[Xplor-nih] posSymmPot IVM problems

[Charles at Schwieters.org]

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Hello Jakob--

> I am trying to calculate the structure of a symmetric multimer.
> 
> I get problems when introducing the "new style nonstrict symmetry  
> term" created by "create_posSymmPot" (see code snippet below).
> I use a modified version of the "gb1_rdc/refine.py" script.
> 
> from "test.py"
> '''
> # Set up NCS potential
> from posSymmPotTools import create_PosSymmPot
> psp1 = create_PosSymmPot("ncs1")
> psp1.addEquivAtomSelPair("segid E and resid 1:6","segid C and resid 1:6")
> psp1.addEquivAtomSelPair("segid F and resid 1:6","segid D and resid 1:6")

this will not do what you expect: each line will restrain the center of
the first selection to the center of the second. You need to specify one
addEquivSelPair for each pair of *atoms*.

>      def step(*args): return _publicIVM.PublicIVM_step(*args)
> SystemError: xplor-nih error: eigen: 2 off-diagonal elements on an  
> intermediate tridiagonal form did not converge to zero.
> PyInterp::command: error executing: >execfile('test.py')<
> 

I believe the algorithm does not behave properly unless there are at
least three (maybe four?) EquivAtomPairs specified. We will add a check
for this condition in future releases.

> Can you help me to find the error, switching to generic NCS term from  
> the generic xplor interface produces no errors.
> 

The next release of Xplor-NIH will have a simplified interface to
PosSymmPot for this case. Until then the NCS XplorPot term maybe
easier to use.

> 
> Furthermore, I use a distance symmetry potential. It seems to be  
> impossible to set potential type to "symmetry" with:
> 
> pot.setPotType("symmetry")
> 

are you referring to the XPLOR NOE distance symmetry term? The Python
NOEPot does not support this: use the NOE XplorPot term instead.

best regards--
Charles
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