Hi David, Just to clarify, what ConSurf puts in the b-factor field are probably the ConSurf conservation values (not B-factor, not AlphaFold pLDDT confidence scores, etc.). Elaine
On Jul 29, 2024, at 11:50 AM, Eric Pettersen via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi David, Looking at a ChimeraX session created by ConSurf, it seems that it sets bfactors in the range 0-9, not 0-100 — which you can see with the Render By Attribute tool. So "hide @@bfactor<5 ribbon” might do what you want.
—Eric
On Jul 28, 2024, at 8:29 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi David, There is no option to call the ConSurf web service from inside ChimeraX (or Chimera), I just meant to ask whether you could display the output in ChimeraX. I didn't know the recent version of the ConSurf server provided ChimeraX sessions, so that is helpful, thanks!
You would have to talk to the ConSurf website developers about what information they put into the session. However, I would not expect it to have any Alphafold information (pLDDT or PAE values). It probably just has whatever atomic coordinates you uploaded (if that's how you input the structure), or atomic coordinates straight from the PDB.
Regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 26, 2024, at 8:04 PM, David S. Fay <DavidFay@uwyo.edu> wrote:
Hi Elaine,
I was able to open the ConSurf .cxs files using ChimeraX, which were part of the Consurf download. I have tried using ConSurf through Chimera or ChimeraX yet. I’ve attached an example image I recently obtained using ChimeraX. One limitation I haven’t worked is how to display PAE contacts between peptides when using this ConSurf file in ChimeraX. I can do it with AF2/3 files – no problem, but not with the ConSurf files. Also, the .cxs files don't seem to work for other ChimeraX functions, such as: hide @@bfactor<50 ribbon. It’s also unfortunate that ConSurf doesn’t allow you to visualize conservation for more than one of the two peptide chains, at least as far as I can tell. But it’s still quite useful.
If you have any additional hints I’d be glad to try them.
David
<Screenshot 2024-07-26 at 8.54.04 PM.png>
On Jul 26, 2024, at 3:11 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi David, Thanks for the info about the ConSurf website. Did you ever use the ConSurf website output in ChimeraX or were all the outputs only suitable for Chimera (which was my experience)?
Some other notes, in case you or others didn't know...
(1) ChimeraX also plots PAE data from AlphaFold2 or AlphaFold3 <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#pae>
example command: alphafold fetch LDLR_HUMAN pae true
screenshot of result: <Screen Shot 2024-07-26 at 2.10.24 PM.png>
(2) ChimeraX can convert mmCIF to PDB, i.e. you could just open the mmCIF file and then save the structure as PDB. Can be done with the File menu or with the commands "open" and "save":
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#formats> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html>
Elaine
On Jul 26, 2024, at 1:54 PM, David S. Fay via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Real quick followup for those who might be interested.
I did contact ConSurf. They suggested using a different browser and clearing the cache. I did both and it now works but only on Chrome and NOT on Safari (for those using Macs). This isn’t the first time I’ve had problems with Safari. ConSurf is helpful for looking at conservation of a protein sequence and/or a 3D structure.
Incidentally, for converting cif to pdb, which is necessary for ConSurf, this site worked well. https://project-gemmi.github.io/wasm/convert/cif2pdb.html
Also, some may be interested in using this site to generate AF2-like red/blue PAE diagrams as well as creating spreadsheets of predicted peptide interactions from AF3. https://predictomes.org/tools/af3/
David
On Jul 25, 2024, at 9:42 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
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Hi David, Did you try asking the Consurf developers? There is a "contact us" link on their website:
<https://consurf.tau.ac.il/consurf_contact.php>
I haven't used this web service recently. I have only used its outputs in Chimera so far (never ChimeraX).
If I go to a page for precalculated results there is a "Chimera" download that gives a Chimera session (.py file), e.g.
<https://consurfdb.tau.ac.il/main_output.php?pdb_ID=2GBP&view_chain=A&unique_...>
I tried downloading that just now, and it works in Chimera. In Chimera you can use File... Export Scene... and export a .py file that you can open with ChimeraX. Only the ribbon and carbon atoms are colored by the Consurf values, however, not the heteroatoms.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
> On Jul 24, 2024, at 8:08 PM, David S. Fay via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: > > Hi, > > I’m curious if anyone else is having trouble getting results from ConSurf? The site appears to be up, which maybe wasn’t the case a while back. But trying various kinds of inputs doesn’t lead to any results. Rather, it just seems to just get hung up. (It’s also possible I’m doing something incorrectly.) > > Thanks in advance! > > David