add residues at the beginnning of a chain

[17dacheng]

Hello,

i have a protein complex with chain A and B, want to add 0-20 residues at the beginning of the chain A, i have try two jsons which are not work

json1: { "partial_diffusion": { "input": "1.cif", "partial_t": 15.0, "contig": "0-20,A1-97,/0,B1-177", "select_fixed_atoms": "A1-97,/0,B1-177" } }

json2: { "partial_diffusion": { "input": "1.cif", "partial_t": 15.0, "contig": "0-20,/0", "unindex": "A1-97,/0,B1-177" } }

is there anyone can tell me the reason and give the corrent json.

Thanks,

[rclune]

Can you say more about what is not working? Are you getting an error message or unexpected outputs?

If you are just trying to add 20 residues to the start of chain A, but otherwise keep everything that is in your input CIF file, you don't need to add the select_fixed_atoms option, having the portions of chain A and B that you want to keep in your contig should be enough.

For your second JSON script, by not providing the portions of your system that you want to keep from your input in your contig I believe that RFD3 will not know what you are trying to reference in the unindex section.

[17dacheng]

Can you say more about what is not working? Are you getting an error message or unexpected outputs?

If you are just trying to add 20 residues to the start of chain A, but otherwise keep everything that is in your input CIF file, you don't need to add the select_fixed_atoms option, having the portions of chain A and B that you want to keep in your contig should be enough.

For your second JSON script, by not providing the portions of your system that you want to keep from your input in your contig I believe that RFD3 will not know what you are trying to reference in the unindex section.

Hi, rclune

there is no error reported, i check the results found no residues are added at the beginning of chain A

i have also tried following, which dropped the select_fixed_atoms, still no residues are added

{ "partial_diffusion": { "input": "input_pdbs/fold_cd58_v22_cd2_model_0.cif", "partial_t": 15.0, "contig": "0-20,A1-97,/0,B1-177" } }

hope to hear from u soon,

thanks!

[DieHof]

Hello, the problem is, that you are using partial_t as an setting, which is used for partial diffusion. Looking at the input parsing for partial diffusion, it looks like partial diffusion works the exact same way as in RFdiffusion(1). This means that the input and output of rfd must have the exact same number of residues. So it is not possible to add new residues in a partial diffusion run, as the model has no prior information of where these new residues are located. To add residues, you should just remove the partial_t argument, so your json should look like:

{
"diffusion": {
"input": "input_pdbs/fold_cd58_v22_cd2_model_0.cif",
"contig": "0-20,A1-97,/0,B1-177"
}}

I hope this solves your problem.

[Ubiquinone-dot]

+1 to DieHof's reply!

[17dacheng]

Hello, the problem is, that you are using partial_t as an setting, which is used for partial diffusion. Looking at the input parsing for partial diffusion, it looks like partial diffusion works the exact same way as in RFdiffusion(1). This means that the input and output of rfd must have the exact same number of residues. So it is not possible to add new residues in a partial diffusion run, as the model has no prior information of where these new residues are located. To add residues, you should just remove the partial_t argument, so your json should look like:

{
"diffusion": {
"input": "input_pdbs/fold_cd58_v22_cd2_model_0.cif",
"contig": "0-20,A1-97,/0,B1-177"
}}

I hope this solves your problem.

very clear, many thanks!