This page summarizes some helpful command line tools to find and display restraints.
Phenix has three databases of CIF files related to ligands:
The first, Chemical Components (CC), is obtained from the Protein Data Bank (PDB). It contains information about all entities in the PDB including protein, nucleic acids and ligands. The information includes bonding but no other internal coordinates, so these are not restraints files. The second, Monomer Library, is a curated copy of the Monomer Library containing restraints for many common ligands. The third, GeoStd, contains all protein entities (amino acids, modified amino acids), all glycans, many nucleic acids and ligands. This is a curated set of restraints that is maintained as the “best” possible.
In some cases, restraints are be required to run a tool, for example when we want to create the geometry_restraints_manager(). It is then useful to determine whether there is a restraints file in the Phenix distribution and if so where. Otherwise, it would be necessary to get restraints, for example with ReadySet. The following command returns the contents of the restraints file and the path for the molecule hoh (water molecule):
elbow.where_is_that_cif_file hoh
The command elbow.where_is_that_cif_file is followed by the 3-letter code of a ligand or component. The output is:
Looking for ligand code hoh
--------------------------------------------------------------------------------
CIF file
/Users/nigel/phenix/conda/modules/chem_data/geostd/h/data_HOH.cif
--------------------------------------------------------------------------------
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
HOH . 'water ' solvent 3 1 . 2012-10-17 2013-01-10
;
Copy of CCP4 Monomer Library entry.
Added neutron distances
;
#
data_comp_HOH
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.partial_charge
HOH O O OH2 -0.408
HOH H1 H HOH2 0.204
HOH H2 H HOH2 0.204
loop_
_chem_comp_tree.comp_id
_chem_comp_tree.atom_id
_chem_comp_tree.atom_back
_chem_comp_tree.atom_forward
_chem_comp_tree.connect_type
HOH O n/a . END
HOH H1 O . .
HOH H2 O . .
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
HOH O H1 coval 0.840 0.020 0.950
HOH O H2 coval 0.840 0.020 0.950
loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
HOH H1 O H2 106.800 3.000
--------------------------------------------------------------------------------
CIF file
/Users/nigel/phenix/conda/modules/chem_data/geostd/h/data_HOH.cif
--------------------------------------------------------------------------------
According to the output, the restraints file for hoh is in GeoStd.
If the file is not in the GeoStd, the code looks in the Monomer Library and returns it it is found. This scenario occurs for example in the case of GTP. If the component is not found in the Monomer Library, the output displays the contents of the Chemical Components file. An example for this is the component 000.
elbow.where_is_that_cif_file 000
The output for this command is:
Looking for ligand code 000
--------------------------------------------------------------------------------
CIF file
/Users/nigel/phenix/conda/modules/chem_data/chemical_components/0/data_000.cif
--------------------------------------------------------------------------------
data_000
#
_chem_comp.id 000
_chem_comp.name "methyl hydrogen carbonate"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type ATOMP
_chem_comp.formula "C2 H4 O3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2010-04-27
_chem_comp.pdbx_modified_date 2011-06-04
_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 76.051
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 000
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 3LIN
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
#
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_component_atom_id
_chem_comp_atom.pdbx_component_comp_id
_chem_comp_atom.pdbx_ordinal
000 C C C 0 1 N N N 32.880 -0.090 51.314 -0.456 0.028 -0.001 C 000 1
000 O O O 0 1 N N N 32.160 0.180 50.105 -0.376 1.240 0.001 O 000 2
000 OA OA O 0 1 N N N 34.147 -0.940 51.249 0.662 -0.720 0.001 OA 000 3
000 CB CB C 0 1 N N N 33.872 -2.227 50.459 1.929 -0.010 -0.001 CB 000 4
