SzmapGrid

Overview

The szmap_grid utility reads an OEBinary (.oeb or .oeb.gz) file generated by SZMAP and displays information about the grids within. If atom property tags from a SZMAP -at_coords calculation are found, it will list the all property names.

Example Commands

> szmap_grid 4std_stbl.oeb.gz

szmap-meta-data attached to molecule 1, 'complex: PROTEIN (SCYTALONE DEHYDRATASE) + residue 'BFS''.
'mask_grid' dimensions: 38 29 33
'neut_diff_free_energy_grid' dimensions: 38 29 33
'vdw_grid' dimensions: 38 29 33
'order_grid' dimensions: 38 29 33

szmap-meta-data attached to molecule 2, 'ligand: residue 'BFS''.
'lig_mask_grid' dimensions: 38 29 33
'neut_diff_lig_free_energy_grid' dimensions: 38 29 33
'lig_vdw_grid' dimensions: 38 29 33
'lig_order_grid' dimensions: 38 29 33

szmap-meta-data attached to molecule 3, 'apo: PROTEIN (SCYTALONE DEHYDRATASE)'.
'apo_mask_grid' dimensions: 38 29 33
'neut_diff_apo_free_energy_grid' dimensions: 38 29 33
'apo_vdw_grid' dimensions: 38 29 33
'apo_order_grid' dimensions: 38 29 33

szmap-meta-data attached to molecule 4, 'stabilization'.
'stbl_mask_grid' dimensions: 38 29 33
'neut_diff_stbl_free_energy_grid' dimensions: 38 29 33
'stbl_vdw_grid' dimensions: 38 29 33
'stbl_order_grid' dimensions: 38 29 33

Input appears to be the results file from a SZMAP grid calculation.
SZMAP grids but no -at_coords property tags in input file.

> szmap_grid 2w3a_coords.oeb.gz

szmap-meta-data attached to molecule 1, 'apo: TOP'.
atom property tags: szmap_mask, szmap_neut_diff_free_energy, szmap_neut_diff_enthalpy,
szmap_neut_diff_entropy, szmap_vdw, szmap_order, szmap_vac_diff_free_energy,
szmap_vac_diff_enthalpy, szmap_vac_diff_entropy, szmap_free_energy, szmap_enthalpy,
szmap_entropy, szmap_neutral_free_energy, szmap_neutral_enthalpy,
szmap_neutral_entropy, szmap_interaction, szmap_psolv, szmap_wsolv, szmap_intvdw,
szmap_probe_burial, szmap_clash

szmap-meta-data attached to molecule 2, 'apo: DIHYDROFOLATE REDUCTASE+ion+cofact'.

Input appears to be the results file from a SZMAP -at_coords calculation.
SZMAP -at_coords property tags but no grids in input file.

szmap_grid can also split a given grid out into a separate grid file. The output grid can be in OEBinary, Grasp, CCP4, or ascii format. Since PyMOL can read Grasp .phi maps, they provide a way to transfer grids from SZMAP to PyMOL.

> szmap_grid 4std_stbl.oeb.gz neut_diff_apo_free_energy_grid 4std_nddG.phi

The options -output_all_format and -prefix will generate a separate grid file for all grids in the SZMAP results.

> szmap_grid -output_all_format .phi -prefix 4std 4std_stbl.oeb.gz

If the szmap_grid option -at_coords is used, the specified grid’s values will be interpolated at the coordinates of any atoms in the input coordinates file and written out attached to those atoms in a file defined by -mol for use by other tools. A tab-delimited table of these results is written to standard-output.

> szmap_grid -at_coords coords.sdf -mol out.oeb szmap.oeb.gz vdw_grid >table.txt

Note

A direct calculation at these coordinates using SZMAP will be superior to these interpolated values.

Meta-data

SZMAP attaches meta-data to molecules in the results file that documents run conditions. This data is displayed when the szmap_grid option -verbose is used.

szmap-meta-data attached to molecule 1, 'complex: PROTEIN (SCYTALONE DEHYDRATASE) + residue 'BFS''.

points: grid
system: complex
prot-title: PROTEIN (SCYTALONE DEHYDRATASE)
prot-num-atoms: 2680
prot-num-bonds: 2720
lig-title: residue 'BFS'
lig-num-atoms: 33
lig-num-bonds: 34
dielectric-model: gaussian
eps-outer: 80
eps-inner: 1
salt-conc: 0.05M
probe-type: water
orientations: 60
rotation-matrices: symmetrical
mask-cutoff: 0
mask: calculation=1.01
mask: bulk solvent=0.99
mask: clash=0
grid-spacing: 0.5A
zap-spacing: 0.5A
zap-iters: 5
run-date: Jan 23 2013
run-time: 10:48:03
version: 20130123
release: 1.1.1
arch: redhat-RHEL5-x64
platform: redhat-RHEL5-g++4.1-x64
licensee: Initech
site: Austin

The meta-data includes the version and release of SZMAP used to generate the results. Early releases used a different format, version: 110 for version 1.1.0.

Command Line Help

A description of the command line interface can be obtained by executing SzmapGrid with the --help option.

