ADP does not have these synonyms. I can add this but it will be short
term solution. We need long term solution with backward
compatibility. I am working on that.
For short term synonyms for ADP (AMP, ATP, NAD, NDP etc) could be added.
Garib
On 8 Oct 2008, at 11:01, Martyn Winn wrote:
I believe Garib handles a lot of these things through the use of
synonyms, see mon_lib_list.html The section
data_comp_synonym_atom_list
has things like:
Ad . C1* 'C1''
Ad . C2* 'C2''
Is that what you wanted? Not sure if it is complete, e.g. not sure
if it
works for ADP.
Martyn
On Wed, 2008-10-08 at 10:06 +0100, Phil Evans wrote:
As far as I understand it (not very far), the PDB version 3 format
changes the naming of ribose ring atoms in nucleic acid to the
conventional C1', C2' etc from the version 2 C1* etc
The dictionaries supplied with Coot & Refmac have the V2 style names
C1* etc
eg a/ADP.cif
data_comp_ADP
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
ADP O2A O OP -0.500 0.000 0.000
0.000
ADP PA P P 0.000 1.026 1.100
0.106
ADP O1A O OP -0.500 1.921 1.136
1.326
ADP O3A O O2 0.000 2.021 1.042
-1.149
ADP PB P P 0.000 1.545 0.853
-2.667
ADP O3B O OP -0.660 2.802 0.361
-3.341
ADP O2B O OP -0.660 0.421 -0.149
-2.613
ADP O1B O OP -0.660 1.204 2.233
-3.157
ADP O5* O O2 0.000 0.378 2.570
0.052
ADP C5* C CH2 0.000 -0.566 2.955
-0.916
ADP H5*1 H H 0.000 -1.399 2.252
-0.844
ADP H5*2 H H 0.000 -0.084 2.847
-1.890
ADP C4* C CH1 0.000 -1.083 4.370
-0.761
ADP H4* H H 0.000 -1.632 4.428
0.189
ADP C3* C CH1 0.000 -2.090 4.668
-1.916
... etc
Should these dictionaries be changed?
Phil
--
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*
*
*
* Dr. Martyn
Winn *
*
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* STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD,
U.K. *
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Garib Murshudov
http://www.ysbl.york.ac.uk/YSBLPrograms/index.jsp
Erice 2010: Structure and Function from Macromolecular
Crystallography: Organization in Space and Time
http://www.crystalerice.org/erice2010/2010.htm
