The EMAP module
Modeling macromolecular assemblies with map objects
by Xiongwu Wu and Bernard R. Brooks
Laboratory of Biophysical Chemistry, NHLBI, NIH
The EMAP module is designed to manipulate map objects as well as
interexchange between atomic objects and map objects.
A map object is defined as a rectangular space with grid distributions
of certain properties. A map object may have its reference atom set which
defines the atomic structure used to transfer map to atoms or verse versa.
A rigid domain is defined to represent a map at the position and
orientation of an atomic structure. A rigid domain can be moved around
as a molecular structure. Many rigid domains can be defined for a map object.
Map objects can be manipulated so as to initialization, resizing,
addition, substruction, reduction, and comparison. With rigid domains, one
can perform fiting individual maps to a complex map, constructing complex
structure from many components.
Map object manipulation is highly efficient for large system modeling. It
is also the necessary approach to derive structure information from electon
microscopy experiment.
Field map is defined to describe the electrostatic field generated from
a molecule. In addition to the density map used in electron microscopy (EM)
image fitting, molecular maps are defined to describe the distribution of
atomic properties such as partial charges, vdw cores. Field maps and
molecular maps provide a convenient way to evaluate interactions between
map objects. Through map energies, the structure of macromolecular
assemblies can be modeled through docking or simulation approaches.
* Menu:
* Syntax:: Syntax of the EMAP commands
* Description:: Description of the EMAP functions
* Substitution:: Description of substitution values
* Examples:: Usage example of the EMAP commands
Syntax of EMAP Manipulation commands
[SYNTAX EMAP manipulation]
! default parameter setting:
EMAP { PARAmeters [RESO real] [RCUT real] -
[DX real] [DY real] [DZ real] [ICORE int] -
[AX real] [AY real] [AZ real] [EPS real] -
[PSOLV real] [PSELE real] [PCORE int] }
! Map file IO:
EMAP { READ mapid NAME filename }
{ WRITe mapid NAME filename [DDR|CORE] }
! Map object manipulation
EMAP { CORE mapid [CUT real] [DENSity|DDR] }
{ DDR mapid }
{ GENErate mapid [atom-selection] [COMParison-set] [RESO real] -
[DX real DY real DZ real] [AS existing_mapid] -
[FMAP [GRID] [AX real AY real AZ real] }
{ INITialize emapid [BASE real] }
{ REDUce mapid BY mapid [TO mapid] }
{ REFErence mapid atom-selection }
{ RESIze mapid AS mapid [GRID-only] [BOUNdary-only] }
{ SCALe mapid BY real }
{ STATistics emapid }
! Rigid domain manipulation
EMAP { ASSIgn mapid AS rigid [atom-selection] }
{ COMPlex RIGId rigid [RIGId mapid ...] [APPEnd] [FIX]}
{ PROJect rigid [ atom-selection ] }
{ RESTore rigid }
{ ROTAte rigid XDIR real YDIR real ZDIR real PHI real }
{ SAVE rigid }
{ TRANslate rigid XDIR real YDIR real ZDIR real [DIST real] }
! Rigid domain IO
EMAP { TRAJectory [OPEN|CLOSe] [READ|WRITe] UNIT integer [NAME filename| -
! Map object and rigid domain manipulation:
EMAP { ADD rigid TO mapid }
{ COPY [MAPId mapid|RIDId rigid] TO [mapid|rigid] }
{ DELEte [MAPId mapid|RIGId rigid]}
{ DUPLicate [MAPId mapid|RIDId rigid] TO [mapid|rigid] }
{ PSF [MAPId mapid|RIGId rigid] [SKIP int] [RCUT real] }
{ QUERy [MAPId mapid|RIDId rigid] }
{ SUBStract rigid FROM mapid }
{ SUM mapid }
! Conformational evaluation:
EMAP { CORR [MAPId mapid|RIGId rigid] [MAPId mapid|RIGId rigid] [CORE] [DDR] }
{ INTEraction [MAPId mapid|RIGId rigid] [MAPId mapid|RIGId rigid] -
[EPS real] [PSOLV real] [PSELE real] [PCORE int] }
! Conformational optimization:
EMAP { DOCK [FMAP][GTMC [SPACE]] [MANY] [TRAJectory integer] -
[MAPId mapid] [RIGId rigid [RIGId rigid [...]]] -
grid-properties MC-parameters Correlation-type -
Fitting-criteria }
grid-properties::= NTRAnslation int NROTation int [SPACE]
MC-parameters::=NCYLc int NSTEp int TEMP real TRAN real ROTA real
Correlation-type::=[CORE [ACORe int] [BCORe real] [CCORe real]] [DDR] [CORE]
Fitting-criteria::=[LOOP int] [DTCO real] [CFIX real]
! Rigid domain trajectory file IO:
EMAP { TRAJectory [OPEN|CLOSE] UNIT integer [NAME filename] }
{ TRAJectory [READ|WRITE] UNIT integer RIGId integer }
________________________________________________
! A shortcut READ command is implmented to simplify the process of creating
! molecular segments from coordinate files or PDB (default) files.
