Demo Rigi¶
Run it by typing MMMx demo_Rigi. This example generates logfile demo_rigi.log. The logfile is automatically displayed after completion by the #report directive at the end.
Modules used¶
Modules Prepare and Rigi are used.
Source code¶
#log
!prepare
getpdb 2MF1 RSM0
merge RSM1 % only backbone coordinates are used for pseudo-symmetry transform
RSM0 {1}(A)1-59
RSM0 {1}(B)1-59
RSM0 {1}(C)1-59
RSM0 {1}(D)1-59
RSM0 {1}(E)1-59
RSM0 {1}(F)1-59
RSM0 {1}(G)20-35
RSM0 {1}(G)44-56
RSM0 {1}(G)1-15
RSM0 {1}(G)59-72
RSM0 {1}(G)38-40
.merge
save RsmE_RsmZ_rigid_bodies RSM1 RSM1 % save a PDB file that contains only the rigid bodies
.prepare
!rigi % call the Rigi method
rbtemplate RsmE_RsmZ_rigid_bodies.pdb
separate on
maxtrials 50000
save RsmE_RsmZ_rba
probability 0.5
rigid (A) (B) (G) (H)
(A)8 mtsl
(A)40 mtsl
(B)40 mtsl
.rigid
rigid (C) (D) (I) (J)
(C)8 mtsl
(C)40 mtsl
(D)40 mtsl
.rigid
rigid (E) (F) (K)
(E)8 mtsl
(E)40 mtsl
(F)40 mtsl
.rigid
ddr mtsl
% 18 core restraints
(A)8 (C)8 34.8 3.7
(A)8 (C)40 65.4 2.8
(A)8 (D)40 66.1 3.1
(A)40 (C)8 54.9 3.2
(A)40 (C)40 83.8 2.5
(B)40 (C)40 86.2 3.2
(A)8 (E)40 20.5 2.2
(A)40 (E)8 53.1 3.0
(A)40 (E)40 51.5 2.9
(B)40 (E)40 49.2 2.6
(A)8 (F)40 21.7 2.4
(A)40 (F)40 50.8 2.6
(B)40 (F)40 49.0 2.4
(C)8 (E)8 16.0 2.1
(C)8 (E)40 46.6 2.8
(D)40 (E)8 49.3 2.8
(D)40 (E)40 77.8 2.6
(C)40 (F)40 77.7 2.4
% 6 auxiliary protein-protein restraints
(B)8 (D)40 54.0 2.9
(B)8 (C)40 54.4 3.0
(D)8 (F)40 49.4 3.6
(C)40 (F)8 51.3 3.1
(A)8 (D)8 33.6 3.4
(B)40 (D)8 55.2 2.9
.ddr
nlink
(I)15 (G)20 5 30 % SL1 16/ SL2 19
(G)35 (K)38 3 18 % SL2 36/ Link(2,3) 38
(K)40 (H)44 4 24 % Link(2,3) 40/ SL3 44
(H)56 (J)59 3 18 % SL3 56/ SL4 59
.nlink
.rigi
# report
Functionality¶
This example reassembles the RsmE/RsmZ complex, excluding flexible RNA linkers, from its parts and from simulated distance distribution restraints.
First, the prepare module is used to generate a rigid-body template containing only the copies of the RsmE protein and the RNA stemloops of RsmZ.
To this end, structure 2MF1 is downloaded from the PDB and stored in entity RSM0. The six RsmE copies are chains A-F, residues 1-59. They are extracted from the first model {1} of this NMR structure ensemble.
The stemloops are extracted from chain G of this model. All these parts are merged into entity RSM1. This entity is then saved to file Rsme_Rsmz_rigid_bodies.pbd with pseudo-PDB identifier RSM1.
In the rigi module, this PDB file is specified as rigid-body template. The rigid bodies are separated from each other. A maximum number of 50000 trials is specified.
The rigid-body arrangements are saved in MMMx-internal format to file RsmE_RsmZ_rba.mat. The rigid-body arrangements cover 50% of total probability.
Rigid body 1 is assmebled from an RsmE dimer (chains A and B of the tempalte) and the stemlops attached to this dimer (chains G and H of the template, corresponding to (G)20-35 and (G)44-56 in PDB structure 2MF1).
Residues 8 and 40 in chain A and residue 40 in chain B are specified as reference labelling sites with spin label mtsl.
Rigid body 2 is assembled analogously. Rigid body 3 features only one stemloop.
Then, 18 distance distribution restraints with mtsl labels are specified between reference sites (core restraints) and six further restraints are specified that involve equivalent sites, which are not reference sites (auxiliary restraints). Each restraint is specified by the mean distance and standard deviation of the distance distribution.
Finally, the nucleotide links between the stemloops are specified, each by the number of nucleotide links and the maximum distance. For the maximum distance, 6 Å per nucleotide link are assumed.
Outputs¶
Outputs are the rigid-body template file RsmE_RsmZ_rigid_bodies.pdb and the rigid-body arrangement file RsmE_RsmZ_rba.mat.