unread mercury

Axel T. Brunger brunger at LAPLACE.CSB.YALE.EDU
Mon Sep 2 21:05:35 EST 1996


Your definition of the chemical atom type of mercury probably
doesn't match chemical HG+* .  Do a 

vector show elem ( chemical ) ( <select mercury atom here>) 


Note, that complete scattering tables are avaiable in the
developmental version of X-PLOR (file $XTALLIB/scatter.lib for
normal scattering, and two anomalous scattering libraries).  

Axel Brunger


A Rashid wrote:
> 
> Dear xplorers,
> 
>         I have been doing refinments on my protein (rigid body, positional, etc.)
> and I just noticed that the program does not seem to recognize an atom in the
> structure, namely a mercury. The output from the check,inp ( or any other routine
> for that matter) is:
> 
> ==================================
>  XREFINE>   SCATter ( chemical C* )
>  SELRPN:   1468 atoms have been selected out of   2773
>  a1=      2.31000 20.8439 1.02000 10.2075 1.58860 .568700 .865000 51.6512 .215600
>  XREFINE>   SCATter ( chemical N* )
>  SELRPN:    392 atoms have been selected out of   2773
>  a1=      12.2126 .005700 3.13220 9.89330 2.01250 28.9975 1.16630 .582600 -11.529
>  XREFINE>   SCATter ( chemical O* )
>  SELRPN:    409 atoms have been selected out of   2773
>  a1=      3.04850 13.2771 2.28680 5.70110 1.54630 .323900 .867000 32.9089 .250800
>  XREFINE>   SCATter ( chemical S* )
>  SELRPN:      4 atoms have been selected out of   2773
>  a1=      6.90530 1.46790 5.20340 22.2151 1.43790 .253600 1.58630 56.1720 .866900
>  XREFINE>   SCATter ( chemical P* )
>  SELRPN:      0 atoms have been selected out of   2773
>  a1=      6.43450 1.90670 4.17910 27.1570 1.78000 0.52600 1.49080 68.1645 1.11490
>  XREFINE>   SCATter ( chemical FE* )
>  SELRPN:      2 atoms have been selected out of   2773
>  a1=      11.1764 4.61470 7.38630 0.30050 3.39480 11.6729 0.07240 38.5566 0.97070
>  XREFINE>   SCATter ( chemical HG+* )
>  SELRPN:      0 atoms have been selected out of   2773
>  a1=      29.5641 1.21152 18.0600 7.05639 12.8374 0.28473 6.89912 20.7482 10.6268
> 
> ==================================
> 
> at the end you can see that the program thinks that there are 0 HG+ atoms. The
> program recognizes all the rest including the FE on the HEM.
> If anyone has an idea as to why this is happening please let me know.
> Thank you in advance and have a nice labor day weekend.
> 
>                         Sincerely,
>                         Ali

-- 
=======================================================================
| Axel T. Brunger          Dept. Molecular Biophysics and Biochemistry|
| Professor/Investigator   Bass Center, 266 Whitney Avenue            |
| Office: 203-432-6143     Howard Hughes Medical Institute/Yale Univ. |
| FAX:    203-432-6946     New Haven, CT 06520, USA.                  |
| http://xplor.csb.yale.edu/~brunger                                  |
| mailto://brunger@laplace.csb.yale.edu                               |
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