Huw, I guess you're referring to my original posting of this problem.
When I used binary version 5.5.0109 (compiled by gfortran I assume)
downloaded from Garib's site as he suggested instead of the 5.5.0102
version I compiled myself using ifort (because gfortran had given
trouble in the past), the problem went away. Admittedly I didn't do a
thorough analysis of the circumstances under which the problem is
observed - sorry but I was just happy to see it working!
Thomas Eriksson suggested it was a problem with the ifort v11 LAPACK
library, and that may well be the cause, but again I never got around to
testing that.
Cheers
-- Ian
> -----Original Message-----
> From: [log in to unmask]
> [mailto:[log in to unmask]] On Behalf Of Huw Jenkins
> Sent: 09 November 2009 15:48
> To: [log in to unmask]
> Subject: Re: [ccp4bb] Alterate conformers destroyed by Refmac!
>
> 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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