ChimeraX "color by conservation" tutorial
In case anyone is interested, there's a new tutorial on coloring by sequence conservation using ChimeraX (requires version 1.1 or newer). It has click-to-execute links if you view it in the ChimeraX built-in browser. <https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/conservation-c...> Happy holidays! Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
Thanks for this update Elaine. I’ll pass it on to those in the lab as well. Take care. Sean
On Dec 24, 2020, at 5:12 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
In case anyone is interested, there's a new tutorial on coloring by sequence conservation using ChimeraX (requires version 1.1 or newer). It has click-to-execute links if you view it in the ChimeraX built-in browser.
Happy holidays! Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
Dear Elaine, This is gorgeous, thanks a lot! ConSurf grades are easy to use here and easy to present. I love chimeraX is really.a big big improvement. The only thing is I tried to open https…. But it does not work for me, I can do the tutorial downloading the file, but not with open http.. command. Best, Fabian Fabian Glaser PhD Bioinformatics Knowledge Unit - BKU The Lorry I. Lokey Center for Life Sciences and Engineering Technion - Israel Institute of Technology, Haifa, Israel Web https://lokey.technion.ac.il/bioinformatic-knowledge-unit/ Tel +972 (0) 4 8293701
On 25 Dec 2020, at 0:12, Elaine Meng <meng@cgl.ucsf.edu> wrote:
In case anyone is interested, there's a new tutorial on coloring by sequence conservation using ChimeraX (requires version 1.1 or newer). It has click-to-execute links if you view it in the ChimeraX built-in browser.
<https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/conservation-c...>
Happy holidays! Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Fabian, Oops, I changed the location of the tutorial and forgot to update the open command inside the tutorial. I just fixed it, so thanks for letting me know! The command should instead be: open https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/conservation-c... (because that's where the tutorial is, <https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/conservation-c...>) In example 1, I used the Consurf sequence alignment to calculate values in ChimeraX (because the Consurf server is one good way to get alignments), but I agree it would also be useful to show the Consurf values directly. Thanks, Elaine
On Dec 29, 2020, at 1:16 AM, Fabian Glaser <fabian.glaser@gmail.com> wrote:
Dear Elaine,
This is gorgeous, thanks a lot! ConSurf grades are easy to use here and easy to present.
I love chimeraX is really.a big big improvement.
The only thing is I tried to open https…. But it does not work for me, I can do the tutorial downloading the file, but not with open http.. command.
Best,
Fabian
Fabian Glaser PhD
Bioinformatics Knowledge Unit - BKU The Lorry I. Lokey Center for Life Sciences and Engineering Technion - Israel Institute of Technology, Haifa, Israel Web https://lokey.technion.ac.il/bioinformatic-knowledge-unit/ Tel +972 (0) 4 8293701
On 25 Dec 2020, at 0:12, Elaine Meng <meng@cgl.ucsf.edu> wrote:
In case anyone is interested, there's a new tutorial on coloring by sequence conservation using ChimeraX (requires version 1.1 or newer). It has click-to-execute links if you view it in the ChimeraX built-in browser.
<https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/conservation-c...>
Happy holidays! Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
_______________________________________________ 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 -
Fabian Glaser -
Sean Moore