Hi
I'm reviving this thread as I've found some new information.
I don't know if this will help find the source of the problem but the
alternative conformers seem not to be correctly recognised when the
co-ordinates are read in -
I've tested this by removing all alternate conformations from a pdb
file (using pdbcur) and then re-inserting 1 alternative conformation
followed by manually deleting the lines for the B conformer and
setting the occupancies back to 1.00 - i.e so the only difference is
that the label is "AXXX" compared to " XXX" (XXX=SER in this case but
I'm sure that's not relevant).
diff 0_alt.pdb 1_alt_label.pdb
1170,1172c1170,1172
< ATOM 1025 CA SER A 120 21.031 -30.854 53.830 1.00
11.60 C
< ATOM 1027 CB SER A 120 19.633 -30.312 54.097 1.00
11.90 C
< ATOM 1029 OG SER A 120 18.941 -30.270 52.880 1.00
13.91 O
---
> ATOM 1025 CA ASER A 120 21.031 -30.854 53.830 1.00
11.60 C
> ATOM 1027 CB ASER A 120 19.633 -30.312 54.097 1.00
11.90 C
> ATOM 1029 OG ASER A 120 18.941 -30.270 52.880 1.00
13.91 O
The relevant lines from the Refmac logfiles when the structures are
refined are below. When there are AXXX style atom labels but no extra
atoms the number of bond, angle, and torsion restraints and
chiralities has *decreased* which suggests to me the atoms labelled
AXXX are not correctly recognised.
Using the same files as imput for Refmac 5.5.0106 (which doesn't mess
up alternate conformers) gives exactly the same values for the number
of restraints for both files.
No alternative conformations Refmac_5.5.0102
CRYST1 142.393 142.393 112.233 90.00 90.00 120.00 H 3 2
Number of atoms : 3223
Number of residues : 769
Number of chains : 6
I am reading library. Please wait.
mon_lib.cif
--------------------------------
--- title of input coord file ---
PDB_code:xxxx
PDB_name:----
PDB_date:XX-XXX-9-
--------------------------------
Number of chains : 6
Total number of monomers : 769
Number of atoms : 3223
Number of missing atoms : 0
Number of rebuilt atoms : 0
Number of unknown atoms : 0
Number of deleted atoms : 0
Number of bonds restraints : 2848
Number of angles restraints : 3831
Number of torsions restraints : 1955
Number of chiralities : 423
Number of planar groups : 495
1 alternative conformation labelled Refmac_5.5.0102
CRYST1 142.393 142.393 112.233 90.00 90.00 120.00 H 3 2
Number of atoms : 3223
Number of residues : 769
Number of chains : 6
I am reading library. Please wait.
mon_lib.cif
--------------------------------
--- title of input coord file ---
PDB_code:xxxx
PDB_name:----
PDB_date:XX-XXX-9-
--------------------------------
Number of chains : 6
Total number of monomers : 769
Number of atoms : 3223
Number of missing atoms : 0
Number of rebuilt atoms : 0
Number of unknown atoms : 0
Number of deleted atoms : 0
Number of bonds restraints : 2844
Number of angles restraints : 3824
Number of torsions restraints : 1950
Number of chiralities : 422
Number of planar groups : 495
I hope this helps...
Huw
--
Dr Huw Jenkins
Astbury Centre for Structural Molecular Biology
University of Leeds
Leeds, LS2 9JT
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