Double and triple bond sticks
Dear ChimeraX, Greetings from Australia. I use ChimeraX animations to teach elementary school children how food is converted into the CO₂ we exhale, so: A) thank you for this invaluable resource B) is there any way to display double and triple bonds? And, if not, are you planning to add this feature in future versions? C) apologies for repeating this question - originally asked by Chase Smith (28 November 2019) - but I couldn’t find a response Many thanks in advance, Ruben ______________________ Ruben Meerman M: 0414 680 271 E: rubenmeerman@me.com
Greetings Ruben! Ah, I see the response was in the next month... apparently the archive doesn't connect the threads across month boundaries: <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2019-December/000734.html> As far as I know, the answer is still the same. Alas, our manpower is fairly limited these days. We are excited to hear you are using ChimeraX to teach elementary school children! Carbohydrate catabolism can be pretty advanced, but given the right visuals and level of detail, I'm sure you can teach them effectively. I can see how representing double and triple bonds would help to make the reactions clearer. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 13, 2021, at 8:24 PM, Ruben Meerman <rubenmeerman@me.com> wrote:
Dear ChimeraX,
Greetings from Australia.
I use ChimeraX animations to teach elementary school children how food is converted into the CO₂ we exhale, so:
A) thank you for this invaluable resource
B) is there any way to display double and triple bonds? And, if not, are you planning to add this feature in future versions?
C) apologies for repeating this question - originally asked by Chase Smith (28 November 2019) - but I couldn’t find a response
Many thanks in advance,
Ruben ______________________ Ruben Meerman M: 0414 680 271 E: rubenmeerman@me.com
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Ruben, Elaine is correct in that the answer is still the same right now. With yours being the second request, we will certainly put some thought into whether there is anything reasonable we can do here -- balanced against our other development priorities. I don't know whether this will be of any help to you, but you could make the double bonds visually identifiable by changing the bond thickness. I've attached an image of a small molecule where I've made the double bond twice as thick as the single bonds and aromatic bonds 1.5 times as thick. You can change bond thickness/radius with the "size" command. Bonds normally have a radius of .2 (angstroms). To make the image I first set all bond radii to .1 with: size #1 stick .1 Then I used the mouse to select the double bond and set it to .2 with: size sel stick .2 Then I set all aromatic bonds to .15 with: size aromatic stick .15 --Eric Eric Pettersen UCSF Computer Graphics Lab
On Feb 14, 2021, at 10:29 AM, Elaine Meng <meng@cgl.ucsf.EDU> wrote:
Greetings Ruben! Ah, I see the response was in the next month... apparently the archive doesn't connect the threads across month boundaries:
<https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2019-December/000734.html>
As far as I know, the answer is still the same. Alas, our manpower is fairly limited these days.
We are excited to hear you are using ChimeraX to teach elementary school children! Carbohydrate catabolism can be pretty advanced, but given the right visuals and level of detail, I'm sure you can teach them effectively. I can see how representing double and triple bonds would help to make the reactions clearer.
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 13, 2021, at 8:24 PM, Ruben Meerman <rubenmeerman@me.com> wrote:
Dear ChimeraX,
Greetings from Australia.
I use ChimeraX animations to teach elementary school children how food is converted into the CO₂ we exhale, so:
A) thank you for this invaluable resource
B) is there any way to display double and triple bonds? And, if not, are you planning to add this feature in future versions?
C) apologies for repeating this question - originally asked by Chase Smith (28 November 2019) - but I couldn’t find a response
Many thanks in advance,
Ruben ______________________ Ruben Meerman M: 0414 680 271 E: rubenmeerman@me.com
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (3)
-
Elaine Meng -
Eric Pettersen -
Ruben Meerman