[phenixbb] hydrogen-bond restraints for Watson-Crick base pairs

[Scott Classen]

Hi all,

I set main.secondary_structure_restraints = True
and it appears that protein ss elements are found and added to the geo file, but watson crick pairs are not.

From the log file:

============================= Secondary structure =============================

No existing secondary structure definitions found.
  Interpreting HELIX and SHEET records from PDB file
  Running PROBE to identify base pairs

  34 helices and 4 sheets defined
  52.1% alpha, 9.0% beta

The eff file shows only helix and sheet records and no nucleic_acid records

My DNA looks like this:


HETATM    1  O5*  Ad D   1     -47.740 -49.121 -17.972  1.00 91.44           O  
ANISOU    1  O5*  Ad D   1    13002   6701  15042   3404   -258  -1747       O  
HETATM    2  C5*  Ad D   1     -47.012 -48.219 -17.145  1.00 89.95           C  
ANISOU    2  C5*  Ad D   1    12785   6488  14904   3328   -133  -1848       C  
HETATM    3  C4*  Ad D   1     -45.570 -48.166 -17.612  1.00 87.82           C  
ANISOU    3  C4*  Ad D   1    12704   6315  14346   3354    213  -1700       C  
HETATM    4  O4*  Ad D   1     -45.517 -47.624 -18.952  1.00 85.51           O  
ANISOU    4  O4*  Ad D   1    12694   6248  13549   3345     56  -1589       O  
HETATM    5  C3*  Ad D   1     -44.642 -47.267 -16.812  1.00 88.97           C  
ANISOU    5  C3*  Ad D   1    12860   6436  14508   3299    389  -1783       C  
HETATM    6  O3*  Ad D   1     -43.312 -47.719 -17.004  1.00 87.64           O  
ANISOU    6  O3*  Ad D   1    12793   6290  14216   3376    787  -1645       O  
HETATM    7  C2*  Ad D   1     -44.883 -45.902 -17.456  1.00 88.06           C  
ANISOU    7  C2*  Ad D   1    12951   6509  13998   3224     84  -1819       C  
HETATM    8  C1*  Ad D   1     -45.055 -46.290 -18.922  1.00 86.43           C  
ANISOU    8  C1*  Ad D   1    12944   6475  13420   3268     -4  -1650       C  
HETATM    9  N9   Ad D   1     -46.030 -45.477 -19.640  1.00 88.99           N  
ANISOU    9  N9   Ad D   1    13415   6923  13476   3202   -408  -1684       N  
HETATM   10  C8   Ad D   1     -47.262 -45.061 -19.205  1.00 91.41           C  
ANISOU   10  C8   Ad D   1    13632   7157  13943   3159   -766  -1828       C  
HETATM   11  N7   Ad D   1     -47.919 -44.338 -20.086  1.00 91.51           N  
ANISOU   11  N7   Ad D   1    13857   7306  13606   3115  -1076  -1814       N  
HETATM   12  C5   Ad D   1     -47.057 -44.279 -21.180  1.00 89.60           C  
ANISOU   12  C5   Ad D   1    13841   7242  12960   3112   -900  -1656       C  
HETATM   13  C4   Ad D   1     -45.889 -44.979 -20.917  1.00 87.68           C  
ANISOU   13  C4   Ad D   1    13517   6968  12828   3174   -500  -1580       C  
HETATM   14  N1   Ad D   1     -46.108 -43.812 -23.301  1.00 83.38           N  
ANISOU   14  N1   Ad D   1    13478   6809  11393   3063   -789  -1439       N  
HETATM   15  C2   Ad D   1     -45.046 -44.522 -22.903  1.00 82.39           C  
ANISOU   15  C2   Ad D   1    13235   6642  11427   3141   -430  -1387       C  
HETATM   16  N3   Ad D   1     -44.840 -45.143 -21.741  1.00 83.98           N  
ANISOU   16  N3   Ad D   1    13201   6650  12057   3203   -253  -1442       N  
HETATM   17  C6   Ad D   1     -47.151 -43.666 -22.454  1.00 87.19           C  
ANISOU   17  C6   Ad D   1    13821   7135  12171   3057  -1043  -1571       C  
HETATM   18  N6   Ad D   1     -48.209 -42.954 -22.862  1.00 88.07           N  
ANISOU   18  N6   Ad D   1    14074   7286  12102   2999  -1409  -1621       N  

Is there any reason it wouldn't be recognized by PROBE?

Thanks,
Scott

On Jun 22, 2010, at 2:21 PM, Scott Classen wrote:

> Hello friendly Phenix developers,
> 
> According to the CHANGES for phenix.refine 1.6.2-432 there is a new feature:
> 
> "hydrogen-bond restraints for Watson-Crick base pairs"
> 
> How do I use this? I couldn't find any documentation... or is it automagic?
> 
> Thanks,
> Scott