My software notes

February 8, 2012

water refinement in Xplor-NIH

Filed under: xplor/xplor-nih/cns — kpwu @ 1:23 pm

Starting at Xplor-NIH 2.26 (now it’s version 2.29 on Feb. 8th, 2012), official Xplor-NIH package provides an example script doing explicit solvent refinement. The short description made by Xplor-NIH author:

refinement with explicit solvent and full electrostatics. Includes rdcs, noes, jcoupling terms and dihedral restraints. This is a work-in-progress. Please compare with other protocols. In particular, this protocol seems to result in structures for which the DIHE term is large.

Note on J-coupling violations:

Calculated structures exhibit at least four consistently violated J-coupling restraints. These restraints are at or near mobile loop regions where the single structure approximation breaks down. In these regions an ensemble of structures must be used to fit all experimental data. Please see the gb3_ensemble directory for an example of ensemble refinement.

The script can be found (after version 2.26) at : XPLOR-NIH HOME/eginput/gb1_rdc

I did a quick try using a 90-aa protein–a small protein I am working on determining the solution structure. The input structure was originally refined by the refinement script provided by Xplor-NIH (with NOE, CDIH, RDC) from simulated annealed  templates. The structural quality after regular refinement has been improved a lot ( by checking the Ramachandran plot: from ~60% to 85%). But the water refinement makes the solution structure better (85% –> 95%) although a lot of DIHE violations are noted by Xplor-NIH (same issue as issued by the author).

Here is the analysis done by Molprobity ( showing improved scores and structural quality.

1. Ramachandran plot of structure refined by NOE, CDIH and RDC only.

2. Structure in #1 was refined by water refinement

3. Molprobity analysis of structures in 1 (up) and 2 (down) (click to see full sized snapshots)


  1. I also find that the DIHE terms is really high in version 2.32. Regardless, the final structure using the script is better than without the water refinement according to procheck. Does anynone know why the DIHE term is so high?

    Comment by Marie Tremblay — May 13, 2013 @ 11:10 am | Reply

  2. The author has said something about it at Xplor-NIH forum on Jan16, 2013:

    Hash: SHA256

    Hello Gary–

    >we are planning to do some refinement in a water box and with
    >electrostatics turned on. I found a pointer to your example scripts in
    >blog post from a while back:
    >According the the post there seemed to be a known problem with large
    >DIHE terms, however, the comment on the file hasd dissapeared so i
    >presume this has been fixed (It didn’t seemed to be mentioned in the
    >release notes)?

    The “issue” is that a large number of DONE violations are reported. This is likely due to a threshold value which is too small. I think everything should be working fine.

    Best regards–

    Comment by kpwu — May 13, 2013 @ 11:55 am | Reply

  3. I would like to include ensemble files in the water refinement script. I tried give file names in the script.

    could you please let me know how to include pdb files in water refinement.

    import glob
    #this could also be a list of filenames

    Comment by srini2201 — December 16, 2016 @ 12:17 pm | Reply

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