sitemap Command Help
Command: $SCHRODINGER/sitemap
usage:
$SCHRODINGER/sitemap [options] -j <jobname> -prot <file.mae>
or
$SCHRODINGER/sitemap [options] <input_file.in>
$SCHRODINGER/sitemap carries out a site-finding job, then calculates SiteMaps
for each qualifying site-point grouping, and finally evaluates the SiteMap
results and summarizes the characteristics of the sites in a series of Maestro
properties. SiteMap can be invoked from Maestro or can be run from the command
line.
positional arguments:
input_file A file with lines such as "KEYWORD value", which are
equivalent to "-keyword value" command-line arguments.
(Except for job control options such as -HOST)
options:
-j <jobname>, -job <jobname>, -jobname <jobname>
A unique descriptor for this data set, used to make
some file names unique. Required when not using an
input file.
-h, -help Show this help message and exit.
Job Control Options:
-HOST <hostname> Run job remotely on the indicated host entry.
Standard Options:
-NSTRUCTS NSTRUCTS Divide the overall job into subjobs with no more than
NSTRUCTS structures.
Common SiteMap Options:
-prot <file.mae> [<file.mae>...], -protein <file.mae> [<file.mae>...]
A required protein file in Maestro format. Multiple
such options may be specified to run multiple jobs.
-lig <file>, -ligmae <file>, -ligsdf <file>
include optional ligand file in Maestro or SD format
-receptortype <auto, protein, rna>
Specify the type of receptor to be protein or RNA.
auto mode will determine the receptor type
automatically
-siteasl <asl> ASL expression used instead of a ligand to restrict
the site-finding step.
-sitebox <dist> If an optional ligand file or ASL expression is
specified, restrict the site-finding step to a box
placed around the ligand plus a margin of <dist>
(default 6.0)
-addsp [yes|no] Add additional "extend" site points to the site-point
set if they fall in regions that satisfy the threshold
criteria for phobicity or philicity (default, "yes")
-xcent XCENT X coordinate of grid center, to be used instead of
ligand-, receptor-, or ASL-based centroid
-ycent <float> Y coordinate of grid center
-zcent <float> Z coordinate of grid center
-xrange <float> X size of grid box, to be used instead of receptor-,
or ASL-based box size
-yrange <float> Y size of grid box
-zrange <float> Z size of grid box
-reportsize <size> Minimum number of site points needed to report a site
grouping (default, 15)
-maxeval <max_evaluated_sites>
Evaluate the top N largest sites (default: 2x max
reported site)
-maxsites <max> Report up to this number of sites (default, 5)
-modphobic {0|1|2|3} Set definition to be used in defining hydrophobic
regions (default, 3)
-grid <gridsize> Grid size to be used in the SiteMap calculations
(default, 0.7 A)
-resolution <val> Alternative means for specifying the grid size
(<val>="low" for 1.0 A, "standard" for 0.7 A or "high"
for 0.35 A)
-mapdist <dist> Restrict displayed SiteMaps to <dist> from the nearest
site point (default, 4 A). Can be overriden, up to the
"-margin <margin>" distance, by using the Surface
Limit facility
-ffield <OPLS version>
Version of OPLS to use (default, OPLS_2005)
-extend <intdist> In evaluating exposure in site-evaluation stage, try
adding additional site points at grid points +/-
<intdist> from an original site point (default, 3 A)
-compact_mode_threshold <float>
If SiteMap generates sites with volumes above this
threshold, a 2nd sitemap run will start with settings
for the compact mode. To disable the 2nd sitemap run,
set a negative number like -1. (default, 800 ų)
-compress [yes|no] Compress the final _out.mae file using gzip. (default,
"yes")
-writestructs [yes|no]
include a copy of the receptor structure (and ligand,
if any) in the output file (default, "yes")
-writevis [yes|no] write .vis and .smap files for surface visualization
(default, "yes")
Additional Options:
-enclosure <fraction>
Fraction of ray directions from a grid point that must
intersect the protein within a specified distance for
that grid point to be considered as a potential site
point (default, 0.5)
-maxdist <dist> Distance within which a directional ray from a
candidate grid point must intersect the protein
surface (default, 8 A)
-maxvdw <vdw-energy> vdW interaction-energy threshold (kcal/mol) for a grid
point to qualify as a potential site point (default,
1.1). Note this quantity is the negative of the
computed interaction energy, so that the argument
supplied must be positive. A smaller positive value
keeps more candidate site points
-verbosity {0|1|2|3} Control level of detail in output log files (default,
0)
-margin <margin> Grid-box margin to be used in the SiteMap calculations
(default, 6 A)
-addphob <thresh> Set criterion for adding additional phobic points to
<thresh> (default, -0.50 kcal/mol if modphobic
argument is 2 or 3, otherwise -0.75 kcal/mol)
-addphil <thresh> Set criterion for adding additional philic points
(default, -8 kcal/mol)
Advanced Options:
-dvscale <float> When multiplied by the square of a protein-atom vdW
radius, the argument sets the squared distance from a
candidate site point to a protein atom for determining
whether the site point is "inside" or "outside" the
protein (default, 2.5)
-nthresh <int> Minimum number of candidate site-point neighbors
required to be within a distance of sqrt(d2thresh) for
a candidate site point to be eligible for inclusion in
a site-point grouping (default, 3)
-d2thresh <float> Squared distance used in nthresh test (default 3.1
A**2)
-kmax <int> Maximum sum of differences in grid indices to nearest
site point allowed to add a candidate site point to a
site-point group (default, 3)
-kmax2 <int> Maximum sum of squares of differences in grid indices
to nearest site point allowed for a candidate site
point to be added to a site-point group (default, 5)
-mingroup <int> Minimum number of points in a site-point grouping
required to constitute a site (default, 3)
-dthresh <float> Maximum acceptable value for the minimum distance
separating site points in two site-point groupings for
them to be considered for merger into a single group
(default, 6.5 A)
-rthresh <float> Minimum acceptable ratio of the distance between the
centroids of two site-point groups relative to the
effective sizes of the groups (default, 5.)
-r2thresh <float> Squared distance used in determining whether two site-
point groupings being considered for merger have
successfully been interconnected by solvent-exposed
bridging points (default, 4.1 A**2)
-cutoff <cutdist> The cutdist value restricts the calculation of vdW and
electrostatic potentials to protein atoms that lie
within this distance of a grid point (default, 20 A)
-modcharges [yes|no] The default value of "yes" scales down formal-charge
contributions to the protein partial atomic charges by
50%
-nearres <float> Maximum distance between sitepoints and residues to
list in the s_sitemap_residues property (default, 3.5
A).