READ { SEGId segment { PDB [BUILd [SETUp]] }} [UNIT integer]
{ { CARD }}
{ { FREE }}
__________________________________________________
Descriptions of the map manipulation commands
Map objects are created only by READ, GENErate, or DUPLicate commands.
Rigid domains are created only by ASSIgn or DUPLicate commands. All of other
commands manipulate existing map objects or rigid domains.
All rigid domains has a storage for backup purpose. Current position and
orientation of a rigid domain can be SAVEd to the storage and can be RESTored
from the storage.
------------------------------------------------------------------------------
1) The PARAmeter command
The PARA command will set the default values for parameters that
would be used in other EMAP commands.
RESO--Map resolution, angstroms;
RCUT--the base density to tell the noise level;
DX, DY, DZ-- Grid interval in map objects;
AX, AY, AZ-- Scaling lengths for reduced coordinates in field maps;
EPS-- Dielectric constant for electrostatic interaction;
PSOLV-- Desolvation energy parameter
PSELE-- Electrostatic solvation parameter
PCORE-- vdw core interaction parameter
------------------------------------------------------------------------------
2) The READ command
The READ command will create a map object by readin the map information
from a map file. Currectly, only CCP4 format is supported.
------------------------------------------------------------------------------
3) The WRITe command
The WRITe command will write a map object to a map file. Currectly,
only CCP4 format is available. Option DDR specify the Laplacian filtered
density will be written out, and CORE specify the core indics will be
written out.
------------------------------------------------------------------------------
4) The CORE command
The CORE command will rebuild the core indice of the map object. Two
methods, density or Laplacain, can be used for the build up. CUT defines the
cutoff density used in the build up.
------------------------------------------------------------------------------
5) The DDR command
The DDR command will recalculate the Laplacian of the map object.
------------------------------------------------------------------------------
6) The GENE command
The GENErate command will generate a map object from the coordinates of
a selected atom set. The default resolution is 15 angstroms but can be
specified for other values. The default map gid properties is DX=DY=DZ=3
angstroms. The grid intervals can be specified by DX, DY, and DZ or taken from
other map objects by AS. The generated map object takes the atom set as its
reference atom set.
If FMAP is specified, a molecular map will be generated using atomic
properties of the molecule. This map contains charge distribution, electro-
static field distribution, and vdw core distribution. GRID option can speed
up the calculation in electrostatic field distribution with less accuracy. The
field map uses AX, AY, and AZ to define the coordinate scales. Normally, AX,
AY, and AZ is set to the gyration radius of the molecule.
------------------------------------------------------------------------------
7) The INITialize command
The INITialize command set the distribution properties of a map object
to be zero, or BASE value, including core indices , throughout its space.
The map object should be generated before it can be initialized.