000 OXT OXT O 0 1 N Y N 32.419 0.429 52.564 -1.663 -0.566 -0.000 OXT 000 5
000 HB HB H 0 1 N N N 34.788 -2.834 50.416 1.996 0.613 -0.892 HB 000 6
000 HBA HBA H 0 1 N N N 33.076 -2.800 50.957 1.995 0.618 0.888 HBA 000 7
000 HBB HBB H 0 1 N N N 33.555 -1.969 49.438 2.748 -0.730 0.002 HBB 000 8
000 HXT HXT H 0 1 N Y N 31.625 0.931 52.425 -2.438 0.013 0.002 HXT 000 9
#
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
000 C OXT SING N N 1
000 O C DOUB N N 2
000 OA C SING N N 3
000 CB OA SING N N 4
000 CB HB SING N N 5
000 CB HBA SING N N 6
000 CB HBB SING N N 7
000 OXT HXT SING N N 8
#
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
000 SMILES ACDLabs 12.01 "O=C(O)OC"
000 SMILES_CANONICAL CACTVS 3.370 "COC(O)=O"
000 SMILES CACTVS 3.370 "COC(O)=O"
000 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "COC(=O)O"
000 SMILES "OpenEye OEToolkits" 1.7.0 "COC(=O)O"
000 InChI InChI 1.03 "InChI=1S/C2H4O3/c1-5-2(3)4/h1H3,(H,3,4)"
000 InChIKey InChI 1.03 CXHHBNMLPJOKQD-UHFFFAOYSA-N
#
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
000 "SYSTEMATIC NAME" ACDLabs 12.01 "methyl hydrogen carbonate"
000 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 "methyl hydrogen carbonate"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
000 "Create component" 2010-04-27 RCSB
000 "Modify descriptor" 2011-06-04 RCSB
#
--------------------------------------------------------------------------------
CIF file
/Users/nigel/phenix/conda/modules/chem_data/chemical_components/0/data_000.cif
--------------------------------------------------------------------------------
Should you wish to see the Chemical Components file for an entity in the restraints databases use the option cc.
elbow.where_is_that_cif_file hoh cc
The output of this command is:
Looking for ligand code hoh
--------------------------------------------------------------------------------
CIF file
/Users/nigel/phenix/conda/modules/chem_data/chemical_components/h/data_HOH.cif
--------------------------------------------------------------------------------
data_HOH
#
_chem_comp.id HOH
_chem_comp.name WATER
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAS
_chem_comp.formula "H2 O"
_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 2011-06-04
_chem_comp.pdbx_ambiguous_flag N
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces MTO
_chem_comp.formula_weight 18.015
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code HOH
_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 1NHE
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
#
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_component_atom_id
_chem_comp_atom.pdbx_component_comp_id
_chem_comp_atom.pdbx_ordinal
HOH O O O 0 1 N N N -23.107 18.401 -21.626 -0.064 0.000 0.000 O HOH 1
HOH H1 1H H 0 1 N N N -22.157 18.401 -21.626 0.512 0.000 -0.776 H1 HOH 2
HOH H2 2H H 0 1 N N N -23.424 18.401 -20.730 0.512 0.000 0.776 H2 HOH 3
#
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
HOH O H1 SING N N 1
HOH O H2 SING N N 2
#
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
HOH SMILES ACDLabs 10.04 O
HOH SMILES_CANONICAL CACTVS 3.341 O
HOH SMILES CACTVS 3.341 O
HOH SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 O
HOH SMILES "OpenEye OEToolkits" 1.5.0 O
HOH InChI InChI 1.03 InChI=1S/H2O/h1H2
HOH InChIKey InChI 1.03 XLYOFNOQVPJJNP-UHFFFAOYSA-N
#
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
HOH "SYSTEMATIC NAME" ACDLabs 10.04 water
HOH "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 oxidane
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
HOH "Create component" 1999-07-08 RCSB
HOH "Modify descriptor" 2011-06-04 RCSB
#
--------------------------------------------------------------------------------
CIF file
/Users/nigel/phenix/conda/modules/chem_data/chemical_components/h/data_HOH.cif
--------------------------------------------------------------------------------
Note the different locations compared to the first example. Also, this cif file only has coordinates.
Perform these commands to follow along.
phenix.fetch_pdb 1yjp --mtz
phenix.refine 1yjp.{pdb,mtz} write_final_geo=True
These commands will download a model from the PDB and then refine it.
