Your cif-file contains coordinates, but as far as I could see it does not 
contain bond lengths, and angles and their deviations. That is what coot 
complains about.

Unless your cif-file describes a modified spermine you could use the 
spermine already described in the refmac5 library:
In coot, go to the "File->Get Monomer" menu and enter the three letter 
code SPM.

It should load a spermine together with geometric restrains (have a look 
at $CLIB/data/monomers/s/SPM.cif to compare with your cif-file and see 
that it contains bond length information etc.).

Tim

--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A


On Tue, 22 Jan 2008, Vineet Gaur wrote:

> Hi all
> I am using COOT for model building and refinement.
> i have to introducea ligand in my model
> i have downloaded .cif file from RCSB.
> However while importing the cif file i m getting the warning message of
> having No restraints in the CIF file
>
> is there any problem in the format of the following cif file
>
> data_SPM
> #
> _chem_comp.id                                    SPM
> _chem_comp.name                                  SPERMINE
> _chem_comp.type                                  NON-POLYMER
> _chem_comp.pdbx_type                             HETAI
> _chem_comp.formula                               "C10 H26 N4"
> _chem_comp.mon_nstd_parent_comp_id               ?
> _chem_comp.pdbx_synonyms                         ?
> _chem_comp.pdbx_formal_charge                    0
> _chem_comp.pdbx_initial_date                     1999-07-08
> _chem_comp.pdbx_modified_date                    2007-08-16
> _chem_comp.pdbx_ambiguous_flag                   N
> _chem_comp.pdbx_release_status                   REL
> _chem_comp.pdbx_replaced_by                      ?
> _chem_comp.pdbx_replaces                         ?
> _chem_comp.formula_weight                        202.340
> _chem_comp.one_letter_code                       ?
> _chem_comp.three_letter_code                     SPM
> _chem_comp.pdbx_model_coordinates_details        ?
> _chem_comp.pdbx_model_coordinates_missing_flag   N
> _chem_comp.pdbx_ideal_coordinates_details        ?
> _chem_comp.pdbx_ideal_coordinates_missing_flag   N
> _chem_comp.pdbx_model_coordinates_db_code        1DPL
> _chem_comp.pdbx_processing_site                  ?
> #
> loop_
> _chem_comp_atom.comp_id
> _chem_comp_atom.atom_id
> _chem_comp_atom.alt_atom_id
> _chem_comp_atom.type_symbol
> _chem_comp_atom.charge
> _chem_comp_atom.pdbx_align
> _chem_comp_atom.pdbx_aromatic_flag
> _chem_comp_atom.pdbx_leaving_atom_flag
> _chem_comp_atom.pdbx_stereo_config
> _chem_comp_atom.model_Cartn_x
> _chem_comp_atom.model_Cartn_y
> _chem_comp_atom.model_Cartn_z
> _chem_comp_atom.pdbx_model_Cartn_x_ideal
> _chem_comp_atom.pdbx_model_Cartn_y_ideal
> _chem_comp_atom.pdbx_model_Cartn_z_ideal
> _chem_comp_atom.pdbx_ordinal
> SPM N1   N1   N 0 1 N N N -1.386 5.560  25.140 -0.292 0.012  7.961  1
> SPM C2   C2   C 0 1 N N N -2.248 4.344  25.282 0.514  -0.023 6.734  2
> SPM C3   C3   C 0 1 N N N -1.844 3.214  24.376 -0.408 0.014  5.515  3
> SPM C4   C4   C 0 1 N N N -2.834 2.063  24.495 0.432  -0.022 4.237  4
> SPM N5   N5   N 0 1 N N N -2.313 0.871  23.720 -0.453 0.013  3.066  5
> SPM C6   C6   C 0 1 N N N -3.235 -0.310 23.760 0.411  -0.024 1.880  6
> SPM C7   C7   C 0 1 N N N -2.669 -1.391 22.871 -0.451 0.011  0.617  7
> SPM C8   C8   C 0 1 N N N -3.306 -2.753 23.219 0.450  -0.028 -0.617 8
> SPM C9   C9   C 0 1 N N N -2.886 -3.777 22.188 -0.412 0.006  -1.880 9
> SPM N10  N10  N 0 1 N N N -3.212 -5.172 22.585 0.453  -0.031 -3.066 10
> SPM C11  C11  C 0 1 N N N -2.084 -5.778 23.391 -0.433 0.005  -4.237 11
> SPM C12  C12  C 0 1 N N N -2.443 -7.162 23.912 0.407  -0.032 -5.515 12
> SPM C13  C13  C 0 1 N N N -1.448 -8.158 23.367 -0.515 0.005  -6.734 13
> SPM N14  N14  N 0 1 N N N -0.553 -8.726 24.427 0.292  -0.029 -7.961 14
> SPM HN11 1HN1 H 0 0 N N N -1.660 6.326  25.754 -0.739 0.916  7.988  15
> SPM HN12 2HN1 H 0 0 N N N -1.355 5.869  24.168 0.354  -0.014 8.735  16
> SPM H21  1H2  H 0 1 N N N -2.281 4.005  26.343 1.181  0.838  6.713  17
