Hi Meng, Below is from alphafold21_predict_colab.ipynb. Does this mean the two proteins is predicated to form a dimer(homo-dimer)? Best, Junyi [cid:37184ba2-34bc-485e-a93d-00801d5d7ba0] ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Thursday, January 19, 2023 1:00 PM To: Liang, Junyi <LIANGJ3@ccf.org> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] [EXT] Re: missing or invalid sequences CAUTION CYBER RISK: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender, expected to receive this content and trust that it’s safe. If you determine that the email isn’t from a trusted source, you can delete the email, submit it via the BlueFish button in Outlook for investigation or forward the email as an attachment to phishtanktriage@ccf.org if you don’t have the Bluefish button or are on a mobile device. 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@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<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> Below is a screenshot of interface. I would like to do a protein-protein interaction predication. <image.png> Best,
Junyi From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Thursday, January 19, 2023 11:34 AM To: Liang, Junyi <LIANGJ3@ccf.org> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: [EXT] Re: [chimerax-users] missing or invalid sequences
CAUTION CYBER RISK: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender, expected to receive this content and trust that it’s safe. If you determine that the email isn’t from a trusted source, you can delete the email, submit it via the BlueFish button in Outlook for investigation or forward the email as an attachment to phishtanktriage@ccf.org if you don’t have the Bluefish button or are on a mobile device.
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@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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