PBcount

PBcount computes the frequency of PBs at each position along the amino acid sequence.

Note

The following examples require psi_md_traj.PB.fasta and
psi_md_traj2.PB.fasta obtained with PBassign:
$ wget https://raw.githubusercontent.com/pierrepo/PBxplore/master/demo_doc/psi_md_traj_1.gro
$ wget https://raw.githubusercontent.com/pierrepo/PBxplore/master/demo_doc/psi_md_traj_1.xtc
$ PBassign -x psi_md_traj_1.xtc -g psi_md_traj_1.gro -o psi_md_traj_1
Frame 1/225.
Frame 100/225.
Frame 200/225.
Frame 225/225.
wrote psi_md_traj_1.PB.fasta

$ wget https://raw.githubusercontent.com/pierrepo/PBxplore/master/demo_doc/psi_md_traj_2.gro
$ wget https://raw.githubusercontent.com/pierrepo/PBxplore/master/demo_doc/psi_md_traj_2.xtc
$ PBassign -x psi_md_traj_2.xtc -g psi_md_traj_2.gro -o psi_md_traj_2
Frame 1/225.
Frame 100/225.
Frame 200/225.
Frame 225/225.
wrote psi_md_traj_2.PB.fasta

If needed, you can download [psi_md_traj_1.PB.fasta](https://raw.githubusercontent.com/pierrepo/PBxplore/master/demo_doc/psi_md_traj_1.PB.fasta) and [psi_md_traj_2.PB.fasta](https://raw.githubusercontent.com/pierrepo/PBxplore/master/demo_doc/psi_md_traj_2.PB.fasta).

Example

$ PBcount -f psi_md_traj_1.PB.fasta -o psi_md_traj_1
read 225 sequences in psi_md_traj_1.PB.fasta
wrote psi_md_traj_1.PB.count

Content of psi_md_traj_1.PB.count:

         a     b     c     d     e     f     g     h     i     j     k     l     m     n     o     p
1        0     0     0     0     0     0     0     0     0     0     0     0     0     0     0     0
2        0     0     0     0     0     0     0     0     0     0     0     0     0     0     0     0
3        0     0     0     4     0   221     0     0     0     0     0     0     0     0     0     0
4        0     0     0     0     0     5     0     0     0     0   220     0     0     0     0     0
[snip]
51       0     0     0     0     0    56     0    98     0     0    71     0     0     0     0     0
52       0    56     0     0     0     0     0     0    94     3     3    69     0     0     0     0
53     144     0    60     2     0     0     0     0     0     0     0     0     1     0     0    18
54       0     0   225     0     0     0     0     0     0     0     0     0     0     0     0     0
55       0     0     0     0     0     0     0     0     0     0     0     0     0     0     0     0
56       0     0     0     0     0     0     0     0     0     0     0     0     0     0     0     0

Note that residues 1, 2, 55 and 56 have a null count of all PBs. These residues are the first and last residues of the structure and no PB can be assigned to them.

If needed, you can download [psi_md_traj_1.PB.count](https://raw.githubusercontent.com/pierrepo/PBxplore/master/demo_doc/psi_md_traj_1.PB.count).

Usage

Here’s the PBcount help text.

usage: PBcount [-h] -f F -o O [--first-residue FIRST_RESIDUE]

Compute PB frequency along protein sequence.

optional arguments:
  -h, --help            show this help message and exit
  -f F                  name(s) of the PBs file (in fasta format)
  -o O                  name for results
  --first-residue FIRST_RESIDUE
                        define first residue number (1 by default)
  -v, --version         show program's version number and exit

-f option

can be used several times:

$ PBcount -f psi_md_traj_1.PB.fasta -f psi_md_traj_2.PB.fasta -o psi_md_traj_all
read 225 sequences in psi_md_traj_1.PB.fasta
read 225 sequences in psi_md_traj_2.PB.fasta
wrote psi_md_traj_all.PB.count

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

–first-residue option

By default, the number of the first residue is 1, this option allows to adjust the number associated to the first residue (and to the followings automaticaly).

$ PBcount --first-residue 5 -f psi_md_traj_1.PB.fasta -o psi_md_traj_1_shifted
read 225 sequences in psi_md_traj_1.PB.fasta
wrote psi_md_traj_1_shifted.PB.count

Content of psi_md_traj_1_shifted.PB.count:

         a     b     c     d     e     f     g     h     i     j     k     l     m     n     o     p
5        0     0     0     0     0     0     0     0     0     0     0     0     0     0     0     0
6        0     0     0     0     0     0     0     0     0     0     0     0     0     0     0     0
7        0     0     0     4     0   221     0     0     0     0     0     0     0     0     0     0
8        0     0     0     0     0     5     0     0     0     0   220     0     0     0     0     0
9        0   222     0     0     0     0     0     0     0     0     0     3     0     0     0     0
10       6     0   201     0     0     5     0     0     0     0     0     0    12     0     1     0
[snip]

If needed, you can download [psi_md_traj_1_shifted.PB.count](https://raw.githubusercontent.com/pierrepo/PBxplore/master/demo_doc/psi_md_traj_1_shifted.PB.count).