How to use zip PDBs with IMP-FOXS (such as with the online version of FOXS)
Hello,
I am attempting to run FOXS with 200+ PDBs. For this purpose I have downloaded IMP since the online version of FOXS can only use 100PDBs. However, I don't see an option in the tutorial or the help command for uploading a zip containing multiple PDBs. It appears you have to upload the PDBs individually from what I can see.
This is what I'm entering:
>>>foxs -g -h pdb.zip saxs_data.dat
begin IMP::atom::`anonymous-namespace'::read_pdb: WARNING Sorry, unable to read atoms from PDB file. Thanks for the effort. end IMP::atom::`anonymous-namespace'::read_pdb WARNING can't parse input file pdb.zip
On 1/19/23 11:06 AM, sammahdi1994--- via IMP-users wrote: > I am attempting to run FOXS with 200+ PDBs. For this purpose I have > downloaded IMP since the online version of FOXS can only use 100PDBs. > However, I don't see an option in the tutorial or the help command for > uploading a zip containing multiple PDBs.
It's a command line tool - there's no reason for it to handle zip files since you can already do that (with other command line tools). FoXS can handle any number of PDBs and/or profiles on the command line, so just unzip your file first and then give FoXS as many of the PDBs as you want.
Ben
Oh ok.
So I'm getting a strange error when I try to run FOXS.
>>>>>>foxs -h file.pdb saxs_data.dat begin IMP::atom::`anonymous-namespace'::read_pdb: WARNING Sorry, unable to read atoms from PDB file. Thanks for the effort. end IMP::atom::`anonymous-namespace'::read_pdb file.pdb 5864 atoms file.pdb saxs_data.dat Chi^2 = 2107.33 c1 = 1.05 c2 = 4 default chi^2 = 4489.64
So it's able to read it, but I get a warning saying it can't? The output also generates 2 .dat outputs, and 1 .fit output, is there an option to exclude the generation of the 2 .dat and only generate the fit file (I only care for the fitted theoretical profile).
On 1/19/23 2:30 PM, sammahdi1994--- via IMP-users wrote: > So I'm getting a strange error when I try to run FOXS. > >>>>>>> foxs -h file.pdb saxs_data.dat > begin IMP::atom::`anonymous-namespace'::read_pdb: > WARNING Sorry, unable to read atoms from PDB file. Thanks for the effort.
That's not an error, it's a warning. It says so in capitals ;)
> So it's able to read it, but I get a warning saying it can't?
It's able to read file.pdb as PDB, but it cannot read saxs_data.dat as PDB - that's the file it is warning about. This is fine because it will just go and assume it's a profile instead (which it is).
> The output also generates 2 .dat outputs, and 1 .fit output, is > there an option to exclude the generation of the 2 .dat and only generate the > fit file (I only care for the fitted theoretical profile).
No, FoXS always generates these .dat files.
Ben
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