Thursday, 20 October 2011

How to get formfactor for Zn +2.

From: Eleanor Dodson
Date: 4 October 2011 15:31



Can anyone advise me how to get the Zn+2 formfactor from atomsf.lib

The input coordinate is given atom type ZN+2 but the formfactor is that for Zn:
I changed the atom name to Zn+2 but that made no difference...

ATOM   1893  O   UNK A 258      -8.934  52.268  49.467  0.00 66.53      O
ATOM   1894 ZN+2  ZN B   1     -10.456  38.580  26.267  1.00  57.36    ZN+2
ATOM   1895  O   HOH C   1      -5.932  42.917  25.589  1.00 24.02      O

refmac log says:

loop_
    _atom_type_symbol
    _atom_type_scat_Cromer_Mann_a1
    _atom_type_scat_Cromer_Mann_b1
    _atom_type_scat_Cromer_Mann_a2
    _atom_type_scat_Cromer_Mann_b2
    _atom_type_scat_Cromer_Mann_a3
    _atom_type_scat_Cromer_Mann_b3
    _atom_type_scat_Cromer_Mann_a4
    _atom_type_scat_Cromer_Mann_b4
    _atom_type_scat_Cromer_Mann_c


 N     12.2126   0.0057   3.1322   9.8933   2.0125  28.9975   1.1663  0.5826 -11.5290
 C      2.3100  20.8439   1.0200  10.2075   1.5886   0.5687   0.8650 51.6512   0.2156
 O      3.0485  13.2771   2.2868   5.7011   1.5463   0.3239   0.8670 32.9089   0.2508
 SE    17.0006   2.4098   5.8196   0.2726   3.9731  15.2372   4.3543 43.8163   2.8409
 S      6.9053   1.4679   5.2034  22.2151   1.4379   0.2536   1.5863 56.1720   0.8669
 ZN    14.0743   3.2655   7.0318   0.2333   5.1625  10.3163   2.4100 58.7097   1.3041


Eleanor

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From: Garib N Murshudov


If you will put element names in correct positions then refmac may have a chance to find it. Here is corrected positions:

ATOM   1893  O   HOH A 258      -8.934  52.268  49.467  0.00 66.53           O
ATOM   1894 ZN    ZN B   1     -10.456  38.580  26.267  1.00 57.36          ZN+2
In your case all element names are moved towards left and B value of ZN is in incorrect position also.
Regards
Garib
Garib N Murshudov 
Structural Studies Division
MRC Laboratory of Molecular Biology





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From: Eleanor Dodson
OK

So the ATOM TYPE has ZN O C S etc in column 77/78 and the +2 etc in 79/80

Is there any documentation for this?

E

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From: Garib N Murshudov

I think it is a pdb rule. Here are some of the rules:


Charges (confusingly) could be 2+ etc. 

Regards
Garib

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From: Ian Tickle





Yes, see: ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions/Format_v33_A4.pdf

Though this has been the format for ATOM/HETATM records ever since I can remember.

Cheers

-- Ian


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From: Frances C. Bernstein


I checked back and the 1992 format decscription did not use
columns 77 - 80 for ATOM/HETATM records.  But the 1996 document
did use them.  I then checked the old Newsletters and the proposed
use of columns 77 - 80 was discussed in April 1995.

                     Frances

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From: Eleanor Dodson


Thank you all. I had forgotten about checking pdb record formats..

Eleanor


It works when you follow the rules!


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