Hi Martin, According to this open-access paper, the ConSurf web server https://consurf.tau.ac.il/ has been upgraded to provide ChimeraX sessions:

Using evolutionary data to make sense of macromolecules with a "face-lifted" ConSurf. Yariv B, Yariv E, Kessel A, Masrati G, Chorin AB, Martz E, Mayrose I, Pupko T, Ben-Tal N. Protein Sci. 2023 Mar;32(3):e4582. doi: 10.1002/pro.4582. PMID: 36718848 https://onlinelibrary.wiley.com/doi/10.1002/pro.4582

However, it appears that the ConSurf web server is down for maintenance right now, so I couldn't try it.

Regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Dec 4, 2023, at 7:04 AM, martin.brehm--- via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:

Dear ChimeraX developers,

I have a question regarding a potential upgrade of ChimeraX. Would it be possible to include the functionality of ConSurf, a tool to plot the degree of sequence conservation onto a model, into ChimeraX? The code for this is publically available on GitHub: https://github.com/Rostlab/ConSurf See this publication for more information: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987940/ Thanks a lot in advance and have a nice day!

Best regards Martin Brehm

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Martin Brehm – PhD Student Falk Lab – Max Perutz Labs Vienna Room 1.624 – Phone +43 14277 74361 martin.brehm@univie.ac.at

I can confirm: I used the ConSurf server last February and got a ChimeraX session with the results. So they had added this feature before the paper was published.

Guillaume

On 4 Dec 2023, at 19:02, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> wrote:

Looking at my older notes, I believe I did try their web server back in March 2023 when I first saw this paper, but the download was a Chimera session (not ChimeraX) at that time and their "contact us" webform didn't work. I don't know if they changed the server to really provide a ChimeraX session since then, or if it was a mistake in the paper.

Elaine

On Dec 4, 2023, at 9:55 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> wrote:

Hi Martin, According to this open-access paper, the ConSurf web server https://consurf.tau.ac.il/ has been upgraded to provide ChimeraX sessions:

Using evolutionary data to make sense of macromolecules with a "face-lifted" ConSurf. Yariv B, Yariv E, Kessel A, Masrati G, Chorin AB, Martz E, Mayrose I, Pupko T, Ben-Tal N. Protein Sci. 2023 Mar;32(3):e4582. doi: 10.1002/pro.4582. PMID: 36718848 https://onlinelibrary.wiley.com/doi/10.1002/pro.4582

However, it appears that the ConSurf web server is down for maintenance right now, so I couldn't try it.

Regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Dec 4, 2023, at 7:04 AM, martin.brehm--- via ChimeraX-users <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> wrote:

Dear ChimeraX developers,

I have a question regarding a potential upgrade of ChimeraX. Would it be possible to include the functionality of ConSurf, a tool to plot the degree of sequence conservation onto a model, into ChimeraX? The code for this is publically available on GitHub: https://github.com/Rostlab/ConSurf See this publication for more information: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987940/ Thanks a lot in advance and have a nice day!

Best regards Martin Brehm

<image001.png>

Martin Brehm – PhD Student Falk Lab – Max Perutz Labs Vienna Room 1.624 – Phone +43 14277 74361 martin.brehm@univie.ac.atmailto:martin.brehm@univie.ac.at

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Hi Martin, In case you didn't already know, ChimeraX itself has several options for computing conservation (in turn provided by the AL2CO program included with ChimeraX) from a multiple sequence alignment, and these conservation values can be used to color any structure associated with that sequence alignment. We have a tutorial on coloring by conservation using ChimeraX, with three different examples:

https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/conservation-coloring.html

See also Sequence Viewer documentation in the User Guide: https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#headers

However, unlike ConSurf, ChimeraX does not automatically generate the sequence alignment for you. There are many ways to obtain a sequence alignment completely separate of ChimeraX, and you could save that as a file and open it in ChimeraX, which understands several sequence alignment file formats:

https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#sequence

Alternatively, it is possible to generate the sequence alignment entirely within ChimeraX (although that may not be the best way to get a representative set of sequences) using the ChimeraX Blast Protein tool, and then choosing which set of hits from the Blast results to open as a multiple sequence alignment. https://rbvi.ucsf.edu/chimerax/docs/user/tools/blastprotein.html

Some years ago I wrote an informal summary of several ways to get a multiple sequence alignment for use in Chimera or ChimeraX:

https://www.rbvi.ucsf.edu/home/meng/sources.html

I haven't checked all the links for a while, so some of them may be out of date. It includes the Blast approach, but using Chimera. Now ChimeraX also has a Blast Protein tool; the steps would be similar as outlined, although not identical.

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Dec 5, 2023, at 1:08 PM, Eric Pettersen via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:

Hi Martin, I don't think including ConSurf directly in ChimeraX is feasible. The source code seems to be oriented for server use and likely only compiles on Linux. It also requires multiple additional packages (including Perl) with various licenses and compilation needs of their own. It also requires the installation of the SwissProt and TrEMBL databases. The latter is 58GB compressed. So I think I'm going to hold out for the ConSurf website to come back online. :-) Unfortunately the message the site gives today says it has been down since mid-September due to "serious security problems", but that nonetheless they are working on getting it back online.

--Eric

Eric Pettersen UCSF Computer Graphics Lab

...

On Dec 4, 2023, at 7:04 AM, martin.brehm--- via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:

Dear ChimeraX developers,

I have a question regarding a potential upgrade of ChimeraX. Would it be possible to include the functionality of ConSurf, a tool to plot the degree of sequence conservation onto a model, into ChimeraX? The code for this is publically available on GitHub: https://github.com/Rostlab/ConSurf See this publication for more information: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987940/ Thanks a lot in advance and have a nice day!

Best regards Martin Brehm