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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