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: (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
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