Fails to depict and answer the polymeric forms

[pachterlab]

Fails to depict and answer the polymeric forms

[lauraluebbert]

Hi! It might be worth playing around with the mono- versus multimer function in gget alphafold. If you pass each sequence of the hexamer separately as a list (or in a .fa), the program will automatically use the multimer model. This will take much longer but might yield results closer to the expected structure.

[Harpreet525]

HiThe sequence is at 58% identity and is a homohexadimer. So i dont know how but the pdb database showed the same monomer arranged in a circular 6mer perimeter. Plus i cannot put same sequences 6 times, is it ?I mean prodigal captured only one sequenceRegardsHarpreet SinghOn Aug 17, 2022 12:22 AM, Laura Luebbert ***@***.***> wrote: Hi! It might be worth playing around with the mono- versus multimer function in gget alphafold. If you pass each sequence of the hexamer separately as a list (or in a .fa), the program will automatically use the multimer model. This will take much longer but might yield results closer to the expected structure. —Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you authored the thread.Message ID: ***@***.***>

[Harpreet525]

i also happen to face an issue with supplying a fasta file to read as it returns an error that fasta file starts with '>' but myt file does contain the '>' symbol at the starting.

And i am plotting the pdb file separately in pymol, is the plotting function embedded in gget alphafold as i couldnt get any plot

[lauraluebbert]

Hi, I ran gget alphafold on a fasta file containing the chloride dismutase sequence (from PDB 2VXH) 6 times (pasted below) (terminal command: gget alphafold 2VXH.fa). (Note: I had no problem inputting the fasta file. Please make sure your fasta is formatted correctly, starting with a single-line description without any characters/lines preceding the ">".) Inputting several sequences automatically uses the multimer model. The resulting prediction looks as follows:

>1
GSHMQPMQAMKIERGTILTQPGVFGVFTMFKLRPDWNKVPAMERKGAAEEVKKLIEKHKDNVLVDLYLTRGLETNSDFFFRINAYDLAKAQTFMREFRSTTIGKNADVFETLVGVTKPLNYISKDKSPGLNAGLSSATYSGPAPRYVIVIPVKKNAEWWNMSPEERLKEMEVHTTPTLAYLVNVKRKLYHSTGLDDTDFITYFETDDLTAFNNLMLSLAQVKENKFHVRWGSPTTLGTIHSPEDVIKALAD
>2
GSHMQPMQAMKIERGTILTQPGVFGVFTMFKLRPDWNKVPAMERKGAAEEVKKLIEKHKDNVLVDLYLTRGLETNSDFFFRINAYDLAKAQTFMREFRSTTIGKNADVFETLVGVTKPLNYISKDKSPGLNAGLSSATYSGPAPRYVIVIPVKKNAEWWNMSPEERLKEMEVHTTPTLAYLVNVKRKLYHSTGLDDTDFITYFETDDLTAFNNLMLSLAQVKENKFHVRWGSPTTLGTIHSPEDVIKALAD
>3
GSHMQPMQAMKIERGTILTQPGVFGVFTMFKLRPDWNKVPAMERKGAAEEVKKLIEKHKDNVLVDLYLTRGLETNSDFFFRINAYDLAKAQTFMREFRSTTIGKNADVFETLVGVTKPLNYISKDKSPGLNAGLSSATYSGPAPRYVIVIPVKKNAEWWNMSPEERLKEMEVHTTPTLAYLVNVKRKLYHSTGLDDTDFITYFETDDLTAFNNLMLSLAQVKENKFHVRWGSPTTLGTIHSPEDVIKALAD
>4
GSHMQPMQAMKIERGTILTQPGVFGVFTMFKLRPDWNKVPAMERKGAAEEVKKLIEKHKDNVLVDLYLTRGLETNSDFFFRINAYDLAKAQTFMREFRSTTIGKNADVFETLVGVTKPLNYISKDKSPGLNAGLSSATYSGPAPRYVIVIPVKKNAEWWNMSPEERLKEMEVHTTPTLAYLVNVKRKLYHSTGLDDTDFITYFETDDLTAFNNLMLSLAQVKENKFHVRWGSPTTLGTIHSPEDVIKALAD
>5
GSHMQPMQAMKIERGTILTQPGVFGVFTMFKLRPDWNKVPAMERKGAAEEVKKLIEKHKDNVLVDLYLTRGLETNSDFFFRINAYDLAKAQTFMREFRSTTIGKNADVFETLVGVTKPLNYISKDKSPGLNAGLSSATYSGPAPRYVIVIPVKKNAEWWNMSPEERLKEMEVHTTPTLAYLVNVKRKLYHSTGLDDTDFITYFETDDLTAFNNLMLSLAQVKENKFHVRWGSPTTLGTIHSPEDVIKALAD
>6
GSHMQPMQAMKIERGTILTQPGVFGVFTMFKLRPDWNKVPAMERKGAAEEVKKLIEKHKDNVLVDLYLTRGLETNSDFFFRINAYDLAKAQTFMREFRSTTIGKNADVFETLVGVTKPLNYISKDKSPGLNAGLSSATYSGPAPRYVIVIPVKKNAEWWNMSPEERLKEMEVHTTPTLAYLVNVKRKLYHSTGLDDTDFITYFETDDLTAFNNLMLSLAQVKENKFHVRWGSPTTLGTIHSPEDVIKALAD

The plotting functions are only called when using gget in a Python environment (e.g. Jupyter Lab/Google Colab). If using from terminal, I would indeed recommend to open the pdb result in PyMol or here.