To get the RMSD and RMSZ values for the initial model broken into all residues, residues without alt. loc. and residues with alt. loc.
elbow.refine_geo_display 1yjp_refine_001.geo
The output of the command is:
RMS results for model
RMS(D/Z)
d-all d-none d-alt z-all z-none z-alt
bond 0.015( 59) 0.015( 59) 0.000( 0) 0.932( 59) 0.932( 59) 0.000( 0)
angle 1.354( 79) 1.354( 79) 0.000( 0) 0.825( 79) 0.825( 79) 0.000( 0)
dihedral 18.725( 34) 18.725( 34) 0.000( 0) 1.170( 34) 1.170( 34) 0.000( 0)The overall bond RMSD is 0.015Å while the overall bond RMSZ is 0.93. We can do the same for the .geo obtained after refinement:
elbow.refine_geo_display 1yjp_refine_001_final.geo
RMS results for model
RMS(D/Z)
d-all d-none d-alt z-all z-none z-alt
bond 0.006( 59) 0.006( 59) 0.000( 0) 0.315( 59) 0.315( 59) 0.000( 0)
angle 0.844( 79) 0.844( 79) 0.000( 0) 0.447( 79) 0.447( 79) 0.000( 0)
dihedral 3.051( 34) 3.051( 34) 0.000( 0) 0.645( 34) 0.645( 34) 0.000( 0)
The output shows that after refinement, the RMSD and RMSZ are reduced to 0.06Å and 0.32, respectively.
The output for a geo file of a large molecule can be overwhelming. If it is desired to look at restraints of a particular residue (such as a ligand), it is handy to apply the command on a subset. The syntax does not follow the standard Phenix atom selection syntax, but it is straightforward. For example, the selection string GLY will show restraints for all glycine residues in the model. The output also shows the RMSD/Z for the selection. The selection is therefore particular useful to display information about ligands.
elbow.refine_geo_display 1yjp_refine_001_final.geo GLY
The output is:
RMS results for selection
RMS(D/Z)
d-all d-none d-alt z-all z-none z-alt
bond 0.004( 4) 0.004( 4) 0.000( 0) 0.235( 4) 0.235( 4) 0.000( 0)
angle 1.901( 5) 1.901( 5) 0.000( 0) 0.679( 5) 0.679( 5) 0.000( 0)
dihedral 4.330( 1) 4.330( 1) 0.000( 0) 0.866( 1) 0.866( 1) 0.000( 0)
----- bonds ----- bonds ----- bonds ----- bonds ----- bonds ----- bonds
1 " CA GLY A 1 " - " C GLY A 1 " [ 1.516, 1.508, 0.008, 1.80e-02, 3.09e+03, 2.14e-01] Z= 0.44
2 " N GLY A 1 " - " CA GLY A 1 " [ 1.451, 1.453, -0.002, 1.60e-02, 3.91e+03, 1.87e-02] Z= -0.12
3 " C GLY A 1 " - " N ASN A 2 " [ 1.330, 1.329, 0.001, 1.31e-02, 5.83e+03, 1.13e-02] Z= 0.08
4 " C GLY A 1 " - " O GLY A 1 " [ 1.231, 1.230, 0.001, 2.00e-02, 2.50e+03, 1.19e-03] Z= 0.05
---- angles ---- angles ---- angles ---- angles ---- angles ---- angles
1 " N GLY A 1 " - " CA GLY A 1 " - " C GLY A 1 " [ 113.30, 109.17, 4.13, 2.90, 0.119, 2.02e+00] Z= 1.42
2 " CA GLY A 1 " - " C GLY A 1 " - " N ASN A 2 " [ 116.20, 116.86, -0.66, 2.00, 0.250, 1.09e-01] Z= -0.33
3 " CA GLY A 1 " - " C GLY A 1 " - " O GLY A 1 " [ 120.80, 120.18, 0.62, 2.10, 0.227, 8.69e-02] Z= 0.30
4 " C GLY A 1 " - " N ASN A 2 " - " CA ASN A 2 " [ 120.94, 120.50, 0.44, 1.57, 0.406, 7.81e-02] Z= 0.28
