CHARMM c30b1 emap.doc



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            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



File: emap ]-[ Node: Syntax
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                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]
 
________________________________________________
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)
__________________________________________________
__________________________________________________



File: emap ]-[ Node: Description
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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.

------------------------------------------------------------------------------
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.

------------------------------------------------------------------------------
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.

------------------------------------------------------------------------------
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.

------------------------------------------------------------------------------
4)  the DUPLicate command

        The DUPLicate command will create an identical map or rigid domain of
an existing object .  

------------------------------------------------------------------------------
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.

------------------------------------------------------------------------------
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.

------------------------------------------------------------------------------
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.

------------------------------------------------------------------------------
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.

------------------------------------------------------------------------------
7)  The STATistics command

        The STATistics command calculate and print the statistic  properties 
of the distribution properties of the map.

------------------------------------------------------------------------------
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.

------------------------------------------------------------------------------
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.

------------------------------------------------------------------------------
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.

------------------------------------------------------------------------------
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.

------------------------------------------------------------------------------
12) The SCALE command

        The SCALe command will scale the  distribution properties of the
map object by the real number spedified after "BY". 

------------------------------------------------------------------------------
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.

------------------------------------------------------------------------------
14) The SAVE command

        The SAVE command will copy the position and orientation of the rigid
domain to its storage.

------------------------------------------------------------------------------
15) The RESTore command

        The RESTore command will copy the stored position and orientation to
the rigid domain.

------------------------------------------------------------------------------
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.

------------------------------------------------------------------------------
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 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.

------------------------------------------------------------------------------
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.

------------------------------------------------------------------------------
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. 

------------------------------------------------------------------------------
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.

------------------------------------------------------------------------------
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.


------------------------------------------------------------------------------
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.



File: Emap ]-[ Node: Substitution
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                      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.




File: Emap ]-[ Node: Examples
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                        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

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FDA/CBER/OVRR Biophysics Laboratory
Modified, updated and generalized by C.L. Brooks, III
The Scripps Research Institute