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CCP4BB  January 2008

CCP4BB January 2008

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Subject:

Lipid not restrained during ShelX refinement

From:

"Neutze Gp. CCP4ibb account" <[log in to unmask]>

Reply-To:

Neutze Gp. CCP4ibb account

Date:

Tue, 29 Jan 2008 16:30:08 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (164 lines)

Hi everyone,

I am trying to build and refine a phosphatidylserine (PSF) lipid
molecule, using ShelX for the refinment.

I have taken the ideal coordinates from the Hic-up server and bond
length/angles from PRODRG (see below). After approximately modelling
the atom positions using Coot I started refinement with the ideal bond
length/angles pasted into my ShelX .ins file. However, most of the
bonds in PSF are not restrained by ShelX, only a couple are
maintained, and the atoms drift away. [I also tried creating bond
length/angles .dfx in from the ideal PSF pdb fiel in ShelXPro but had
no joy there either]. Atom and residue naming for PSF appears to agree
between my pdb file and the ideal values, as far as I can see.

Does any one have any ideas here? Am I missing something trivial?
Thanks in advance.

Best wishes, Rob
_________________________________________________

Rob Horsefield Ph.D.

[log in to unmask]            www.csb.gu.se/rob

University of Gothenburg - GU
Lundberg Laboratory (office 1209),
Medicinaregatan 9E, Gothenburg, 41390 Sweden
Tel: 00 46 31 78 63936     Mob: 00 46 706 707 871
_________________________________________________

COMPND PSF 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE; PHOSPHATIDYLSERINE
REMARK PSF Part of HIC-Up: http://xray.bmc.uu.se/hicup
REMARK PSF Extracted from PDB file pdb1dsy.ent
REMARK PSF Formula C18 H34 N1 O10 P1
REMARK PSF Nr of non-hydrogen atoms  25
REMARK PSF Eigen-values covariance X/Y/Z      213.5      80.1      45.6
REMARK PSF Residue type PSF
REMARK PSF Residue name   6041
REMARK PSF Original residue name (for O) $401
REMARK PSF  RESOLUTION. 2.60 ANGSTROMS.
REMARK PSF occurs in        0 other PDB entries
REMARK PSF
HETATM    1  O2  PSF  6041       3.938  -8.474   5.875  1.00 20.00           O+0
HETATM    2  O1  PSF  6041       4.810  -7.227   3.847  1.00 20.00           O+0
HETATM    3  P   PSF  6041       5.297  -8.205   5.042  1.00 20.00           P+0
HETATM    4  O4  PSF  6041       6.454  -7.693   5.852  1.00 20.00           O+0
HETATM    5  O3  PSF  6041       5.577  -9.625   4.316  1.00 20.00           O+0
HETATM    6  C2  PSF  6041       2.801  -8.960   5.170  1.00 20.00           C+0
HETATM    7  C3  PSF  6041       1.635  -9.144   6.134  1.00 20.00           C+0
HETATM    8  O11 PSF  6041       1.348  -7.888   6.752  1.00 20.00           O+0
HETATM    9  O12 PSF  6041       0.917  -6.964   4.683  1.00 20.00           O+0
HETATM   10  C1  PSF  6041       1.000  -6.877   5.901  1.00 20.00           C+0
HETATM   11  C4  PSF  6041       1.973 -10.143   7.233  1.00 20.00           C+0
HETATM   12  C5  PSF  6041       1.016 -11.120   9.164  1.00 20.00           C+0
HETATM   13  O51 PSF  6041       2.014 -11.791   9.391  1.00 20.00           O+0
HETATM   14  O52 PSF  6041       0.855 -10.253   8.121  1.00 20.00           O+0
HETATM   15  C6  PSF  6041      -0.231 -11.095  10.020  1.00 20.00           C+0
HETATM   16  C7  PSF  6041      -0.120 -11.966  11.272  1.00 20.00           C+0
HETATM   17  C13 PSF  6041       0.697  -5.634   6.709  1.00 20.00           C+0
HETATM   18  C14 PSF  6041       1.910  -5.101   7.471  1.00 20.00           C+0
HETATM   19  C15 PSF  6041       3.065  -4.717   6.540  1.00 20.00           C+0
HETATM   20  N   PSF  6041       5.881  -5.519   0.771  1.00 20.00           N+0
HETATM   21  CA  PSF  6041       4.999  -5.951   1.828  1.00 20.00           C+0
HETATM   22  CB  PSF  6041       5.709  -6.870   2.811  1.00 20.00           C+0
HETATM   23  C   PSF  6041       4.496  -4.707   2.531  1.00 20.00           C+0
HETATM   24  OT1 PSF  6041       5.152  -3.692   2.723  1.00 20.00           O+0
HETATM   25  OT2 PSF  6041       3.223  -4.859   2.982  1.00 20.00           O+0
HETATM   26  C8  PSF  6041      -1.394 -11.935  12.121  1.00 20.00           C+0
HETATM   27  C9  PSF  6041      -1.240 -12.787  13.381  1.00 20.00           C+0
HETATM   28  C10 PSF  6041      -2.485 -12.726  14.251  1.00 20.00           C+0
HETATM   29  C16 PSF  6041       4.274  -4.221   7.333  1.00 20.00           C+0
HETATM   30  C17 PSF  6041       5.439  -3.880   6.418  1.00 20.00           C+0
REMARK PSF ENDHET