5 " O GLY A 1 " - " C GLY A 1 " - " N ASN A 2 " [ 123.00, 122.95, 0.05, 1.60, 0.391, 8.63e-04] Z= 0.03
---- dihedrals ---- dihedrals ---- dihedrals ---- dihedrals ---- dihedrals ---- dihedrals
1 " CA GLY A 1 " - " C GLY A 1 " - " N ASN A 2 " - " CA ASN A 2 " [ 180.00, 175.67, 4.33, 0, 5.00, 0.04, 0.75]
---- chirals ---- chirals ---- chirals ---- chirals ---- chirals ---- chirals
None
To get just the information for the ASN with residue number "3" use
elbow.refine_geo_display 1yjp_refine_001_final.geo “ASN 3”
RMS results for selection
RMS(D/Z)
d-all d-none d-alt z-all z-none z-alt
bond 0.004( 9) 0.004( 9) 0.000( 0) 0.248( 9) 0.248( 9) 0.000( 0)
angle 0.664( 14) 0.664( 14) 0.000( 0) 0.419( 14) 0.419( 14) 0.000( 0)
dihedral 5.645( 6) 5.645( 6) 0.000( 0) 1.139( 6) 1.139( 6) 0.000( 0)
----- bonds ----- bonds ----- bonds ----- bonds ----- bonds ----- bonds
1 " C ASN A 3 " - " N GLN A 4 " [ 1.331, 1.337, -0.006, 1.29e-02, 6.01e+03, 1.88e-01] Z= -0.47
2 " CA ASN A 3 " - " CB ASN A 3 " [ 1.532, 1.526, 0.006, 1.82e-02, 3.02e+03, 1.13e-01] Z= 0.33
3 " CG ASN A 3 " - " ND2 ASN A 3 " [ 1.328, 1.323, 0.005, 2.10e-02, 2.27e+03, 5.49e-02] Z= 0.24
4 " CG ASN A 3 " - " OD1 ASN A 3 " [ 1.231, 1.235, -0.004, 1.90e-02, 2.77e+03, 5.24e-02] Z= -0.21
5 " CB ASN A 3 " - " CG ASN A 3 " [ 1.516, 1.521, -0.005, 2.50e-02, 1.60e+03, 3.53e-02] Z= -0.20
6 " N ASN A 3 " - " CA ASN A 3 " [ 1.456, 1.454, 0.002, 1.21e-02, 6.83e+03, 3.20e-02] Z= 0.17
7 " C ASN A 3 " - " O ASN A 3 " [ 1.236, 1.237, -0.002, 1.20e-02, 6.94e+03, 1.84e-02] Z= -0.17
8 " CA ASN A 3 " - " C ASN A 3 " [ 1.521, 1.523, -0.002, 1.19e-02, 7.06e+03, 1.62e-02] Z= -0.17
9 " C ASN A 2 " - " N ASN A 3 " [ 1.331, 1.329, 0.001, 1.34e-02, 5.57e+03, 6.14e-03] Z= 0.07
…
Two “selections” will show those restraints that involve both. Note that the selection 4 will select the residue number (resseq).
elbow.refine_geo_display 1yjp_refine_001_final.geo “ASN 3” 4
----- bonds ----- bonds ----- bonds ----- bonds ----- bonds ----- bonds
1 " C ASN A 3 " - " N GLN A 4 " [ 1.331, 1.337, -0.006, 1.29e-02, 6.01e+03, 1.88e-01] Z= -0.47
---- angles ---- angles ---- angles ---- angles ---- angles ---- angles
1 " C ASN A 3 " - " N GLN A 4 " - " CA GLN A 4 " [ 122.77, 123.55, -0.78, 1.41, 0.503, 3.06e-01] Z= -0.55
2 " O ASN A 3 " - " C ASN A 3 " - " N GLN A 4 " [ 123.30, 123.53, -0.23, 1.19, 0.706, 3.65e-02] Z= -0.19
3 " CA ASN A 3 " - " C ASN A 3 " - " N GLN A 4 " [ 116.29, 116.19, 0.10, 1.30, 0.592, 5.54e-03] Z= 0.08
---- dihedrals ---- dihedrals ---- dihedrals ---- dihedrals ---- dihedrals ---- dihedrals
1 " CA ASN A 3 " - " C ASN A 3 " - " N GLN A 4 " - " CA GLN A 4 " [ 180.00, 168.44, 11.56, 0, 5.00, 0.04, 5.35]
To get the information for all connections use the exclamation mark !.
elbow.refine_geo_display 1yjp_refine_001_final.geo “ASN 3” !
