[chimerax-users] Using ChimeraX to predict protein-protein interaction/binding via Alphafold.

[Elaine Meng]

It is #1,2  -- not #1,#2.  Before I sent the previous message, tried the first one myself with alphafold predict and it worked.

Elaine


> On Oct 5, 2022, at 9:03 AM, Tan, Wei Ren via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> 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 at cgl.ucsf.edu>
> Sent: Wednesday, 5 October 2022, 4:55 pm
> To: Tan, Wei Ren
> Cc: chimerax-users at cgl.ucsf.edu
> Subject: Re: [chimerax-users] Using ChimeraX to predict protein-protein interaction/binding via Alphafold.
> 
> [You don't often get email from meng at cgl.ucsf.edu. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ]
> 
> 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&data=05%7C01%7Cwei.r.tan%40kcl.ac.uk%7C45362ac10b09483ca7b708daa6ea0866%7C8370cf1416f34c16b83c724071654356%7C0%7C0%7C638005821343017939%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=3pM0d%2FKrmBZh1pS1oAcERI1EKLCILoJyjNcs9wGwLJY%3D&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 at 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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