Hi there,
I'm trying to use the *IMP.pmi.tools.set_coordinates_from_rmf *to start modelling a complex from a previous modelled frame. In a first step, I set the whole structure as a single rigid body and perform 100 rex frames. In the second step I want to use the frame 99 of this modelling as starting point, but now I want to divide the structure into several rigid parts and super rigid bodies.
However, the first frame has not the exact same coordinates as in the 99th from the first step using the method mentioned above.
I'm using two different topology files:
For instance: topology1.txt |molecule_name ... |chain|residue_range ... |rigid_body |super_rigid_body subunit1 A 1,10 1 1 subunit1 A 11,20 1 1 subunit2 B 1,15 1 1 subunit2 B 6,25 1 1 ...
topology2.txt |molecule_name ... |chain|residue_range ... |rigid_body |super_rigid_body subunit1 A 1,10 1 1 subunit1 A 11,20 2 1 subunit2 B 1,15 3 2 subunit2 B 6,25 4 2 ....
I tried also by not shuffling the system in case that was the error, but the same output was obtained. What may be wrong?
Thanks in advance!
Altair
On 12/10/20 2:44 PM, Altair Hernández wrote: > I'm trying to use the *IMP.pmi.tools.set_coordinates_from_rmf *to start > modelling a complex from a previous modelled frame.
This will only work if the topologies of the two complexes are the same.
> In a first step, I > set the whole structure as a single rigid body and perform 100 rex > frames. In the second step I want to use the frame 99 of this modelling > as starting point, but now I want to divide the structure into several > rigid parts and super rigid bodies.
This won't work because the RMF file doesn't save the global coordinates of each particle in the rigid body - it saves the reference frame of the body and the body-frame coordinates (relative to that frame) of each particle. So there's only one reference frame in the RMF (for the one rigid body in the original modeling) and you're trying to apply it to multiple rigid bodies. If you have the same set of particles in both cases, you should be able to read in their global coordinates, then map them to body-frame coordinates for each new rigid body. (There are methods in the RigidBody class to do this.) Or you could just set all your new rigid bodies to have the same reference frame. But this would be an "exercise for the reader" - there is no code in PMI (to my knowledge) to do this.
Another option would be to write out PDB or mmCIF files for each subunit from your first simulation, then use these in the topology file for the second one.
Ben
Thanks Ben!
Writing out PDB files from the first simulation and using them in the top file for the second one worked well!
Best
Altair
On Sat, 12 Dec 2020 at 02:13, Ben Webb ben@salilab.org wrote:
> On 12/10/20 2:44 PM, Altair Hernández wrote: > > I'm trying to use the *IMP.pmi.tools.set_coordinates_from_rmf *to start > > modelling a complex from a previous modelled frame. > > This will only work if the topologies of the two complexes are the same. > > > In a first step, I > > set the whole structure as a single rigid body and perform 100 rex > > frames. In the second step I want to use the frame 99 of this modelling > > as starting point, but now I want to divide the structure into several > > rigid parts and super rigid bodies. > > This won't work because the RMF file doesn't save the global coordinates > of each particle in the rigid body - it saves the reference frame of the > body and the body-frame coordinates (relative to that frame) of each > particle. So there's only one reference frame in the RMF (for the one > rigid body in the original modeling) and you're trying to apply it to > multiple rigid bodies. If you have the same set of particles in both > cases, you should be able to read in their global coordinates, then map > them to body-frame coordinates for each new rigid body. (There are > methods in the RigidBody class to do this.) Or you could just set all > your new rigid bodies to have the same reference frame. But this would > be an "exercise for the reader" - there is no code in PMI (to my > knowledge) to do this. > > Another option would be to write out PDB or mmCIF files for each subunit > from your first simulation, then use these in the topology file for the > second one. > > Ben > -- > ben@salilab.org https://salilab.org/~ben/ > "It is a capital mistake to theorize before one has data." > - Sir Arthur Conan Doyle >
participants (2)
-
Altair Hernández -
Ben Webb