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