Demo FlexRNA¶
This example generates logfile demo_FlexRNA.log
. The logfile is automatically displayed after completion by the #report
directive at the end.
Modules used¶
Modules Prepare
, FlexRNA
, and YasaraRefine
are used.
Functionality¶
This example excises dlexible RNA linkers from a model of the RsmE/RsmZ complex, regenerates them by FlexRNA, and refines the model by calling Yasara.
First, the prepare module is used to generate a template containing only the copies of the RsmE protein, the RNA stemloops of RsmZ, and a short piece of an RNA linker that is bound to an RsmE molecule.
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 and linker piece 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 order to regenerate the four excised short flexible RNA linkers, FlexRNA
is called four times. Each call specifies 75% coverage of the conformation space, generation of one model per template, and a maximum computation time of 0.1 h.
In the first call, the input read by addpdb
is the rigid-body file generated by the previous Prepare
block.
The sequence ACAG
of the missing nucleotides 16-19 is specified and the 5’-anchor (I)15
and 3’-anchor (G)20
are specified as well.
The output PDB file is saved with basis name RsmE_RsmZ_SL1_SL2
. This example does not specify distance distribution restraints for the RNA.
In the second call, the addpdb
statement refers to the output of the first call. This requires a wildcard filename RsmE_RsmZ_SL1_SL2_*.pdb
.
The 5’-anchor nucleotide, which would have been (G)35
in the rigid-body file save by Prepare
must be referred to as (I)35
.
This is because the previous FlexRNA
module linked chains (I)
and (G)
and, since the first piece was chain (I)
, named the resulting chain (I)
.
The two remaining calls of FlexRNA
are analogous to the second call.
Finally, the complete model is refined by a call to YasaraRefine with maximum computatipn time of 1 h.
Outputs¶
Outputs are the rigid-body template file RsmE_RsmZ_rigid_bodies.pdb
and the PDB files of all intermediate models and of the final model.