----- bonds ----- bonds ----- bonds ----- bonds ----- bonds ----- bonds
1 " C ASN A 3 " - " N GLN A 4 " [ 1.331, 1.337, -0.006, 1.29e-02, 6.01e+03, 1.88e-01] Z= -0.47
2 " C ASN A 2 " - " N ASN A 3 " [ 1.331, 1.329, 0.001, 1.34e-02, 5.57e+03, 6.14e-03] Z= 0.07
---- angles ---- angles ---- angles ---- angles ---- angles ---- angles
1 " C ASN A 3 " - " N GLN A 4 " - " CA GLN A 4 " [ 122.77, 123.55, -0.78, 1.41, 0.503, 3.06e-01] Z= -0.55
2 " O ASN A 2 " - " C ASN A 2 " - " N ASN A 3 " [ 122.86, 123.11, -0.25, 1.18, 0.718, 4.35e-02] Z= -0.21
3 " O ASN A 3 " - " C ASN A 3 " - " N GLN A 4 " [ 123.30, 123.53, -0.23, 1.19, 0.706, 3.65e-02] Z= -0.19
4 " C ASN A 2 " - " N ASN A 3 " - " CA ASN A 3 " [ 122.99, 122.77, 0.22, 1.41, 0.503, 2.49e-02] Z= 0.16
5 " CA ASN A 2 " - " C ASN A 2 " - " N ASN A 3 " [ 115.51, 115.61, -0.10, 1.27, 0.620, 6.56e-03] Z= -0.08
6 " CA ASN A 3 " - " C ASN A 3 " - " N GLN A 4 " [ 116.29, 116.19, 0.10, 1.30, 0.592, 5.54e-03] Z= 0.08
---- dihedrals ---- dihedrals ---- dihedrals ---- dihedrals ---- dihedrals ---- dihedrals
1 " CA ASN A 3 " - " C ASN A 3 " - " N GLN A 4 " - " CA GLN A 4 " [ 180.00, 168.44, 11.56, 0, 5.00, 0.04, 5.35]
2 " CA ASN A 2 " - " C ASN A 2 " - " N ASN A 3 " - " CA ASN A 3 " [ -180.00, -172.49, -7.51, 0, 5.00, 0.04, 2.26]
To see the worst restraints use top=3.
elbow.refine_geo_display 1yjp_refine_001_final.geo “ASN 3” top=3
----- bonds ----- bonds ----- bonds ----- bonds ----- bonds ----- bonds
1 " CG GLN A 4 " - " CD GLN A 4 " [ 1.516, 1.537, -0.021, 2.50e-02, 1.60e+03, 6.77e-01] Z= -0.84
2 " CA ASN A 6 " - " CB ASN A 6 " [ 1.527, 1.513, 0.014, 1.75e-02, 3.27e+03, 6.15e-01] Z= 0.80
3 " CB ASN A 6 " - " CG ASN A 6 " [ 1.516, 1.497, 0.019, 2.50e-02, 1.60e+03, 5.99e-01] Z= 0.76
---- angles ---- angles ---- angles ---- angles ---- angles ---- angles
1 " N GLY A 1 " - " CA GLY A 1 " - " C GLY A 1 " [ 113.30, 109.17, 4.13, 2.90, 0.119, 2.02e+00] Z= 1.42
2 " N ASN A 3 " - " CA ASN A 3 " - " C ASN A 3 " [ 108.90, 111.07, -2.17, 1.63, 0.376, 1.77e+00] Z= -1.33
3 " CB GLN A 4 " - " CG GLN A 4 " - " CD GLN A 4 " [ 112.60, 114.29, -1.69, 1.70, 0.346, 9.91e-01] Z= -0.99
---- dihedrals ---- dihedrals ---- dihedrals ---- dihedrals ---- dihedrals ---- dihedrals
1 " CA ASN A 3 " - " C ASN A 3 " - " N GLN A 4 " - " CA GLN A 4 " [ 180.00, 168.44, 11.56, 0, 5.00, 0.04, 5.35]
