Dear Elaine,

Thank you very much for your quick response. I have actually tried the #1,#2 but the code does not recognize the protein sequence as a sequence.

Missing or invalid "sequences" argument. Sequence argument #1 is not a chain-specifier, alignment ID, UniProt ID or sequence character.

I downloaded the pdb from RCSB.

May I know what other methods can I use to perform the task?

Thank you very much.

Sincerely Yours,
William Tan

From: Elaine Meng <meng@cgl.ucsf.edu>
Sent: Wednesday, 5 October 2022, 4:55 pm
To: Tan, Wei Ren
Cc: chimerax-users@cgl.ucsf.edu
Subject: Re: [chimerax-users] Using ChimeraX to predict protein-protein interaction/binding via Alphafold.

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Hi William,
The "&" is wrong -- that symbol is for intersection, and the intersection between the two different models is nothing (none of the atoms are in both #1 and #2 at the same time).  I.e. to specify both models together try #1,2 instead:

alphafold predict #1,2

<https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fatomspec.html%23combinations&amp;data=05%7C01%7Cwei.r.tan%40kcl.ac.uk%7C45362ac10b09483ca7b708daa6ea0866%7C8370cf1416f34c16b83c724071654356%7C0%7C0%7C638005821343017939%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&amp;sdata=3pM0d%2FKrmBZh1pS1oAcERI1EKLCILoJyjNcs9wGwLJY%3D&amp;reserved=0>

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


> On Oct 5, 2022, at 6:44 AM, Tan, Wei Ren via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Dear Sir/Mdm,
>
> Sorry to disturb you with regards to this matter, as I am unable to find any resources online, or on your YouTube channel to solve my problem. I am William, a medical student at King’s College London, UK, who have been using your software, ChimeraX, for the past few months to elucidate possible protein structure for one of the protein I am currently studying. I have faced a problem with predicting a protein interaction between a heterodimer (6z1n) and a novel protein that I am studying now. When I loaded both pdbs, I am unable to run the alphafold via the command:
>
> alphafold predict #1&#2 (where #1 is 6z1n and #2 is my protein of interest)
>
> Hence, how can I load the pdb of 6z1n (the heterodimer) and the sequence of the protein of interest to predict what is the possible interaction between the 2, instead of putting all 3 monomers as a sequence and for Alphafold to repredict the interactions between the2 monomers within 6z1n instead?
>
> Thank you very much and sorry to disturb you!
>
> Sincerely Yours,
> William Tan



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