PBassign¶

PBassign assigns a PB sequence to a protein structure.

Example¶

First download data:

$ wget https://files.rcsb.org/view/3ICH.pdb

Then perform PBs assignment:

$ PBassign -p 3ICH.pdb -o 3ICH
1 PDB file(s) to process
Read 1 chain(s) in 3ICH.pdb
wrote 3ICH.PB.fasta

Content of 3ICH.PB.fasta :

>3ICH.pdb | chain A
ZZccdfbdcdddddehjbdebjcdddddfklmmmlmmmmmmmmnopnopajeopacfbdc
ehibacehiamnonopgocdfkbjbdcdfblmbccfbghiacdddebehiafkbccddfb
dcfklgokaccfbdcfbhklmmmmmmmpccdfkopafbacddfbgcddddfbacddddZZ

Note that Protein Blocs assignment is only possible for proteins (as its name suggests). As a consequence, processed PDB files must contain protein structures only (please remove any other molecule). In addition, the PDB parser implemented here is pretty straightforward. Be sure your PDB files complies with the ATOM field of the PDB format.

Usage¶

Here’s the PBassign help text.

Usage: PBassign [options] -p file.pdb|dir [-p file2.pdb] -o output_root_name -g gro_file -x xtc_file

optional arguments:
  -h, --help     show this help message and exit
  -p P           name of a pdb file or name of a directory containing pdb
                 files
  -o O           name for results
  -v, --version  show program's version number and exit

other options to handle molecular dynamics trajectories:
  -x X           name of the topology file
  -g G           name of the trajectory file

`-p` option¶

can be used several times. For instance:

$ wget https://files.rcsb.org/view/3ICH.pdb
$ wget https://files.rcsb.org/view/1BTA.pdb
$ wget https://files.rcsb.org/view/1AY7.pdb
$ PBassign -p 3ICH.pdb -p 1BTA.pdb -p 1AY7.pdb -o test1
3 PDB file(s) to process
Read 1 chain(s) in 3ICH.pdb
Read 1 chain(s) in 1BTA.pdb
Read 2 chain(s) in 1AY7.pdb
wrote test1.PB.fasta

All PB assignments are written in the same output file. If a PDB file contains several chains and/or models, PBs assignments are also written in a single output file. From the previous example, the ouput of test1.PB.fasta is:

>3ICH.pdb | chain A
ZZccdfbdcdddddehjbdebjcdddddfklmmmlmmmmmmmmnopnopajeopacfbdc
ehibacehiamnonopgocdfkbjbdcdfblmbccfbghiacdddebehiafkbccddfb
dcfklgokaccfbdcfbhklmmmmmmmpccdfkopafbacddfbgcddddfbacddddZZ
>1BTA.pdb | chain A
ZZdddfklonbfklmmmmmmmmnopafklnoiaklmmmmmnoopacddddddehkllmmm
mngoilmmmmmmmmmmmmnopacdcddZZ
>1AY7.pdb | chain A
ZZbjadfklmcfklmmmmmmmmnnpaafbfkgopacehlnomaccddehjaccdddddeh
klpnbjadcdddfbehiacddfegolaccdddfkZZ
>1AY7.pdb | chain B
ZZcddfklpcbfklmmmmmmmmnopafklgoiaklmmmmmmmmpacddddddehkllmmm
mnnommmmmmmmmmmmmmnopacddddZZ

One can also use the -p option to provide a directory containing PDB files as an input. PBassign will process all PDB files located in the PBdata directory:

$ wget https://files.rcsb.org/view/1AY7.pdb -P demo
$ wget https://files.rcsb.org/view/2LFU.pdb -P demo
$ wget https://files.rcsb.org/view/3ICH.pdb -P demo
$ wget https://files.rcsb.org/view/1BTA.pdb -P demo
$ PBassign -p demo/ -o test2
4 PDB file(s) to process
Read 1 chain(s) in demo/3ICH.pdb
Read 2 chain(s) in demo/1AY7.pdb
Read 1 chain(s) in demo/1BTA.pdb
Read 10 chain(s) in demo/2LFU.pdb
wrote test2.PB.fasta

`-x` and `-g` options¶

Warning

These options use the MDAnalysis library which is installed by PBxplore.

Instead using the -p option, protein structures could come from a molecular dynamics simulation trajectory file. For this, you have to specify a trajectory file with the -x option and a topology file with the -g option. It will accept any trajectory file format handled by the MDAnalysis library. See their [table of supported formats](https://pythonhosted.org/MDAnalysis/documentation_pages/coordinates/init.html#id1) for the full list. Here an example with GROMACS files.

$ wget https://raw.githubusercontent.com/pierrepo/PBxplore/master/demo_doc/psi_md_traj.gro
$ wget https://raw.githubusercontent.com/pierrepo/PBxplore/master/demo_doc/psi_md_traj.xtc
$ PBassign -x psi_md_traj.xtc -g psi_md_traj.gro -o psi_md_traj
Frame 1/225.
Frame 100/225.
Frame 200/225.
Frame 225/225.
wrote psi_md_traj.PB.fasta

If needed, you can download psi_md_traj.PB.fasta [here](https://raw.githubusercontent.com/pierrepo/PBxplore/master/demo_doc/psi_md_traj.PB.fasta).

Tips’n tricks¶

To flatten the PB sequences obtained in FASTA format, i.e. get PB sequences in a single line each, one solution could be:

$ wget https://files.rcsb.org/view/1AY7.pdb
$ PBassign -p 1AY7.pdb -o 1AY7
$ cat 1AY7.PB.fasta | sed "s/^>.*/\t/" | tr -d "\n" | tr "\t" "\n" > 1AY7.PB.flat

Content of 1AY7.PB.flat :

ZZbjadfklmcfklmmmmmmmmnnpaafbfkgopacehlnomaccddehjaccdddddehklpnbjadcdddfbehiacddfegolaccdddfkZZ
ZZcddfklpcbfklmmmmmmmmnopafklgoiaklmmmmmmmmpacddddddehkllmmmmnnommmmmmmmmmmmmmnopacddddZZ