Miguel wrote:
Hello,
The notation 1Hxx is unfortunately standard in all the PDB files
reporting the coordinates of Hydrogens and it corresponds to Hxx1 in
standard IUPAC notation. It comes from the fact that initially in
the PDB format 3 char slots were reserved for the atom names : it was
enough for the X-Ray diffraction models, the methodology does not
allow to determine the position of Hydrogens. But when the
structures with Hydrogens come out, there was no place for 4 chars
atom names. The solution that have been adopted : place the forth
character before the first ! A very "interesting" solution for all
the designers of PDB parsers !
What a disaster.
A last comment, in RasMol, "select LIP.1H47" is recognized.
OK
I suppose that the Jmol designers didn't know this oddity of the PDB
format.
That is correct.
It's written in the PDB Format Guide, Part 63 about the ATOM record,
cited at this list several times:
- Hydrogen naming sometimes conflicts with IUPAC conventions. For
example, a hydrogen named HG11 in columns 13 - 16 is differentiated from
a mercury atom by the element symbol in columns 77 - 78. Columns 13 - 16
present a unique name for each atom.
it is part of the PDB format like altLoc which is e.g. *;A in RasMolScript
The Jmol parser did not anticipate this. I was unable to find an easy fix
for the parser.
You said:
The notation 1Hxx is unfortunately standard in all the
PDB files reporting the coordinates of Hydrogens and
it corresponds to Hxx1 in standard IUPAC notation.
Q: Could one argue that this should actually be Hxx1? And that the proper
syntax should be:
select [LIP].H471;
yes and no, H471 may be IUPAC but this isn't RasMol compatible and would
cause confusions with all the people working with PDB files in a first
step.
I had no big problem with filtering all relevant scripts with
s/(select\s\S\.)(\d)(\w)/\1\3\2/ but a RasMol compatible parser
shouldn't die on *.1H47 or *.1H47;A
this would translate e.g. "1HB " too, like in 1plc.pdb
ATOM 857 1HB ASER 56 11.046 21.630 13.802 0.50 9.91
1PLC 980
ATOM 858 1HB BSER 56 11.090 21.310 15.620 0.50 9.25
1PLC 981
ATOM 859 2HB ASER 56 10.814 23.064 14.443 0.50 8.56
1PLC 982
ATOM 860 2HB BSER 56 11.172 21.418 14.036 0.50 10.65
1PLC 983
RasMol>select *.1HB;A
If so, then I may be able to fix this at a lower layer, when the .pdb file
is read.
I am not interested in doing this would be considered a hack, but only if
people felt that it was the proper solution.
If *all* of the PDB format is honored, I don't regard this as a hack
and though RasMolScript compatibility has been helpful in giving Jmol a
boost in starting up, now Jmol will be able to define the scripting language
Jmol>select *.HB1%A
but ...
Q: What does the PDB call these things in mmCif files?
1plc.cif
ATOM 857 H HB2 A SER A 1 56 ? 11.046 21.630 13.802 0.50 9.91 ? ?
? ? ?
56 SER A 1HB 1
ATOM 858 H HB2 B SER A 1 56 ? 11.090 21.310 15.620 0.50 9.25 ? ?
? ? ?
56 SER A 1HB 1
ATOM 859 H HB3 A SER A 1 56 ? 10.814 23.064 14.443 0.50 8.56 ? ?
? ? ?
56 SER A 2HB 1
ATOM 860 H HB3 B SER A 1 56 ? 11.172 21.418 14.036 0.50 10.65 ? ?
? ? ?
56 SER A 2HB 1
Q: What does the PDB call these things in their XML format?