REM     This file was generated by PRODRG version 071121.0636
REM     PRODRG written/copyrighted by Daan van Aalten
REM     and Alexander Schuettelkopf
REM
REM     Questions/comments to [log in to unmask]
REM
REM     When using this software in a publication, cite:
REM     A. W. Schuettelkopf and D. M. F. van Aalten (2004).
REM     PRODRG - a tool for high-throughput crystallography
REM     of protein-ligand complexes.
REM     Acta Crystallogr. D60, 1355--1363.
REM
DFIX_PSF 1.530 C10   C9
DFIX_PSF 1.530 C9    C8
DFIX_PSF 1.530 C8    C7
DFIX_PSF 1.530 C7    C6
DFIX_PSF 1.530 C6    C5
DFIX_PSF 1.230 C5    O51
DFIX_PSF 1.360 C5    O52
DFIX_PSF 1.435 O52   C4
DFIX_PSF 1.520 C4    C3
DFIX_PSF 1.435 C3    O11
DFIX_PSF 1.530 C3    C2
DFIX_PSF 1.360 O11   C1
DFIX_PSF 1.230 C1    O12
DFIX_PSF 1.530 C1    C13
DFIX_PSF 1.530 C13   C14
DFIX_PSF 1.530 C14   C15
DFIX_PSF 1.530 C15   C16
DFIX_PSF 1.530 C16   C17
DFIX_PSF 1.430 C2    O2
DFIX_PSF 1.610 O2    P
DFIX_PSF 1.610 P     O3
DFIX_PSF 1.480 P     O4
DFIX_PSF 1.610 P     O1
DFIX_PSF 1.430 O1    CB
DFIX_PSF 1.530 CB    CA
DFIX_PSF 1.530 CA    C
DFIX_PSF 1.470 CA    N
DFIX_PSF 1.250 C     OT2
DFIX_PSF 1.250 C     OT1
DFIX_PSF 1.000 N     HAB
DFIX_PSF 1.000 N     HAC
DFIX_PSF 1.000 N     HAA
DANG_PSF 2.522 C10   C8
DANG_PSF 2.522 C9    C7
DANG_PSF 2.522 C8    C6
DANG_PSF 2.522 C7    C5
DANG_PSF 2.407 C6    O51
DANG_PSF 2.504 C6    O52
DANG_PSF 2.244 O51   O52
DANG_PSF 2.283 C5    C4
DANG_PSF 2.414 O52   C3
DANG_PSF 2.414 C4    O11
DANG_PSF 2.491 C4    C2
DANG_PSF 2.422 O11   C2
DANG_PSF 2.283 C3    C1
DANG_PSF 2.244 O11   O12
DANG_PSF 2.504 O11   C13
DANG_PSF 2.407 O12   C13
DANG_PSF 2.522 C1    C14
DANG_PSF 2.522 C13   C15
DANG_PSF 2.522 C14   C16
DANG_PSF 2.522 C15   C17
DANG_PSF 2.440 C3    O2
DANG_PSF 2.634 C2    P
DANG_PSF 2.520 O2    O3
DANG_PSF 2.526 O2    O4
DANG_PSF 2.520 O2    O1
DANG_PSF 2.526 O3    O4
DANG_PSF 2.520 O3    O1
DANG_PSF 2.526 O4    O1
DANG_PSF 2.634 P     CB
DANG_PSF 2.440 O1    CA
DANG_PSF 2.499 CB    C
DANG_PSF 2.450 CB    N
DANG_PSF 2.450 C     N
DANG_PSF 2.375 CA    OT2
DANG_PSF 2.375 CA    OT1
DANG_PSF 2.228 OT2   OT1
DANG_PSF 2.035 CA    HAB
DANG_PSF 2.035 CA    HAC
DANG_PSF 2.035 CA    HAA
DANG_PSF 1.633 HAB   HAC
DANG_PSF 1.633 HAB   HAA
DANG_PSF 1.633 HAC   HAA
FLAT_PSF C5    C6    O52   O51
FLAT_PSF C1    O11   C13   O12
FLAT_PSF C     CA    OT1   OT2

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