------------------------------------------------------------------------------
8) The REDUce command
The REDUce command will reduce the first map object by the map
object specified after "BY". If a mapid is specified by TO, the result
will be put to the mapid. Otherwise, the first map object will be reduced.
------------------------------------------------------------------------------
9) the REFErence command
The REFErence command will take the atom-selection as the reference
atom set for the map object. ALL rigid domains representing this map object
will not change after the reference atom set change.
------------------------------------------------------------------------------
10) The RESIze command
The RESIze command will change the map object to have the same grid
properties or/and bundary properties as the other map object. Option GRID-only
only resizes the grid properties, and BOUNdary-only only resizes boundary
properties.
------------------------------------------------------------------------------
11) The SCALE command
The SCALe command will scale the distribution properties of the
map object by the real number spedified after "BY".
------------------------------------------------------------------------------
12) The STATistics command
The STATistics command calculate and print the statistic properties
of the distribution properties of the map.
------------------------------------------------------------------------------
13) The ASSIgn command
The ASSIgn command will create a rigid domain representing the map
object. If no atom is selected, a unit vector set at origin will be
created for the rigid domain. If atom-selection is given, the relative
position and orientation related to the reference atom set will be generated
for the rigid domain. The atom-selection should have the same atom number as
the reference atom set of the map object. If the map has no reference atom
set, a initialized rigid domain will be created and the atom selection is
assigned as the reference atom set for the map.
------------------------------------------------------------------------------
14) The COMPlex command
The COMPlex command will define which rigid domains are contained in
a complex that will be built with the DOCK command. A COMPlex command without
APPEnd option will overwrite previous COMPlex command, while with APPEnd option
the command will add the newly defined rigid domains to the complex. The SEEN
option will enable multiple body search during the DOCK procedure, ie., this
rigid domain will be seen when docking other rigid domains.
------------------------------------------------------------------------------
15) The PROJect command
The PROJect command will generate coordinates for the selected atoms
based on the reference atom set and the rigid domain. The selected atoms
should have the same number of atom as the reference set. coordinates are
copied in order of selection and no check is performed.
------------------------------------------------------------------------------
16) The RESTore command
The RESTore command will copy the stored position and orientation to
the rigid domain.
------------------------------------------------------------------------------
17) The ROTAte command
The ROTAte command will cause the specified rigid domain to be rotated
about the specified axis vector through the map center. The vector
need not be normalized, but it must have a non zero length. The PHI value
gives the amount of rotation about this axis in degrees.
------------------------------------------------------------------------------
18) The SAVE command
The SAVE command will copy the position and orientation of the rigid
domain to its storage.
------------------------------------------------------------------------------
19) The TRANslate command
The TRANslate command will cause the position of the rigid domain
to be translated. The translation step may be specified by either X,Y, and Z
displacements, or by a distance along the specified vector. When no distance
is specified, The XDIR,YDIR, and ZDIR values will be the step vector. If a
distance may be specified, the translation will be along the vector for a
distance of DIST.
------------------------------------------------------------------------------
20) The TRAJectory command
The TRAJ command perform open, close, read, or write the trajectory
file of a rigid domain. The trajectory file stores the translation vector
and rotation matrix, configuration energy in a assembly and conformation
number and search index.
When OPEN is specified, the file specified by NAME is opened at UNIT
channel for accessing by the following EMAP TRAJ command.
When WRITe is specified, the translation vector, rotation matrix,
current energy (?EMENG), minimum energy (?EMENGM), and conformational
number (?EMNST), and rigid domain index (?EMNSR) will be written to the
UNIT channel. These information will be read into the rigid domain if
READ is specified and can be shown in CHARMM output by the varable name shown
in above parenthese.
CLOSe is used to close the UNIT channel.
------------------------------------------------------------------------------
21) The ADD command
The ADD command will add the first map object to the map object
specified after "TO". The first map object will not change. The second map
object will change only its distribution properties, but not its grid and
boundary properties.
------------------------------------------------------------------------------
22) the COPY command
The COPY command will COPY an existing object to another existingone.
