# AlignGrid¶

## Overview¶

The AlignGrid utility aligns proteins with electron-density maps on a single reference.

## Example Commands¶

> aligngrid -grid input.ccp4 -query protein1.pdb \
-target protein2.pdb -out output.ccp4


Take the input grid in ccp4 format and protein. Align protein1 to protein2 and rotate and translate the input grid using the same alignment outputting the result to output.ccp4.

## Command Line Help¶

A description of the command line interface can be obtained by executing AlignGrid with the --help option.

> aligngrid --help


will generate the following output:

Help functions:
aligngrid --help simple      : Get a list of simple parameters
aligngrid --help all         : Get a complete list of parameters
aligngrid --help <parameter> : Get detailed help on a parameter
aligngrid --help html        : Create an html help file for this program


## Required Parameters¶

-grid

Input density grid. This is the grid that is to be rotated and translated into the new reference frame.

-out

The output grid in any writable format. These include .ccp4, .map and .grd

-protein

The query protein that corresponds to the input grid.

-target

The target protein that the grid and query protein will be aligned toward.

## Optional Parameters¶

-outprot

An optional file to output the query protein after it is translated and rotated into the new reference frame.

When writing out a .grd file, this indicates the added extents (in Ångströms around the protein when outputting the density.

-scale

The final map spacing in Ångströms. (The default is the minimum spacing in X, Y or Z)

-verbose

Triggers copious logging output.

-autoMTZ

Automatically try to open the mtz file using the DELWT and FDELWT columns from REFMAC5 mtz files.

[default=true]

-Fc <columnname>

Column to use for Fc. Note, to load arbitrary columns, you can use the *-Fc** and -Phic columns and the Fc maptype.*

[default=FC]

-Fdelwt <columnname>

Column to use for Fdelwt or difference map amplitudes

[default=F]

-Fobs <columnname>

Column to use for FObs.

[default=F]

-Fwt <columnname>

Column to use for Fwt or regular map amplitudes.

[default=FWT]

-Phic <columnname>

Column to use for Phic.

[default=PHIC]

-Phidelwt <columnname>

Column to use for Phdelwt or difference map phases.

-Phiwt <columnname>

Column to use for Phwt or regular map phases.

-mtype
The map type to use for fitting. Fo-Fc, Fc, 2Fo-Fc, 3Fo-Fc, Fwt,
Fdelwt...

[default=2Fo-Fc]