> szmap_grid --help

will generate the following output:

Help functions:
  szmap_grid --help simple      : Get a list of simple parameters
  szmap_grid --help all         : Get a complete list of parameters
  szmap_grid --help defaults    : List the defaults for all parameters
  szmap_grid --help <parameter> : Get detailed help on a parameter
  szmap_grid --help html        : Create an html help file for this program
  szmap_grid --help versions    : List the toolkits and versions used in the application

Required Parameters

-input_mol <filename>
-i <filename>

[keyless parameter 1]

OEBinary input file (.oeb or .oeb.gz), with calculated grids attached to copy input molecule(s).

Optional Parameters

Grid Options

-grid <name>
-g <name>

[keyless parameter 2]

Grid to extract or display information about. Name must be one of the grid names listed in Appendix 1: SZMAP Grids.

If not specified, information will be displayed about all grids.

-output_grid <filename>
-o <filename>

[keyless parameter 3]

The file format of the output grid file is automatically determined from the file extension.

File type Extension
OE grid .grd .grd.gz
Grasp grid .phi .phi.gz
Ascii grid .agd .agd.gz
CCP4 map .map .map.gz .ccp .ccp.gz
.ccp4 .ccp4.gz  

Use -output_all_format instead to write all grids into separate files.

-output_all_format <format>
-all <format>

Write out every grid to individual files in the specified format. Used in conjunction with -prefix.

File type Format
OE grid .grd .grd.gz
Grasp grid .phi .phi.gz
Ascii grid .agd .agd.gz
CCP4 map .map .map.gz .ccp .ccp.gz
.ccp4 .ccp4.gz  
-prefix <text>

Filename prefix for grid files written when -output_all_format is specified. Can include file path in addition to the beginning portion of the filename.

[default = szmap_grid]

-slice

Print grid values to standard-output as a series of 2D tabular slices.

-std_box <filename>

Write standard (complex) grid bounding box to output ‘box molecule’ coordinate file.

File type Extension
SDF .sdf .mol .sdf.gz .mol.gz
MOL2 .mol2 .mol2.gz
PDB .pdb .ent .pdb.gz .ent.gz
MacroModel .mmod .mmod.gz
OEBinary .oeb .oeb.gz

To facilitate visualization, box corners are represented by nitrogen atoms and bonds define the box edges.

-lig_box <filename>

Write ligand grid bounding box to output ‘box molecule’ coordinate file.

File type Extension
SDF .sdf .mol .sdf.gz .mol.gz
MOL2 .mol2 .mol2.gz
PDB .pdb .ent .pdb.gz .ent.gz
MacroModel .mmod .mmod.gz
OEBinary .oeb .oeb.gz

To facilitate visualization, box corners are represented by nitrogen atoms and bonds define the box edges.

-apo_box <filename>

Write apo grid bounding box to output ‘box molecule’ coordinate file.

File type Extension
SDF .sdf .mol .sdf.gz .mol.gz
MOL2 .mol2 .mol2.gz
PDB .pdb .ent .pdb.gz .ent.gz
MacroModel .mmod .mmod.gz
OEBinary .oeb .oeb.gz

To facilitate visualization, box corners are represented by nitrogen atoms and bonds define the box edges.

-box_mol <filename>

Write box_mol bounding box to output ‘box molecule’ coordinate file, if a box_mol is found in the input .oeb file.

File type Extension
SDF .sdf .mol .sdf.gz .mol.gz
MOL2 .mol2 .mol2.gz
PDB .pdb .ent .pdb.gz .ent.gz
MacroModel .mmod .mmod.gz
OEBinary .oeb .oeb.gz

To facilitate visualization, box corners are represented by nitrogen atoms and bonds define the box edges.

Interpolation Options

-at_coords <filename>
-coords <filename>

Interpolate the values of the selected grid (and the corresponding mask grid) at the coordinates of atoms in any molecules in the file. Write those molecules, with the (masked) results attached to the atoms, to the output file.

File type Extension
SDF .sdf .mol .sdf.gz .mol.gz
MOL2 .mol2 .mol2.gz
PDB .pdb .ent .pdb.gz .ent.gz
MacroModel .mmod .mmod.gz
OEBinary .oeb .oeb.gz

One of the following tags will be used when assigning values to atoms (without any apo_ or lig_):

  • szmap_mask
  • szmap_neut_diff_free_energy
  • szmap_neut_diff_enthalpy
  • szmap_neut_diff_entropy
  • szmap_vac_diff_free_energy
  • szmap_vac_diff_enthalpy
  • szmap_vac_diff_entropy
  • szmap_free_energy
  • szmap_enthalpy
  • szmap_entropy
  • szmap_neutral_free_energy
  • szmap_neutral_enthalpy
  • szmap_neutral_entropy
  • szmap_interaction
  • szmap_psolv
  • szmap_wsolv
  • szmap_vdw
  • szmap_intvdw
  • szmap_probe_burial
-output_mol <filename>
-mol <filename>

OEBinary output file (.oeb or .oeb.gz), with interpolated grid values attached to -at_coords molecule’s atoms.

[default = szmap_grid_interp.oeb.gz]

-no_table

Do not print a tab-delimited table of interpolated grid values to standard-output when -at_coords is the selection.

-mask_cutoff <number>

Points where interpolated mask values are less than or equal to this cutoff will have values attached to atoms set to 0.0. The default value tries to account for the edges of the masked area where interpolation can generate distorted results.

[default = 0.8]

Other Options

-verbose
-v

Print additional grid details (and SZMAP meta-data) to standard-output.