Hussain Bhukyagps wrote:
> Hi!
>
> their is no connection between the metal and ligand in my pdb..
> how can i generate bonds between them using pymol..??
> by the way the distance between ligands and metal is 1.8-2.0 Ao...??
>
> Hussain
>
>
Hi,
What about specifying the bonds with CONECT records in the PDB file?
From the PDB specs section:
CONECT
Overview
The CONECT records specify connectivity between atoms for which
coordinates are supplied. The connectivity is described using the atom
serial number as found in the entry. CONECT records are mandatory for
HET groups (excluding water) and for other bonds not specified in the
standard residue connectivity table which involve atoms in standard
residues (see Appendix 4 for the list of standard residues). These
records are generated by the PDB.
Record Format
COLUMNS DATA TYPE FIELD DEFINITION
---------------------------------------------------------------------------------
1 - 6 Record name "CONECT"
7 - 11 Integer serial Atom serial number
12 - 16 Integer serial Serial number of bonded
atom
17 - 21 Integer serial Serial number of bonded
atom
22 - 26 Integer serial Serial number of bonded
atom
27 - 31 Integer serial Serial number of bonded
atom
32 - 36 Integer serial Serial number of
hydrogen bonded
atom
37 - 41 Integer serial Serial number of
hydrogen bonded
atom
42 - 46 Integer serial Serial number of salt
bridged
atom
47 - 51 Integer serial Serial number of
hydrogen bonded
atom
52 - 56 Integer serial Serial number of
hydrogen bonded
atom
57 - 61 Integer serial Serial number of salt
bridged
atom
Details
* Intra-residue connectivity within non-standard (HET) residues
(excluding water) is presented on the CONECT records.
* Inter-residue connectivity of HET groups to standard groups (including
water) or to other HET groups are represented on the CONECT records.
* Disulfide bridges specified in the SSBOND records have corresponding
CONECT records.
* Hydrogen bonds and salt bridges have CONECT records.
* No differentiation is made between donor and acceptor for hydrogen bonds.
* No differentiation is made between atoms with excess negative or
positive charge.
* Atoms specified in the connectivity are presented by their serial
numbers as found in the entry.
* All atoms connected to the atom with serial number in columns 7 - 11
are listed in the remaining fields of the record.
* If more than four fields are required for non-hydrogen and
nonsalt-bridge bonds, a second CONECT record with the same atom serial
number in columns 7 - 11 will be used.
* These CONECT records occur in increasing order of the atom serial
numbers they carry in columns 7 - 11. The target-atom serial numbers
carried on these records also occur in increasing order.
* The connectivity list given here is redundant in that each bond
indicated is given twice, once with each of the two atoms involved
specified in columns 7 - 11.
* For nucleic acids, Watson-Crick hydrogen bonds between bases may be
listed, but this is optional.
* For hydrogen bonds, when the hydrogen atom is present in the
coordinates, PDB generates a CONECT record between the hydrogen atom and
its acceptor atom.
* For NMR entries, CONECT records for all models are generated
describing heterogen connectivity and others for LINK records.
Verification/Validation/Value Authority Control
Connectivity is checked for unusual bond lengths.
Relationships to Other Record Types
CONECT records must be present in an entry that contains either
non-standard groups or disulfide bonds.
Example
1 2 3 4 5 6 7
1234567890123456789012345678901234567890123456789012345678901234567890
CONECT 1179 746 1184 1195 1203
CONECT 1179 1211 1222
CONECT 1021 544 1017 1020 1022 1211 1222 1311
Known Problems
Only five digits are available for the atom serial number, but some
structures have already been received with more that 99,999 atoms.
Changing the field length would make earlier entries incorrect.
CONECTs to atoms whose coordinates are not in the entry (e.g.,
symmetry-generated) are not given.
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