Not possible to read.pdb('1ao7.pdb2", multi = TRUE)

[Former user]

Hi, When trying to read the pdb file https://files.rcsb.org/download/1AO7.pdb2.gz it's not possible to load all the models but just one. Thanks

[Xinqiu Yao]

Hi,

Normally, you should use read.pdb(..., multi=TRUE)to read multiple models. That method assumes all the models have exactly the same number of atoms (describing the same system but different conformations, such as in an NMR structure). However, in your case, the multi-model is used to store monomers for building a biological assembly, where models may contain different atoms. I don’t know why PDB chooses such a confusing way to store an assembly but in this case, you cannot use the method above.

Try the following methods (but check carefully if the output is what you want).

pdb <- read.pdb("1ao7")
bio <- biounit(pdb)
## You may ignore the warnings.
## The second biological unit (or assembly) should be what you are looking for
bio[[2]] 

Or, read the assembly from a CIF file:

## First, download the CIF file from PDB.

pdb <- read.cif("1ao7-assembly2.cif") 

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Hope they may help.

[Victoria Isabel Ruiz Serra]

Hi,

It’s me again. Sorry, I didn’t log in when I wrote the issue.

I’m working with pdb biounit files and in principle I cannot change them. Is there any workaround to be able to read the file as usual?

Many thanks

[Xinqiu Yao]

As I mentioned above, some biounit files in PDB format cannot be read properly. One solution is to download the same structure in the PDBx/mmCIF format and read it using read.cif().