Query regarding RCSBPDB

Question

[sharmatina189059]

Dear all Can anybody tell me how can I get co-crystallized structure ID from RCSB PDB or Uniprot. I have 88 PDBIDs and its corresponding Uniprot Ids. Can anybody tell me how can I retrieve this data (it would really be helpful if someone has fetch this type of data programmatically).

[cc]

Perfect, it works perfectly!!! thank you !!!

[GenoMax]

I am not exactly sure what you are looking for but this page allows you to retrieve structures using PDB ID's. Otherwise use the HTTPS services they offer for scripted downloads.

Answer 1

[Joe]

Here's my script that I use regularly to download from PDB via the commandline with a simple wget request. I'm not sure if there is a specific difference in co-crystallised structures, but if it has a 4 letter alphanumeric ID it should work.

Usage:

bash getPDB.sh -i 1ABC

Would download the 1ABC.pdb file in to your current directory. Run the script without arguments or with -h/--help to see the other options.

[cc]

is it possible to download more than one pdb? Like bash getPDB.sh -i 1ABC 3EFD 4NOL Thank you!!

[Joe]

Yeah that should be fairly straight forward, though this is a basic script and can't do it at the moment. I'll need some time to modify it. It'll basically be a case of looping over an array of arguments with bash's ${array[@]} syntax, but I'll have to figure out how nicely that will play with getopt.

In the mean time, a really simple work around would be to call the script in a loop:

for id in 1abc 2def 3ghi ; do bash getPDB.sh -i "$id" ; done

If you want to get a bit more fancy, you could read from a file of IDs. Assuming you had a text file of IDs that looked like :

1abc
2def
3ghi

you can do:

while read id ; do bash getPDB.sh -i "$id" ; done < myIDs.txt

I've not tested these though, so just be careful the newline characters in the text file don't catch you out.

[Joe]

I've updated the script. With getopt, the options are a little limited, but now the following is supported:

bash getpdb.sh -i 1abc -i 2cde -i 3fgh

You have to specify -i multiple times else getopt doesn't understand they should go in to the same array.

I've not tested the new version extensively, but it should work.