Hello HOU--
> I am trying to use a modified version of refine.py ( eginput/gb1_rdc) to
> refine a structure using PCSs only. I have three experimental PCS data-sets
> from three different positions.
>
> There are many error messages when I run the script:
> ---------------------------------------------------------------------------------------------------------------------------------------------
> return _rdcPot.RDCPot1_addRestraints(self, *args, **kwargs)
> SystemError: xplor-nih error: error reading restraint: selection string resid
> 500 and name OO selects no atoms
> PyInterp::command: error executing: >execfile('refinePCS.py')<
> --------------------------------------------------------------------------------------------------------------------------------------------------
> My restraint file is in Xplor format from Numbat:
> assign ( resid 500 and name OO )
> ( resid 500 and name Z )
> ( resid 500 and name X )
> ( resid 500 and name Y )
> ( resid 69 and name H ) -0.02600 0.20000
Apparently, Numbat restraints aren't quite right for Xplor-NIH input.
> For rdcPot, it seems that the Assign command must be followed by six
> selections, but for PCS, only five selections have been generated by Numbat.
> In RDC restraints, the fifth line should be the coupled nuclues, and the sixth
> line is detected nuclues. What I should set in PCS?
In RDCPot, the first 4 atom selections are actually ignored, and can
be anything (but the 4 sets of parentheses are still required).
> Perhaps the OO position( paramagneitc center postion). so I tried again by the
> restraint file as following:
> My restraint file is in Xplor format from Numbat:
> assign ( resid 500 and name OO )
> ( resid 500 and name Z )
> ( resid 500 and name X )
> ( resid 500 and name Y )
> ( resid 500 and name OO )
> ( resid 69 and name H ) -0.02600 0.20000
I suggest that the alignment tensor be completely separate from the
paramagnetic center, and that you instead include the atom explicitly
(like TM+3) in the PSF. A simpler restraint format can be used if you
utilize the rdcPotTools.spaceSeparatedToRestraint function to do the
conversion on input. e.g.
from rdcPotTools import spaceSeparatedToRestraint
restraints = spaceSeparatedToRestraint(open("restraints.txt").read(),
atom1Name='TM+3',
atom2Name='HN',
residCol=1, rdcCol=2, errCol=3)
rdc = create_RDCPot("%s_%s"%(medium,expt),restraints=restraints,
media[medium])
If the local environment of the paramagnetic tags are identical, it
may be useful to use a single alignment tensor with the local
environment defined for each tag. This can be achieved using
rdc.setLocalTensors( [(a1,b1,c1), ...] )
where the argument is a list of three atoms for each tag site,
defining the local coordinate system.
I hope this helps some--
Charles
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