Suggestion for improvement
I love ChimeraX and use it often for my work, e.g. this one <https://www.pnas.org/doi/10.1073/pnas.2421910122>. When using AlphaFold to predict protein structure, the sequence is pasted into the sequence box. It does not allow entering the fasta name ">name" before the sequence.. Allowing a name to be included can avoid much confusion. Presently, the screen shows the output as "best_model" which becomes very confusing when several best models are shown on the screen. James Raymond Univ. Nevada Las Vegas
Hi James, Thanks for your kind words, and congratulations on your work! You can actually rename any of the models in the Model Panel (Models list). E.g. if you doubleclick the name it turns into an editable field. See Model Panel help: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/modelpanel.html> Alternatively, you could use the "rename" command. If you want a name with spaces, you would enclose it quotation marks. See examples in: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/rename.html> 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 Mar 11, 2025, at 11:20 AM, James Raymond via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
I love ChimeraX and use it often for my work, e.g. this one.
When using AlphaFold to predict protein structure, the sequence is pasted into the sequence box. It does not allow entering the fasta name ">name" before the sequence.. Allowing a name to be included can avoid much confusion. Presently, the screen shows the output as "best_model" which becomes very confusing when several best models are shown on the screen. James Raymond Univ. Nevada Las Vegas
thank you! On Tue, Mar 11, 2025 at 11:36 AM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi James, Thanks for your kind words, and congratulations on your work!
You can actually rename any of the models in the Model Panel (Models list). E.g. if you doubleclick the name it turns into an editable field. See Model Panel help: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/modelpanel.html>
Alternatively, you could use the "rename" command. If you want a name with spaces, you would enclose it quotation marks. See examples in: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/rename.html>
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 Mar 11, 2025, at 11:20 AM, James Raymond via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
I love ChimeraX and use it often for my work, e.g. this one.
When using AlphaFold to predict protein structure, the sequence is pasted into the sequence box. It does not allow entering the fasta name ">name" before the sequence.. Allowing a name to be included can avoid much confusion. Presently, the screen shows the output as "best_model" which becomes very confusing when several best models are shown on the screen. James Raymond Univ. Nevada Las Vegas
Hi James, It would be nice if the Colabfold prediction filename were something more reasonable than an fixed name like best_model.pdb. Currently there is no option for that, and you would have to go to your ~/Downloads/ChimeraX/AlphaFold/prediction_N directory and rename the file yourself, not too convenient. I'm working a new AlphaFold 3 / Boltz prediction capability and my prototype already has you enter a name for the prediction that is used in the file names. Tom
On Mar 11, 2025, at 11:50 AM, James Raymond via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
thank you!
On Tue, Mar 11, 2025 at 11:36 AM Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote:
Hi James, Thanks for your kind words, and congratulations on your work!
You can actually rename any of the models in the Model Panel (Models list). E.g. if you doubleclick the name it turns into an editable field. See Model Panel help: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/modelpanel.html>
Alternatively, you could use the "rename" command. If you want a name with spaces, you would enclose it quotation marks. See examples in: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/rename.html>
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 Mar 11, 2025, at 11:20 AM, James Raymond via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
I love ChimeraX and use it often for my work, e.g. this one.
When using AlphaFold to predict protein structure, the sequence is pasted into the sequence box. It does not allow entering the fasta name ">name" before the sequence.. Allowing a name to be included can avoid much confusion. Presently, the screen shows the output as "best_model" which becomes very confusing when several best models are shown on the screen. James Raymond Univ. Nevada Las Vegas
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participants (3)
-
Elaine Meng -
James Raymond -
Tom Goddard