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

[Elaine Meng]

Hi Junyi,
It works fine for me in ChimeraX 1.5 AlphaFold Predict if I paste the following: 

 MPDPLFSAVQGKDEILHKALCFCPWLGKGGMEPLRLLILLFVTELSGAHNTTVFQGVAGQSLQVSCPYDS
MKHWGRRKAWCRQLGEKGPCQRVVSTHNLWLLSFLRRWNGSTAITDDTLGGTLTITLRNLQPHDAGLYQC
QSLHGSEADTLRKVLVEVLADPLDHRDAGDLWFPGESESFEDAHVEHSISRSLLEGEIPFPPTSILLLLA
CIFLIKILAASALWAAAWHGQKPGTHPPSELDCGHDPGYQLQTLPGLRDT,
MPDPLFSAVQGKDEILHKALCFCPWLGKGGMEPLRLLILLFVTELSGAHNTTVFQGVAGQSLQVSCPYDS
MKHWGRRKAWCRQLGEKGPCQRVVSTHNLWLLSFLRRWNGSTAITDDTLGGTLTITLRNLQPHDAGLYQC
QSLHGSEADTLRKVLVEVLADPLDHRDAGDLWFPGESESFEDAHVEHSISRSLLEGEIPFPPTSILLLLA
CIFLIKILAASALWAAAWHGQKPGTHPPSELDCGHDPGYQLQTLPGLRDT

I don't know what was wrong in your case. Remember it has to be plain text, without any quotation marks or other special characters.
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 9:04 AM, Liang, Junyi via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> 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 
> 
> 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
> www.youtube.com
> Below is a screenshot of interface. I would like to do a protein-protein interaction predication.
> <image.png>
> 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>
> 
> 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.
> > 
> > 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
> > 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?
> >