[chimerax-users] [EXT] Re: missing or invalid sequences

[Liang, Junyi]

Hello Elaine,

It's nice to hear from you. I guess I input the sequence in a correct way as I tried to input the sequence the same way as in this video https://www.youtube.com/watch?v=6lXeCPuTePs
[https://www.bing.com/th?id=OVP.95Ygyv4AXQTgCS0WB9iXtgHgFo&pid=Api]<https://www.youtube.com/watch?v=6lXeCPuTePs>
Running AlphaFold to Predict Protein Complexes from ChimeraX<https://www.youtube.com/watch?v=6lXeCPuTePs>
How to predict the structure of a photoreaction center complex of 3 proteins from ChimeraX using AlphaFold-Multimer. Requires a ChimeraX daily build newer than December 2, 2021 or version 1.4. It is not in ChimeraX version 1.3. Web page describing steps https://www.rbvi.ucsf.edu/chimerax/data/alphafold-dec2021/af_multimer.html
www.youtube.com
Below is a screenshot of interface. I would like to do a protein-protein interaction predication.
[cid:c426f420-36c5-4d71-afa5-349318422ae5]
Best,

Junyi
________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Thursday, January 19, 2023 11:34 AM
To: Liang, Junyi <LIANGJ3 at ccf.org>
Cc: chimerax-users at cgl.ucsf.edu <chimerax-users at cgl.ucsf.edu>
Subject: [EXT] Re: [chimerax-users] missing or invalid sequences

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Without the details of what you did, I can only guess that somehow you did not enter the sequences correctly. They should be plain text, with only a comma between sequences of different proteins.

see AlphaFold predict help:
<https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#predict<https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#predict>>

To say anything more informative, we would need to see exactly what you pasted into the sequence area, and what options you chose in the input dialog.

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


> On Jan 19, 2023, at 7:27 AM, Liang, Junyi via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>
> I would like to predicate interaction between two proteins, and tried chimerax version 1.5 after noticing a youtube video https://www.youtube.com/watch?v=6lXeCPuTePs<https://www.youtube.com/watch?v=6lXeCPuTePs>.
>
> Running AlphaFold to Predict Protein Complexes from ChimeraX
> How to predict the structure of a photoreaction center complex of 3 proteins from ChimeraX using AlphaFold-Multimer. Requires a ChimeraX daily build newer than December 2, 2021 or version 1.4. It is not in ChimeraX version 1.3. Web page describing steps https://www.rbvi.ucsf.edu/chimerax/data/alphafold-dec2021/af_multimer.html<https://www.rbvi.ucsf.edu/chimerax/data/alphafold-dec2021/af_multimer.html>
> www.youtube.com<http://www.youtube.com>
> I input the two protein sequences in same way as shown in the video and hit predict. But your software says "missing or invalid sequences". How come?
>


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