2 " CA ASN A 2 " - " C ASN A 2 " - " N ASN A 3 " - " CA ASN A 3 " [ -180.00, -172.49, -7.51, 0, 5.00, 0.04, 2.26]
3 " CA GLN A 4 " - " C GLN A 4 " - " N GLN A 5 " - " CA GLN A 5 " [ 180.00, 173.45, 6.55, 0, 5.00, 0.04, 1.71]
---- chirals ---- chirals ---- chirals ---- chirals ---- chirals ---- chirals
1 " CA ASN A 6 " - " N ASN A 6 " - " C ASN A 6 " - " CB ASN A 6 " [ False, 2.51, 2.58, -0.07, 0.20, 25.00, 0.13]
2 " CA GLN A 5 " - " N GLN A 5 " - " C GLN A 5 " - " CB GLN A 5 " [ False, 2.51, 2.46, 0.06, 0.20, 25.00, 0.08]
3 " CA TYR A 7 " - " N TYR A 7 " - " C TYR A 7 " - " CB TYR A 7 " [ False, 2.51, 2.46, 0.05, 0.20, 25.00, 0.06]
You can use the option only_hydrogens=True to see just the information of the hydrogen atoms. Note that RMSD/Z is zero for the bonds (in our example, H atoms are placed at ideal distances).
phenix.reduce 1yjp.pdb > 1yjp_h.pdb
phenix.pdb_interpretation 1yjp_h.pdb write_geo=True
elbow.refine_geo_display 1yjp_h.pdb.geo "ASN 3" only_hydrogens=True
The above commands will place H atoms with reduce, then the new file will be run by pdb_interpretation and finally, the restraints information is displayed for the H atoms only.
RMS results for selection
RMS(D/Z)
d-all d-none d-alt z-all z-none z-alt
bond 0.000( 6) 0.000( 6) 0.000( 0) 0.000( 6) 0.000( 6) 0.000( 0)
angle 1.575( 14) 1.575( 14) 0.000( 0) 0.525( 14) 0.525( 14) 0.000( 0)
dihedral 0.900( 1) 0.900( 1) 0.000( 0) 0.030( 1) 0.030( 1) 0.000( 0)
----- bonds ----- bonds ----- bonds ----- bonds ----- bonds ----- bonds
1 " CA ASN A 3 " - " HA ASN A 3 " [ 0.970, 0.970, 0.000, 2.00e-02, 2.50e+03, 3.94e-04] Z= 0.00
2 " ND2 ASN A 3 " - "HD21 ASN A 3 " [ 0.860, 0.860, -0.000, 2.00e-02, 2.50e+03, 1.83e-04] Z= -0.00
3 " N ASN A 3 " - " H ASN A 3 " [ 0.860, 0.860, -0.000, 2.00e-02, 2.50e+03, 1.07e-04] Z= -0.00
4 " CB ASN A 3 " - " HB2 ASN A 3 " [ 0.970, 0.970, -0.000, 2.00e-02, 2.50e+03, 4.15e-05] Z= -0.00
5 " ND2 ASN A 3 " - "HD22 ASN A 3 " [ 0.860, 0.860, 0.000, 2.00e-02, 2.50e+03, 1.45e-05] Z= 0.00
6 " CB ASN A 3 " - " HB3 ASN A 3 " [ 0.970, 0.970, -0.000, 2.00e-02, 2.50e+03, 1.30e-07] Z= -0.00
---- angles ---- angles ---- angles ---- angles ---- angles ---- angles
1 " N ASN A 3 " - " CA ASN A 3 " - " HA ASN A 3 " [ 110.00, 106.81, 3.19, 3.00, 0.111, 1.13e+00] Z= 1.06
