C-[0,,2]@C2C
(=[1,,]O)
(-[7,,]@OM2O^-))
(-[3,1.2,,2]H_2C-[1,2,2]C
(=[2,,]O)
(-[7,,]@OM3O^-))))
(-[1,,]@OM4O^-)
chemmove[brown!70!black]%
node (M) at ($(OM1)!0.5!(N2)$) M;
fill let p1=($(M)-(OM1)$),n1=atan2(y1,x1) in
($(OM1.n1)!1mm!(M)$) coordinate (aux1) (M) --
($ (aux1)!1mm!90:(M) $) -- ($ (aux1)!1mm!-90:(M) $)
-- cycle;
fill let p1=($(M)-(N1)$),n1=atan2(y1,x1) in
($(N1.n1)!1mm!(M)$) coordinate (aux2)
(M) --
($ (aux2)!1mm!90:(M) $) -- ($ (aux2)!1mm!-90:(M) $)
-- cycle;
draw[thick,-,shorten >=1mm] (M) to (OM3.south -
enddocument
answered 38 mins ago
marmot
68.2k475147
Placing the M is rather straightforward: use chemmove, which produces an overlay tikzpicture and then e.g. the calc syntax. What I find more difficult is to reproduce the bond styles. I ended up looking up the definitions and then to repeat what I think they do. (EDIT: Minor fine-tuning, big thanks to AndréC for pushing me.)
documentclassarticle
usepackagechemfig
usetikzlibrarycalc
begindocument
chemfig
O=[2,,]C
(-[3,1.8,,1]CH_2-[1,,1]@N1N
(-[7,,,2]H_2C-[0,,]@C1C
(=[7,,]O)
(-[1,,]@OM1O^-))
(-[4,,,2]H_2C-[2,,2,2]H_2C-[0,,]@N2N
(-[1,,,2]H_2C-[0,,2]@C2C
(=[1,,]O)
(-[7,,]@OM2O^-))
(-[3,1.2,,2]H_2C-[1,2,2]C
(=[2,,]O)
(-[7,,]@OM3O^-))))
(-[1,,]@OM4O^-)
chemmove[brown!70!black]%
node (M) at ($(OM1)!0.5!(N2)$) M;
fill let p1=($(M)-(OM1)$),n1=atan2(y1,x1) in
($(OM1.n1)!1mm!(M)$) coordinate (aux1) (M) --
($ (aux1)!1mm!90:(M) $) -- ($ (aux1)!1mm!-90:(M) $)
-- cycle;
fill let p1=($(M)-(N1)$),n1=atan2(y1,x1) in
($(N1.n1)!1mm!(M)$) coordinate (aux2)
(M) --
($ (aux2)!1mm!90:(M) $) -- ($ (aux2)!1mm!-90:(M) $)
-- cycle;
draw[thick,-,shorten >=1mm] (M) to (OM3.south -
enddocument
answered 38 mins ago
marmot
68.2k475147
edited 23 mins ago
answered 38 mins ago
marmot
68.2k475147
answered 38 mins ago
marmot
68.2k475147
answered 38 mins ago
marmot
68.2k475147
68.2k475147
The vertical line from one O- to the other is not well centered, it is slightly too far to the left.
– AndréC
33 mins ago
@AndréC One can either have a vertical line or a centered line in the OP's setup. If one makes the C--H_2C lines a bit longer, it is better centered.
– marmot
31 mins ago
Unfortunately I can't get this to work properly. Can this be used in a figure environment?
– Antidisestablishmentarianism
20 mins ago
+1, perfect now!
– AndréC
19 mins ago
1
@Antidisestablishmentarianism You have to compile twice to get the right placement!
– AndréC
18 mins ago
 |Â
show 1 more comment
The vertical line from one O- to the other is not well centered, it is slightly too far to the left.
– AndréC
33 mins ago
@AndréC One can either have a vertical line or a centered line in the OP's setup. If one makes the C--H_2C lines a bit longer, it is better centered.
– marmot
31 mins ago
Unfortunately I can't get this to work properly. Can this be used in a figure environment?
– Antidisestablishmentarianism
20 mins ago
+1, perfect now!
– AndréC
19 mins ago
1
@Antidisestablishmentarianism You have to compile twice to get the right placement!
– AndréC
18 mins ago
The vertical line from one O- to the other is not well centered, it is slightly too far to the left.
– AndréC
33 mins ago
The vertical line from one O- to the other is not well centered, it is slightly too far to the left.
– AndréC
33 mins ago
@AndréC One can either have a vertical line or a centered line in the OP's setup. If one makes the C--H_2C lines a bit longer, it is better centered.
– marmot
31 mins ago
@AndréC One can either have a vertical line or a centered line in the OP's setup. If one makes the C--H_2C lines a bit longer, it is better centered.
– marmot
31 mins ago
Unfortunately I can't get this to work properly. Can this be used in a figure environment?
– Antidisestablishmentarianism
20 mins ago
Unfortunately I can't get this to work properly. Can this be used in a figure environment?
– Antidisestablishmentarianism
20 mins ago
+1, perfect now!
– AndréC
19 mins ago
+1, perfect now!
– AndréC
19 mins ago
1
1
@Antidisestablishmentarianism You have to compile twice to get the right placement!
– AndréC
18 mins ago
@Antidisestablishmentarianism You have to compile twice to get the right placement!
– AndréC
18 mins ago
 |Â
show 1 more comment
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