Run it by typing
MMMx demo_ExperimentDesign. This example generates logfile
ExperimentDesign is used.
% MMMx Demo: Functionality of the ExperimentDesign module % # log !ExperimentDesign import 2LZM T4L % load T4 lysozyme crystal structure import 2ADC RRM % load NMR structure of an RNA recognition motif sitescan mtsl T4L T4L_sites % sitescan for T4 Lysozyme, default set CILMSTV of residues sitescan mtsl RRM RRM_sites I % sitescan for the protein part of the RRM, only isoleucine sitescan iap-4tu RRM SL_sites u 1 0.1 % sitescan (only uracil) for the RNA part pairlist T4L_sites T4L T4L_pairs 15 80 % a site pair list for T4 lysozyme hetpairlist RRM_sites SL_sites RRM RRM_pairs 15 80 plot T4L_distributions pdf distributions mtsl T4L T4L_distribution 68 131 72 131 75 131 76 131 79 131 86 131 89 131 109 131 .distributions plot RRM_distributions pdf distributions mtsl|iap-4tu RRM RRM_distribution RRM_pairs .distributions import 1BUY EPO % import what was once very popular in professional cycling sitescan mtsl EPO EPO_sites % perform site scan ENMpairs EPO_sites EPO EPO_enm_pairs 15 80 % score site pairs for elastic network modeling .ExperimentDesign # report
The demo imports a T4 Lysozyme structure with PDB identifier
2LZM and stores it with internal identifier
It also imports a RNA recognition motif with bound RNA stemloop with PDB identifier
2ADC and stores it with internal identifier
The first spin-labelling sitescan is performed with spin label
mtsl on entity
T4L and stored in file
T4L_sites.lst. The extension
.lst is appended by default.
The demo then performs two spin-labeling sitescans on the RRM/stemloop complex. First, a scan with label
mtsl is performed on entity
RRM, generating site list
RRM_sites. The RRM is scanned only for substituting isoleucine residues by a spin label.
Second, a scan with label iodoacetamido-proxyl as a thiouracil label is performed on entity
RRM, generating site list
SL_sites. Only uracil nucleotides are considered for labeling.
The demo then generates two site pair lists, one from
T4L_sites.lst referring to entityt
T4L and stores it in file
Site pairs are included only if the mean distance ranges between 15 and 80 Å. The second list combines labels from
RRM_sites.lst with labels from
SL_sites.lst, referring to entity
The pair list is stored as
RRM_pairs.lst and again site pairs are included only if the mean distance ranges between 15 and 80 Å.
Then, basis file name
T4L_distributions is declared for distance distribution output plots and file format
mtsl for entity
T4L and are stored in numerical format with basis file name
A list of 8 spin pairs is declared. Note that this computation of distance distributions does not require a previous site scan or pair list generation.
After this, a new basis file name
RRM_distributions is declared for plots, which are again stored in
An orthogonal spin labelling scheme with labels
iap-4tu is used.
The final example of this demo imports PDB structure
1BUY of erythropoietin into entity
EPO. At sitescan with
mtsl is performed to provide list
Site pairs are generated and scored from this list for elastic network modeling of conformation change of EPO. The list is stored as
EPO_enm_pairs.lst, considering only pairs with mean distance between 15 and 80 Å.
Site and pair list are stored in a self-explaining human-readable format. Figures are stored as vector graphics in PDF format.
Distance distributions are stored as comma-separated value (
.csv) files with the distance in units of Å as the first column and probability density in units of as the second column.