<PDBx:atom_site id="857">
<PDBx:group_PDB>ATOM</PDBx:group_PDB>
<PDBx:type_symbol>H</PDBx:type_symbol>
<PDBx:label_atom_id>HB2</PDBx:label_atom_id>
<PDBx:label_alt_id>A</PDBx:label_alt_id>
<PDBx:label_comp_id>SER</PDBx:label_comp_id>
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_entity_id>1</PDBx:label_entity_id>
<PDBx:label_seq_id>56</PDBx:label_seq_id>
<PDBx:Cartn_x>11.046</PDBx:Cartn_x>
<PDBx:Cartn_y>21.630</PDBx:Cartn_y>
<PDBx:Cartn_z>13.802</PDBx:Cartn_z>
<PDBx:occupancy>0.50</PDBx:occupancy>
<PDBx:B_iso_or_equiv>9.91</PDBx:B_iso_or_equiv>
<PDBx:auth_seq_id>56</PDBx:auth_seq_id>
<PDBx:auth_comp_id>SER</PDBx:auth_comp_id>
<PDBx:auth_asym_id>A</PDBx:auth_asym_id>
<PDBx:auth_atom_id>1HB</PDBx:auth_atom_id>
<PDBx:pdbx_PDB_model_num>1</PDBx:pdbx_PDB_model_num>
</PDBx:atom_site>
<PDBx:atom_site id="858">
<PDBx:group_PDB>ATOM</PDBx:group_PDB>
<PDBx:type_symbol>H</PDBx:type_symbol>
<PDBx:label_atom_id>HB2</PDBx:label_atom_id>
<PDBx:label_alt_id>B</PDBx:label_alt_id>
<PDBx:label_comp_id>SER</PDBx:label_comp_id>
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_entity_id>1</PDBx:label_entity_id>
<PDBx:label_seq_id>56</PDBx:label_seq_id>
<PDBx:Cartn_x>11.090</PDBx:Cartn_x>
<PDBx:Cartn_y>21.310</PDBx:Cartn_y>
<PDBx:Cartn_z>15.620</PDBx:Cartn_z>
<PDBx:occupancy>0.50</PDBx:occupancy>
<PDBx:B_iso_or_equiv>9.25</PDBx:B_iso_or_equiv>
<PDBx:auth_seq_id>56</PDBx:auth_seq_id>
<PDBx:auth_comp_id>SER</PDBx:auth_comp_id>
<PDBx:auth_asym_id>A</PDBx:auth_asym_id>
<PDBx:auth_atom_id>1HB</PDBx:auth_atom_id>
<PDBx:pdbx_PDB_model_num>1</PDBx:pdbx_PDB_model_num>
</PDBx:atom_site>
<PDBx:atom_site id="859">
<PDBx:group_PDB>ATOM</PDBx:group_PDB>
<PDBx:type_symbol>H</PDBx:type_symbol>
<PDBx:label_atom_id>HB3</PDBx:label_atom_id>
<PDBx:label_alt_id>A</PDBx:label_alt_id>
<PDBx:label_comp_id>SER</PDBx:label_comp_id>
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_entity_id>1</PDBx:label_entity_id>
<PDBx:label_seq_id>56</PDBx:label_seq_id>
<PDBx:Cartn_x>10.814</PDBx:Cartn_x>
<PDBx:Cartn_y>23.064</PDBx:Cartn_y>
<PDBx:Cartn_z>14.443</PDBx:Cartn_z>
<PDBx:occupancy>0.50</PDBx:occupancy>
<PDBx:B_iso_or_equiv>8.56</PDBx:B_iso_or_equiv>
<PDBx:auth_seq_id>56</PDBx:auth_seq_id>
<PDBx:auth_comp_id>SER</PDBx:auth_comp_id>
<PDBx:auth_asym_id>A</PDBx:auth_asym_id>
<PDBx:auth_atom_id>2HB</PDBx:auth_atom_id>
<PDBx:pdbx_PDB_model_num>1</PDBx:pdbx_PDB_model_num>
</PDBx:atom_site>
<PDBx:atom_site id="860">
<PDBx:group_PDB>ATOM</PDBx:group_PDB>
<PDBx:type_symbol>H</PDBx:type_symbol>
<PDBx:label_atom_id>HB3</PDBx:label_atom_id>
<PDBx:label_alt_id>B</PDBx:label_alt_id>
<PDBx:label_comp_id>SER</PDBx:label_comp_id>
<PDBx:label_asym_id>A</PDBx:label_asym_id>
<PDBx:label_entity_id>1</PDBx:label_entity_id>
<PDBx:label_seq_id>56</PDBx:label_seq_id>
<PDBx:Cartn_x>11.172</PDBx:Cartn_x>
<PDBx:Cartn_y>21.418</PDBx:Cartn_y>
<PDBx:Cartn_z>14.036</PDBx:Cartn_z>
<PDBx:occupancy>0.50</PDBx:occupancy>
<PDBx:B_iso_or_equiv>10.65</PDBx:B_iso_or_equiv>
<PDBx:auth_seq_id>56</PDBx:auth_seq_id>
<PDBx:auth_comp_id>SER</PDBx:auth_comp_id>
<PDBx:auth_asym_id>A</PDBx:auth_asym_id>
<PDBx:auth_atom_id>2HB</PDBx:auth_atom_id>
<PDBx:pdbx_PDB_model_num>1</PDBx:pdbx_PDB_model_num>
</PDBx:atom_site>
from 1plc.xml
Regards, Jan
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