> SPM H22  2H2  H 0 1 N N N -3.322 4.602  25.135 1.105  -0.939 6.715  18
> SPM H31  1H3  H 0 1 N N N -1.722 3.550  23.320 -1.074 -0.847 5.536  19
> SPM H32  2H3  H 0 1 N N N -0.796 2.883  24.565 -0.999 0.930  5.534  20
> SPM H41  1H4  H 0 1 N N N -3.061 1.809  25.556 1.098  0.839  4.215  21
> SPM H42  2H4  H 0 1 N N N -3.862 2.355  24.178 1.023  -0.938 4.217  22
> SPM HN5  HN5  H 0 1 N N N -1.378 0.612  24.037 -0.976 -0.849 3.071  23
> SPM H61  1H6  H 0 1 N N N -3.427 -0.667 24.798 1.078  0.838  1.889  24
> SPM H62  2H6  H 0 1 N N N -4.284 -0.042 23.493 1.002  -0.940 1.891  25
> SPM H71  1H7  H 0 1 N N N -2.780 -1.142 21.789 -1.117 -0.851 0.608  26
> SPM H72  2H7  H 0 1 N N N -1.555 -1.427 22.916 -1.042 0.927  0.607  27
> SPM H81  1H8  H 0 1 N N N -3.068 -3.077 24.258 1.117  0.833  -0.608 28
> SPM H82  2H8  H 0 1 N N N -4.414 -2.687 23.323 1.041  -0.944 -0.607 29
> SPM H91  1H9  H 0 1 N N N -3.319 -3.536 21.189 -1.079 -0.855 -1.889 30
> SPM H92  2H9  H 0 1 N N N -1.802 -3.675 21.945 -1.003 0.922  -1.891 31
> SPM HN0  HN0  H 0 1 N N N -3.451 -5.748 21.778 0.976  0.831  -3.071 32
> SPM H111 1H11 H 0 0 N N N -1.133 -5.797 22.808 -1.099 -0.857 -4.215 33
> SPM H112 2H11 H 0 0 N N N -1.767 -5.101 24.219 -1.023 0.921  -4.217 34
> SPM H121 1H12 H 0 0 N N N -2.512 -7.194 25.024 1.074  0.830  -5.536 35
> SPM H122 2H12 H 0 0 N N N -3.497 -7.443 23.683 0.998  -0.948 -5.534 36
> SPM H131 1H13 H 0 0 N N N -1.964 -8.969 22.803 -1.181 -0.856 -6.713 37
> SPM H132 2H13 H 0 0 N N N -0.851 -7.712 22.537 -1.105 0.921  -6.714 38
> SPM HN41 1HN4 H 0 0 N N N 0.119  -9.398 24.058 -0.354 -0.003 -8.735 39
> SPM HN42 2HN4 H 0 0 N N N -1.099 -9.133 25.186 0.814  0.833  -7.990 40
> #
> loop_
> _chem_comp_bond.comp_id
> _chem_comp_bond.atom_id_1
> _chem_comp_bond.atom_id_2
> _chem_comp_bond.value_order
> _chem_comp_bond.pdbx_aromatic_flag
> _chem_comp_bond.pdbx_stereo_config
> _chem_comp_bond.pdbx_ordinal
> SPM N1  C2   SING N N 1
> SPM N1  HN11 SING N N 2
> SPM N1  HN12 SING N N 3
> SPM C2  C3   SING N N 4
> SPM C2  H21  SING N N 5
> SPM C2  H22  SING N N 6
> SPM C3  C4   SING N N 7
> SPM C3  H31  SING N N 8
> SPM C3  H32  SING N N 9
> SPM C4  N5   SING N N 10
> SPM C4  H41  SING N N 11
> SPM C4  H42  SING N N 12
> SPM N5  C6   SING N N 13
> SPM N5  HN5  SING N N 14
> SPM C6  C7   SING N N 15
> SPM C6  H61  SING N N 16
> SPM C6  H62  SING N N 17
> SPM C7  C8   SING N N 18
> SPM C7  H71  SING N N 19
> SPM C7  H72  SING N N 20
> SPM C8  C9   SING N N 21
> SPM C8  H81  SING N N 22
> SPM C8  H82  SING N N 23
> SPM C9  N10  SING N N 24
> SPM C9  H91  SING N N 25
> SPM C9  H92  SING N N 26
> SPM N10 C11  SING N N 27
> SPM N10 HN0  SING N N 28
> SPM C11 C12  SING N N 29
> SPM C11 H111 SING N N 30
> SPM C11 H112 SING N N 31
> SPM C12 C13  SING N N 32
> SPM C12 H121 SING N N 33
> SPM C12 H122 SING N N 34
> SPM C13 N14  SING N N 35
> SPM C13 H131 SING N N 36
> SPM C13 H132 SING N N 37
> SPM N14 HN41 SING N N 38
> SPM N14 HN42 SING N N 39
> #
> loop_
> _pdbx_chem_comp_descriptor.comp_id
> _pdbx_chem_comp_descriptor.type
> _pdbx_chem_comp_descriptor.program
> _pdbx_chem_comp_descriptor.program_version
> _pdbx_chem_comp_descriptor.descriptor
> SPM SMILES           ACDLabs              10.04 NCCCNCCCCNCCCN
> SPM InChI            InChI                1.01
> InChI=1/C10H26N4/c11-5-3-9-13-7-1-2-8-14-10-4-6-12/h13-14H,1-12H2
> SPM SMILES_CANONICAL CACTVS               3.341 NCCCNCCCCNCCCN
> SPM SMILES           CACTVS               3.341 NCCCNCCCCNCCCN
> SPM SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C(CCNCCCN)CNCCCN
> SPM SMILES           "OpenEye OEToolkits" 1.5.0 C(CCNCCCN)CNCCCN
> #
> loop_
> _pdbx_chem_comp_identifier.comp_id
> _pdbx_chem_comp_identifier.type
> _pdbx_chem_comp_identifier.program
> _pdbx_chem_comp_identifier.program_version
> _pdbx_chem_comp_identifier.identifier
> SPM "SYSTEMATIC NAME" ACDLabs              10.04
> "N,N'-bis(3-aminopropyl)butane-1,4-diamine"
> SPM "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0
> "N,N'-bis(3-aminopropyl)butane-1,4-diamine"
> #
>
> thanks
> Vineet
>