2 " HB2 ASN A 3 " - " CB ASN A 3 " - " HB3 ASN A 3 " [ 110.00, 106.96, 3.04, 3.00, 0.111, 1.03e+00] Z= 1.01
3 " C ASN A 3 " - " CA ASN A 3 " - " HA ASN A 3 " [ 109.00, 106.68, 2.32, 3.00, 0.111, 6.00e-01] Z= 0.77
4 " CB ASN A 3 " - " CA ASN A 3 " - " HA ASN A 3 " [ 109.00, 110.98, -1.98, 3.00, 0.111, 4.36e-01] Z= -0.66
5 " C ASN A 3 " - " N GLN A 4 " - " H GLN A 4 " [ 123.72, 122.31, 1.41, 3.00, 0.111, 2.22e-01] Z= 0.47
6 " CG ASN A 3 " - " CB ASN A 3 " - " HB2 ASN A 3 " [ 108.00, 109.29, -1.29, 3.00, 0.111, 1.86e-01] Z= -0.43
7 " CG ASN A 3 " - " CB ASN A 3 " - " HB3 ASN A 3 " [ 108.00, 109.26, -1.26, 3.00, 0.111, 1.77e-01] Z= -0.42
8 " CA ASN A 3 " - " N ASN A 3 " - " H ASN A 3 " [ 113.36, 114.17, -0.81, 3.00, 0.111, 7.33e-02] Z= -0.27
9 " CA ASN A 3 " - " CB ASN A 3 " - " HB3 ASN A 3 " [ 109.00, 109.27, -0.27, 3.00, 0.111, 8.37e-03] Z= -0.09
10 " CA ASN A 3 " - " CB ASN A 3 " - " HB2 ASN A 3 " [ 109.00, 109.23, -0.23, 3.00, 0.111, 5.99e-03] Z= -0.08
11 " C ASN A 2 " - " N ASN A 3 " - " H ASN A 3 " [ 123.66, 123.71, -0.05, 3.00, 0.111, 2.83e-04] Z= -0.02
12 "HD21 ASN A 3 " - " ND2 ASN A 3 " - "HD22 ASN A 3 " [ 120.00, 119.97, 0.03, 3.00, 0.111, 8.30e-05] Z= 0.01
13 " CG ASN A 3 " - " ND2 ASN A 3 " - "HD21 ASN A 3 " [ 120.00, 120.02, -0.02, 3.00, 0.111, 3.25e-05] Z= -0.01
14 " CG ASN A 3 " - " ND2 ASN A 3 " - "HD22 ASN A 3 " [ 120.00, 120.01, -0.01, 3.00, 0.111, 1.16e-05] Z= -0.00
---- dihedrals ---- dihedrals ---- dihedrals ---- dihedrals ---- dihedrals ---- dihedrals
1 " CB ASN A 3 " - " CG ASN A 3 " - " ND2 ASN A 3 " - "HD22 ASN A 3 " [ -0.00, -0.90, 0.90, 2, 30.00, 1.11e-03, 1.33e-03]
To see information about non-bonded atoms use show_nonbond=True.
elbow.refine_geo_display 1yjp_refine_001_final.geo “ASN 3” show_nonbond=True
- nonbonded - nonbonded - nonbonded - nonbonded - nonbonded - nonbonded
1 " OD1 ASN A 3 " - " ND2 ASN A 3 " ['2.730', '2.520', 'x,y+1,z']
2 " ND2 ASN A 3 " - " OD1 ASN A 3 " ['2.730', '2.520', 'x,y-1,z']
3 " O ASN A 2 " - " CA ASN A 3 " ['2.801', '2.776']
4 " O ASN A 2 " - " N ASN A 3 " ['2.838', '2.520', 'x,y+1,z']
5 " N ASN A 3 " - " O ASN A 2 " ['2.838', '2.520', 'x,y-1,z']
6 " O ASN A 3 " - " CA GLN A 4 " ['2.844', '2.776']
7 " ND2 ASN A 3 " - " OE1 GLN A 5 " ['2.845', '2.520']
8 " N ASN A 3 " - " O ASN A 3 " ['2.904', '2.496']