Only the distribution properties of a map or the position and orientation of
a rigid domain will be copied.
------------------------------------------------------------------------------
23) The DELEte command
The DELEte command will delelte the specified map object or rigid
domain. They can only be deleted in a last in-first out mode by DELEte command.
If the last map object is deleted, all rigid domains representing the map
object should be deleted first before the map object can be deleted.
------------------------------------------------------------------------------
24) the DUPLicate command
The DUPLicate command will create an identical map or rigid domain of
an existing object .
------------------------------------------------------------------------------
25) The PSF command
The PSF command will create a segment "EM[nseg]" with atoms "C[0-9]"
at grid points. The number [0-9] following C represent the density level at
the grid point. SKIP specifies the grid points to be skipped for every
representing atom. This command is only for the purpose of viewing the map
distribution with a molecular viewer. The segment can be written out in PDB
or CHARMM format for displaying.
------------------------------------------------------------------------------
26) The QUERy command
For map objects, the QUERy command will print out
starting grid numbers (?EMMX,?EMMY,?EMMZ),
grid numbers (?EMLX,?EMLY,?EMLZ),
grid intervals (?EMDX,?EMDY,?EMDZ),
map centers (?EMCX,?EMCY,?EMCZ),
Maximum density(?EMMM),
minimum density (?EMMN),
number of core grids (?EMNC)
For rigid domains, the QUERy command will print out
translation vector (?EMTX,?EMTY,?EMTZ),
rotation matrix (?EMXX,?EMXY,?EMXZ,
?EMYX,?EMYY,?EMYZ,
?EMZX,?EMZY,?EMZZ)
------------------------------------------------------------------------------
27) The SUBStract command
The SUBStract command will substruct the first map object from the map
object specified after "FROM". The first map object will not change. The
second map object will change only its distribution properties, but not its
grid and boundary properties.
------------------------------------------------------------------------------
28) The SUM command
The SUM command creates a map object by summing all rigid fragments
defined by the COMPlex command.
------------------------------------------------------------------------------
29) The CORR command
The CORRelation command will compute the correlation between the two
objects, which can be either map objects or rigid domains or mixed. Option
CORE asks for core-weighted correlations, and DDR asks for Laplacian
correlations. If both options are specified, the core-weighted Laplacian
correlation will be calculated. With the CORE option, the parameters for
core-weighting, ACORE, BCORE, and CCORE can be specified. The correlation
result can be queried by ?EMCT
------------------------------------------------------------------------------
30) The INTEraction command
The INTEraction command will calculate the interaction energy between
two rigid domains and/or map objects. These rigid domains or map objects must
represent molecular map objects. The interaction energies (?EMENG) consist of
VDW core interaction (?EMCORE), electrostatic interaction (?EMELE),
desolvation energy (?EMSOLV), and contact energy (?EMCONS). ?EMENGM stores
the minimum energy over the history of INTEraction commands.
------------------------------------------------------------------------------
31) The DOCK command
The DOCK command will fit the rigid domains defined by COMPlex command
or defined in DOCK command line to a map object or to each other. For single
body docking, the grid-threading Monte Carlo ( GTMC) is used. If chose MANY
option, many-body searching is performed. FMAP will initiate energy-based
searching. When FMAP is specified, the grid will be done over protein surface
except SPACe is specified for GTMC. TRAJ can be used to define the writing
of rigid domain trajectory. A trajectory file must be opened with EMAP TRAJ
OPEN command.
------------------------------------------------------------------------------
32) The TRAJectory command
The TRAJ command manipulates the trajectory file of a rigid domain.
When OPEN is specified, a file is opened for a channel, while CLOSe will close
this channel defined by UNIT. READ or WRITe will read in or write our the
translation vector and rotational matrix of given rigid domain.
------------------------------------------------------------------------------
33) The shortcut READ command
This command provides convenient way to transform a system in PDB file
format into new CHARMM segments with given coordinates. When read in segments
from a PDB file, one can specify BUILd to generate all atom connectivities and
atom types. If there are missing atoms in the PDB file, one can specify SETUp
to generate an internal coordinate table of the segments to be used to
generate the coordiantes of those missing atoms. Each chain in the PDB file
will form a new segment named as the given SEGId followed by its segment
number. These generated segments are well quialified CHARMM segments and
can be used for atom based simulation. This is a very convenient way to
generate simulation systems from PDB files. However, It requires that all
residue and atom names in the input file are consistent with that in the
CHARMM RTF file.
For example:
open read unit 10 card name 1b5s.pdb
read segid b5s PDB build setup unit 10
This command can also be used to create a new segment from either a
PDB file (PDB), a CHARMM coordinate file (CARD), or a free format coordinate
file (FREE). BUILd and SETUp option should not be specified. Please be aware
of that this segment does not have any atom connectivity information and
cannot be used for atom-based molecular simulation. Instead, this segment
can be used to generate a map object needed in the EMAP module.
With this command, a map object can be quickly converted from a PDB structure.
(See examples in this document)
__________________________________________________
MAP object Manipulation Values
There are some variables that can be used in titles or
CHARMM commands that are set by some of the EMAP manipulation commands.
Here is a summary and description of each variable.
'EMCT'
The correlation value calculated by the CORRelation command.
Examples to use EMAP module
1. Read in map file and creat a map object
EMAP READ map NAME "a7n.ccp4"
2.Read in PDB files and creat segments
OPEN READ UNIT 16 CARD NAME a7na.pdb
READ SEGId a7na UNIT 16
OPEN READ UNIT 17 CARD NAME a7nb.pdb
READ SEGId a7nb UNIT 16
3. Generate map objects from structures
EMAP GENErate mapa SELEct SEGId a7na END
EMAP GENErate mapb SELEct SEGId a7nb END
4. Assign rigid domains for fitting
EMAP ASSIgn mapa AS riga SELE SEGId a7na END
EMAP ASSIgn mapb AS rigb SELE SEGId a7nb END
5. Perform GTMC fitting with default parameters
EMAP DOCK GTMC MAPId map RIGId riga RIGId rigb
6. Perform GTMC fitting with defined parameters
EMAP DOCK GTMC MAPId map RIGId riga RIGId rigb ntran 3 nrot 3 -
ncyc 50 nstep 100 tran 15 rota 30 CORE DDR
7. Perform GTMC fitting with many-body search approach
EMAP DOCK GTMC MAPId map RIGId riga RIGId rigb many ntran 2 nrot 2 -
ncyc 50 nstep 100 tran 15 rota 30 DDR
8. Project rigid domain to obtain fitted coordinates
EMAP PROJ RIGA SELE SEGI A7NA END
EMAP PROJ RIGB SELE SEGI A7NB END
9. Compare the fitting of each rigid domain
EMAP CORR MAPID MAP RIGID RIGA DDR CORE
EMAP CORR MAPID MAP RIGID RIGB DDR CORE
10. Generate the result map: mapn
EMAP DUPLicate MAPID map TO mapn
EMAP INITial mapn
EMAP ADD riga TO mapn
EMAP ADD rigb TO mapn
EMAP SUM mapn
11. Read in a PDB file and create segments with given coordinates
and build missing coordinates
OPEN READ UNIT 10 CARD NAME 1B5S.PDB
READ SEGID B5S PDB BUILD SETUP UNIT 10
IC PARA
IC BUILD
12. Dock a protein represented by rigid domain pep2 into a protein represented
by a molecular map pep1 based on map interactions
EMAP DOCK FMAP GTMC MAPI PEP1 RIGI PEP2 -
NTRA 3 NROT 3 NCYC 10 NSTEP 1000 TEMP 300
NIH/DCRT/Laboratory for Structural Biology
FDA/CBER/OVRR Biophysics Laboratory
Modified, updated and generalized by C.L. Brooks, III
The Scripps Research Institute