[chimerax-users] usage for multimer

[Elaine Meng]

Hi Dennis,
Your sequence input is wrong - it should contain only the sequences pasted as plain text, with only a comma between them (NOT the ">description" line because it is not supposed to be in fasta format).  How to input sequence(s) is explained in the AlphaFold help page.

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

"For predicting a complex (multimer), the sequences of all chains in the complex must be given. The same sequence must be given multiple times if it occurs in multiple copies in the complex. The sequences can be specified either collectively as a model number chosen from the menu of currently open models (e.g. when that model contains multiple chains), or individually within a comma-separated list of UniProt identifiers or pasted-in amino acid sequences."

E.g. something like

ACCCC,ALLPAAAA

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

> On Oct 5, 2022, at 4:12 AM, Dennis Poh via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Sorry, I couldn't generate the pdb from chimera colab - is there anything that i may have missed?
> 
> -Dennis
> 
> On Wed, 5 Oct 2022 at 17:11, Dennis Poh <pohdennis90 at gmail.com> wrote:
> Hi 
> 
> I encounter a problem in multimer prediction with the sequences I use as input.
> It's always indicating:
> "Missing or invalid "sequences" argument: Sequences argument"
> and " is not a chain specifier, alignment id, UniProt id, or sequence characters"
> 
> The input format is always something like a fasta format:
> >seq_id
> ACCCC
> 
> >seq_id2
> ALLPAAAA
> 
> May I know how I can rectify this?
> 
> Thanks!
> - Dennis