calcPRE
Given a molecular structure and a PRE restraint table, back-calculate PRE values, and optionally plot the observed and calculated values as a function of residue number. The convention used in this helper program is that the paramagnetic tag is listed in the first selection, while the measured residues are listed in the second selection.
Usage: calcPRE [option] -psf <file.psf> -table <file.tbl> <file.pdb>
where option is one or more of:
-subSel <atom selection> - delete restraints do not include the specified
atoms in sel2 or sel3.
Currently, this program requires that all tag coordinates be present, and that an accompanying PSF be specified.
Options:
-psf <file.psf> - name of PSF file.
-table <file.tbl> - name of file with PRE assignment statements. If the
string "generate" is given as the table name, dummy
restraints are generated from the -genTagSel and
-genSel arguments, so that no input table is required,
but the -genTagSel is required.
-crossTable <file.tbl> - restraints not used in determining tag coordinates
or tau_c, but whose restraints are back-calculated
using the values determined from the argument of
the -table option.
-params <file.par> - name of a parameter file, required for tag optimization
of non-standard systems. This option can be given
multiple times to load multiple parameter files.
-aveType <spec> - type of distance averaging. The argument spec is one of
r-6 : <r^(-6)> averaging
sum : 1/aveSize \sum r^{-6}
-aveSize <val> - Value of aveSize for sum averaging. This can be important
for oligomers.
-singleEns - Treat the files specified as an ensemble instead of a set
of individual structures.
-genTagSel - selection for paramagnetic tag used to generate dummy
restraints if the table is specified as "generate".
-genSel - selection used to generate dummy restraints if
the table is specified as "generate" ["name HN"]
-funType <spec> - the spec argument can be one of correlation, harmonic,
square, or onesixth. [default: harmonic] For
all but correlation, the constant PRE prefactor
components must be accurately specified. These
include
-rlxType <spec> - Type of paramagnetic relaxation mechanism. The
argument spec should be one of
"r2dd" : R2 relaxation enhancement by
dipolar mechanism
"r2curie" : Curie spin relaxation
"r2mix" : r2dd + r2curie
"r1dd" : R1 relaxation enhancement by
dipolar mechanism
"r1curie" : by Curie spin relaxation
"r1mix" : r1dd + r1
-frequency <val> - NMR frequency in MHz [800].
-npc <num> - number of paramagnetic centers [1] - for
oligomers. See the prePot docs for more info.
-sqn <val> - electron spin quantum number [0.5].
-tauc <val> - correlation time. This is optimized if
-fitTags or -fitTauc is specified.
-fitTauc - If specified, tauc will be chosen to optimize the
PRE energy function.
-noFitTauc - If specified, tauc will be not be optimized. By default,
tauc is optimized if -fitTauc or -fitTags are given.
-fitTags - If specified, the sidechain coordinates of the tag
residues are manipulated such that the PRE energy is
optimized. By default, sidechain selection in the
restraint table are updated. This fitting is controlled
through the following flags:
-tagSel <sel> - where sel is an atom selection to move during
tag optimization. Use of this term enables
-fitTags.
-backboneSel <sel> - sel is an atom selection of atoms which should
not be moved during tag optimization.
-tagInteractSel <sel> - sel specifies which atoms interact with the
tag coordinates. By default tag atoms with
the same segid interact with all non-tag atoms.
Tag atoms with different segids do not interact.
["all"]
-groupedSel <sel> - sel is an atom selection of atoms which should
be moved as a rigid body during tag optimization.
This option can be specified multiple times to
specify multiple regions to be grouped separately.
-energyScale <val> - energy scale factor during tag optimization [1].
-scaleType <spec> - where spec is one of const, sigma or obsig. This
value controls the energy scale factor for each
per-restraint contribution [sigma].
-eefx - If specified, uses the EEFx force field during
tag optimization. This requires a custom PSF.
-numTagStructures <num> - for each input structure, the number of
structures calculated during tag
optimization [10].
-highTempTime <val> - length (in ps) of high temperature dynamics
phase [10].
-annealingTime <val>- length (in ps) of molecular dynamics at each
temperature during simulated annealing
phase [0.2].
-writeStructures - if specified, write out the structures calculated
with optimized tag configurations.
-sbmf - By default, the Solomon-Bloembergen eqaution is used for
calculation of PRE from atomic coordinates. If this
option is specified, a model-free modification of this
equation is employed- see JACS 126, 5879 (2004). This
option takes into account internal tag motion with
characteristic time au_i, related to the total
correlation time 1/ au_t by
1/ au_t = 1/tau_c + 1/tau_i
-taut <val> - the total correlation time (in ns). This must
be less than or equal to tauc, and defaults to 0,
corresponding to a case of internal motion fast
compared to tau_c and the inverse spectrometer
frequency. If -sbmf is specified, then this parameter
should be specified, along with -frequency and a
decent estimate for -taut,
-symmetryModule <m>- name of module to configure a
<m symSimulation>.SymSimulation. It must contain a
function named init which returns a
<m simulation>.Simulation.
-distMultMat <mat> - mat is specified as a row-major Python-formatted 2D
list specifying multipliers for the i,j 1/r^6 distance
contributions. This allows one to preferentially weight
a specified contribution, and has been used to simulate
the presence of a dimer/tetramer mixture when only a
single ensemble member's coordinates are present. The
dimensions of the list are len(sel1)xlen(sel2), so that
when this option is specified, the size of these
selections must be the same for each restraint.
-plotVsResid - if specified, a plot of calculated and observed PRE
values is displayed as a function of residue number.
-plotCorrelation - if specified, a plot is made of calculated vs observed PRE
values. Data points on this plot are clickable to
display segid:residue identity. The ``c'' button can be
used to clear picked labels.
-pdbTemplate <spec> - name of the output structures files if -writeStructures
is specified. The literal STRUCTURE is replaced by the
structure number associated with the tag computation
calculation, while the literal FILE is replaced by the
input filename [FILE_STRUCTURE.calcPRE].
-doAnalyze - for each structure, print out analysis of each energy
term.
-wintitle <string> - string to display in the title bar of the plot window(s).