selection of different residue ranges for a NCS group
Dear All, I am trying to select different regions of the same protein to be included in the same NCS group before refinement. This correspond to the core of a protein. Additionally, I would define other NCS groups for external domains. I have 4 protein/RNA complexes in the asu, P1. Here are the residue ranges for the NCS group corresponding to the core of the protein (invariant): Chain A and resseq: 1:156, 188-227, 413:568, 629:794 this should be the reference group, to match the same region in the other 3 monomers (C, E. G). Other NCS groups will include the RNA, as well as other external domains: Chain B and resseq: 1: 87 This is the RNA molecule, that should match the other 3 monomers (D, F, H) Chain A resseq: 157:187 this is a external domain, to match the other protein monomer (C, E, G) and so on.... for other external domain I have seen that there is the possibility to use user-defined NCS groups, by using: * ncs_groups.params * or modifying the GUI by editing the atom selection For the external domains I think is easy as the syntax is only one line, however for the core of the protein I do not manage to select properly the different residue ranges. Could anybody please help on that? what would be the easiest way to do that? Can I for example creat a ncs_groups.params file and add it to phenix.refine in the GUI? Thanks in advance, Andres
On Thu, Mar 7, 2013 at 10:49 AM, Andres PALENCIA
Can I for example creat a ncs_groups.params file and add it to phenix.refine in the GUI?
Yes, you can just drag it into the list of input files. However, I am not sure if this is actually necessary. The older "global" or Cartesian NCS restraints often required manual setup of restraint groups because they were insensitive to local deformations. The torsion restraints (which have been the default for several versions now) only restrain local structure, so there is no reason for instance why you can't restrain chains which contain domain movements. The intent was for them to be completely automatic, although in practice you might want to adjust the restraint settings slightly. Of course if you have an example where the automatic setup is insufficient, I'm sure Jeff would be interested in seeing it. -Nat
Dear All,
I am trying to select different regions of the same protein to be included in the same NCS group before refinement. This correspond to the core of a protein. Additionally, I would define other NCS groups for external domains. I have 4 protein/RNA complexes in the asu, P1. Here are the residue ranges for the NCS group corresponding to the core of the protein (invariant):
Chain A and resseq: 1:156, 188-227, 413:568, 629:794
this should be the reference group, to match the same region in the other 3 monomers (C, E. G). Other NCS groups will include the RNA, as well as other external domains:
Chain B and resseq: 1: 87 This is the RNA molecule, that should match the other 3 monomers (D, F, H)
Chain A resseq: 157:187 this is a external domain, to match the other protein monomer (C, E, G)
and so on.... for other external domain
I have seen that there is the possibility to use user-defined NCS groups, by using:
* ncs_groups.params * or modifying the GUI by editing the atom selection
For the external domains I think is easy as the syntax is only one line, however for the core of the protein I do not manage to select properly the different residue ranges.
Could anybody please help on that? what would be the easiest way to do that?
Thanks in advance,
Andres
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Andres PALENCIA -
Nathaniel Echols