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
----------
From: Garib N Murshudov
----------
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
----------
From: Garib N Murshudov
----------
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
----------
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
=====================================================
**** Bernstein + Sons
* * Information Systems Consultants
**** 5 Brewster Lane, Bellport, NY 11713-2803
----------
From: Eleanor Dodson
Thank you all. I had forgotten about checking pdb record formats..
Eleanor
It works when you follow the rules!
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
----------
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
Structural Studies Division
MRC Laboratory of Molecular Biology
----------
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
----------
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
----------
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
----------
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
=====================================================
**** Bernstein + Sons
* * Information Systems Consultants
**** 5 Brewster Lane, Bellport, NY 11713-2803
----------
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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