Re: [ccp4bb] How to get formfactor for Zn +2.

[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



On 10/04/2011 03:56 PM, Garib N Murshudov wrote:

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
ATOM   1895  O   HOH C   1      -5.932  42.917  25.589  1.00 24.02           O

In your case all element names are moved towards left and B value of ZN is in 
incorrect position also.

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

Regards
Garib


On 4 Oct 2011, at 15:31, Eleanor Dodson wrote:

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

Garib N Murshudov
Structural Studies Division
MRC Laboratory of Molecular Biology
Hills Road
Cambridge
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk
Web http://www.mrc-lmb.cam.ac.uk