Choosing the right presentation format#
By default Deemian uses detailed_conf_first for the readable output format.
There are six available format that can be used:
Priority |
Detailed |
Clustered |
Summarized |
|---|---|---|---|
conformation first |
|
|
|
interaction type first |
|
|
|
By now you should be familiar with the detailed_conf_first format as it is the one used in getting started and tutorials, now is time to find out the clustered and summarized one.
Clustered means that instead of listing the interaction one by one, the interaction will be clustered based on residue id and chain.
While the summarized one means that rather than showing the detail of interaction it will display the number of interaction per residue pair.
To quickly compare the three of them lets use the script from getting started and add a few lines to get three output format at once:
n1-oseltamivir-5nzn-three-format.txt
molecule 5nzn.pdb [
select protein_A = chain A and protein
select oseltamivir = chain A and resname G39
assign bond oseltamivir template CCC(CC)O[C@@H]1C=C(C[C@@H]([C@H]1NC(=O)C)N)C(=O)O
]
measure protein_ligand [
ionizable positive true
ionizable negative true
interactions all
between oseltamivir and protein_A
]
present protein_ligand [
interactions detailed_conf_first n1_g39_5nzn_detailed.txt
interactions clustered_conf_first n1_g39_5nzn_clustered.txt
interactions summarized_conf_first n1_g39_5nzn_summarized.txt
deemiandata n1_g39_5nzn_ionizable_corrected.dd
]
Running the script above will generate three output in readable formats:
Deemian version: 0.0.0.post71+bad1636
interaction for "oseltamivir:protein_A":
conf 1
ELECTROSTATIC as_cation:
oseltamivir protein_A
id 19 281 282 529
atom_name N4 OE1 OE2 OD1
res_name G39 GLU GLU ASP
res_num.chain 503.A 119.A 119.A 151.A
distance 4.206 2.744 3.157
ELECTROSTATIC as_anion:
oseltamivir protein_A
id 1 271 272 273 2202 2203 2204
atom_name O1A CZ NH1 NH2 CZ NH1 NH2
res_name G39 ARG ARG ARG ARG ARG ARG
res_num.chain 503.A 118.A 118.A 118.A 368.A 368.A 368.A
distance 3.646 2.800 3.584 3.625 2.832 3.523
id 2 1624 1625 1626 2202 2203 2204
atom_name O1B CZ NH1 NH2 CZ NH1 NH2
res_name G39 ARG ARG ARG ARG ARG ARG
res_num.chain 503.A 293.A 293.A 293.A 368.A 368.A 368.A
distance 3.547 3.181 3.015 3.702 3.677 2.833
Deemian version: 0.0.0.post71+bad1636
interaction for "oseltamivir:protein_A":
conf 1
ELECTROSTATIC as_cation:
oseltamivir protein_A
G39 GLU ASP
503.A 119.A 151.A
id 19 281 282 529
atom_name N4 OE1 OE2 OD1
distance 4.206 2.744 3.157
ELECTROSTATIC as_anion:
oseltamivir protein_A
G39 ARG ARG
503.A 118.A 368.A
id 1 271 272 273 2202 2203 2204
atom_name O1A CZ NH1 NH2 CZ NH1 NH2
distance 3.646 2.800 3.584 3.625 2.832 3.523
G39 ARG ARG
503.A 293.A 368.A
id 2 1624 1625 1626 2202 2203 2204
atom_name O1B CZ NH1 NH2 CZ NH1 NH2
distance 3.547 3.181 3.015 3.702 3.677 2.833
Deemian version: 0.0.0.post71+bad1636
interaction for "oseltamivir:protein_A":
conf 1
ELECTROSTATIC as_cation has interactions with interaction numbers
oseltamivir protein_A
G39 503.A GLU 503.A 2
ASP 503.A 1
ELECTROSTATIC as_anion has interactions with interaction numbers
oseltamivir protein_A
G39 503.A ARG 503.A 3
ARG 503.A 3
ARG 503.A 6
As shown above, we can see that in detailed mode and clustered mode the results are pretty similar. The only difference is how the interactions are getting clustered based on the residue id in clustered mode. The summarized mode give much simpler output as it leave the atom id and atom name details and only present the number of interactions.
The other format choice is conformation first versus interaction type first.
This option is only useful when there are multiple conformation being analyzed.
Sometime we would like to compare the interaction between conformations for specific interaction type (such as electrostatic), in this case using detailed_type_first or clustered_type_first would be more effective.