Deploy MSA database on my local server

[shiyu-wangbyte]

Hello, I do not have MSA information on the input json file, so I can use --use_msa_server flag.

But now, i am interested in deploying the MSA database on my local server, So that i can finished all calculations on my local server.

What should i do?

Thanks.

[zhangyuxuann]

@shiyu-wangbyte we are compatiable with colabfold local. you can refer to https://github.com/bytedance/Protenix/blob/main/docs/colabfold_compatiable_msa.md

[shiyu-wangbyte]

OK, thank you

[YoelShoshan]

@zhangyuxuann

In a scenario of a complex (for example - 2 protein chains) what is the correct way to use scripts/colabfold_msa.py ?

Should the user create a .fasta file per chain, and call colabfold_msa.py on it?
or is there another way?

Asking because if I provide a .fasta file with two chains, 'colabfold_msa.py' will take just one and ignore the rest in its postprocessing step of dealing with taxonomy.

I was able to bypass this by running it separately per chain, but I'm not sure if it's equivalent to what Protenix expects.

[JinyuanSun]

@zhangyuxuann

In a scenario of a complex (for example - 2 protein chains) what is the correct way to use scripts/colabfold_msa.py ?

Should the user create a .fasta file per chain, and call colabfold_msa.py on it? or is there another way?

Asking because if I provide a .fasta file with two chains, 'colabfold_msa.py' will take just one and ignore the rest in its postprocessing step of dealing with taxonomy.

I was able to bypass this by running it separately per chain, but I'm not sure if it's equivalent to what Protenix expects.

can you provide a copy of the current input fasta file? @YoelShoshan

[YoelShoshan]

@JinyuanSun

sure!
for example:
7vux_needs_msa.fasta:

>A|protein
MWNPPTFSPALLVVTEGDNATFTCSFSNTSESFVLNWYRMSPSNQTDKLAAFPEDRSQPGQDSRFRVTQLPNGRDFHMSVVRARRNDSGTYLCGAISLAPKAQIKESLRAELRVTERRAEVPTAHPSPSPENLYFQ
>B|protein
EVKLVESGGGLVQPGGSLRLSCAASGFAFSSYDMSWVRQAPGKRLEWVATISGGGRYTYYPDTVKGRFTISRDNAKNSHYLQMNSLRAEDTAVYFCASPYGGYFDVWGQGTLVTVSSASTKGPSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTKTYTCNVDHKPSNTKVDKRVE
>C|protein
EIVLTQSPATLSLSPGERATLSCRASQSISNFLHWYQQKPGQAPRLLIKYASQSISGIPARFSGSGSGTDFTLTISSLEPEDFAVYFCQQSNSWPHTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC