The MAP Object Manipulation Commands--The EMAP module
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 high efficient for large system modeling. It
is also the necessary approach to derive structure information from electon
microscopy experiment.
* 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]
EMAP
{ PARAmeters [RESO real] [RCUT real] -
[DX real] [DY real] [DZ real] [ICORE int] }
{ READ mapid NAME filename }
{ WRITe mapid NAME filename [DDR|CORE] }
{ GENErate mapid [atom-selection] [COMParison-set] [RESO real] -
[DX real DY real DZ real] [AS mapid] }
{ ASSIgn mapid AS rigid [atom-selection] }
{ DUPLicate [MAPId mapid|RIDId rigid] TO [mapid|rigid] }
{ COPY [MAPId mapid|RIDId rigid] TO [mapid|rigid] }
{ REFErence mapid atom-selection }
{ DDR mapid }
{ CORE mapid [CUT real] [DENSity|DDR] }
{ INITialize emapid [BASE real] }
{ STATistics emapid }
{ RESIze mapid AS mapid [GRID-only] [BOUNdary-only] }
{ ADD rigid TO mapid }
{ SUBStract rigid FROM mapid }
{ REDUct mapid BY mapid [TO mapid] }
{ SCALe mapid BY real }
{ SAVE rigid }
{ RESTore rigid }
{ TRANslate rigid XDIR real YDIR real ZDIR real [DIST real] }
{ ROTAte rigid XDIR real YDIR real ZDIR real PHI real }
{ PSF [MAPId mapid|RIGId rigid] [SKIP int] [RCUT real] }
{ PROJect rigid [ atom-selection ] }
{ DELEte [MAPId mapid|RIGId rigid]}
{ CORR [MAPId mapid|RIGId rigid] [MAPId mapid|RIGId rigid] [CORE] [DDR] }
{ COMPlex RIGId rigid [RIGId mapid ...] [APPEnd] [FIX]}
{ SUM mapid }
{ DOCK MAPId mapid [GTMC] [MANY]
grid-properties MC-parameters Correlation-type Fitting-criteria}
grid-properties::= NTRAnslation int NROTation int
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]
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A shortcut READ command is implmented to simplify the process of creating
molecular segments from coordinate files or PDB (default) files.
READ SEGId segid UNIT int [CARD]
This command will creat a new segment named: "segid" by reading from unit "int".
A PDB file should be opened for the unit. If CARD is specified, the file
should be CHARMM coordinate file. A segment is created with the atoms read in
from the file without force field parameter check. This segment can only be
used for EMAP and COOR manipulations.(See examples in this document)
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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.
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1) 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.
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2) 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.
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3) 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. They can also be input or taken from other map objects. The
generated map object takes the atom set as its reference atom set.
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4) the DUPLicate command
The DUPLicate command will create an identical map or rigid domain of
an existing object .
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4) 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.
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5) 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.
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6) 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.
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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.
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7) The STATistics command
The STATistics command calculate and print the statistic properties
of the distribution properties of the map.
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8) 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.
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9) 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.
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10) 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.
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11) The REDUct command
The REDUct 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.
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12) The SCALE command
The SCALe command will scale the distribution properties of the
map object by the real number spedified after "BY".
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13) The ASSIgn command
The ASSIgn command will create a rigid domain representing the map
object. If no atom-selection is given, 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.
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14) The SAVE command
The SAVE command will copy the position and orientation of the rigid
domain to its storage.
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15) The RESTore command
The RESTore command will copy the stored position and orientation to
the rigid domain.
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16) 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.
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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.
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18) 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.
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18) 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.
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19) 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.
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20) 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.
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21) 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.
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22) The DOCK command
The DOCK command will fit the rigid domains defined by COMPlex command
to a map object. Corrently the grid-threading Monte Carlo ( GTMC) is
implemented. if chose MANY option, many-body searching is performed.
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. Compare the two maps
EMAP CORR MAPId map MAPId mapn
NIH/DCRT/Laboratory for Structural Biology
FDA/CBER/OVRR Biophysics Laboratory
Modified, updated and generalized by C.L. Brooks, III
The Scripps Research Institute