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<head>
<title>
GRO, GROUP
</title>
</head>
<h1 align=center>
GRO, GROUP
</h1>
<hr size="3">
<font color=#880000>
<b>
NAME
<br>
</b>
</font>
GRO, GROUP - group structures: catch more than one structure.
<br><br>
<font color=#880000>
<b>
SYNOPSIS
<br>
</b>
</font>
GRO identifier1 identifier2 ... identifierN
<br>
GRO ALL
<br>
GRO SAV filename
<br>
GRO SSC filename
<br>
GROUP identifier1 identifier2 ... identifierN
<br>
GROUP ALL
<br>
GROUP SAVE filename
<br>
GROUP SSC filename
<br><br>
<font color=#880000>
<b>
DESCRIPTION
<br>
</b>
</font>
The command GROUP may be used to catch more than one structure. It is possible
to group only one structure, but this doesn't make much sense. A typical usage
will be to unite some inhibitor with a substrate.
<br><br>
The structures which form the group will be rotated about the common rotation
axis and translated as a single object, except it the keyword ALL is used. In
that case, each structure will retain its own rotation center (the old one).
<br><br>
Slab and color fading will be changed simultaneously for all structures.
It is recommended to adjust slab and color fading before forming the group.
Use much wider slab than usual!
<br><br>
Many other commands will be applied simultaneously for all structures
(color, BACKBONE etc.). The exceptions are
<a href="sav.html">
SAVE
</a>
,
<a href="edi.html">
EDIT
</a>
and
<a href="rep.html">
REPLACE
</a>
, which
use only default structure (the one which was caught last or loaded as
the last structure).
<br><br>
To break the group of structures, i.e. to cancel the command GROUP, execute
the command
<a href="cat.html">
CATCH
</a>
with a single identifier as a command parameter, to catch only one structure.
The command
<a href="dis.html">
DISCARD
</a>
may also be used to break the group of structures. Two other commands which
cancel GROUP are
<a href="cre.html">
CREATE
</a>
and
<a href="loa.html">
LOAD
</a>
.
<br><br>
<font color=#880000>
<b>
GROUP ALL
<br>
</b>
</font>
The keyword ALL may be used to group all structures into a single object.
Each structure will retain its old rotation center.
To break the group, use the command
<a href="cat.html">
CATCH
</a>
to catch only one structure.
<br><br>
<font color=#880000>
<b>
GROUP SAVE filename
<br>
</b>
</font>
The keyword SAVE may be used to save the entire group as a single file.
Each structure will be stored as a separate chain. If any of the structures
contained more than one chain, it will be stored as a single chain. The first
structure will be stored as the chain A, the second as the chain B etc.
If there are more than 26 structures, some chain identifiers may be used more
than once. The original chain identifiers will be lost. The original atomic
serial numbers and residue serial numbers will be replaced by new serials.
These changes will affect only data stored to the output file. After breaking
the group, each structure will remain intact. The file name is case sensitive.
<br><br>
<font color=#880000>
<b>
GROUP SSC filename
<br>
</b>
</font>
The keyword SSC may be used to save the entire group into a single file.
All structures will be stored as a single chain. The original chain
identifiers will be lost. The original atomic serial numbers and residue
serial numbers will be replaced by new serials. These changes will affect
only data stored to the output file. After breaking the group, each structure
will remain intact. The file name is case sensitive.
<br><br>
<font color=#880000>
<b>
EXAMPLES
<br>
</b>
</font>
<table border=2 cellspacing=2 cellpading=0>
<td align="left">
COMMAND
</td>
<td align="left">
DESCRIPTION
</td>
<tr>
<td align="left">
gro 1 2 4
</td>
<td align="left">
Group structures 1, 2 and 4. Define a single rotation center
<br>
for all structures.
</td>
<tr>
<td align="left">
gro all
</td>
<td align="left">
Group all structures. Each structure will retain its old
<br>
rotation center.
</td>
<tr>
<td align="left">
group 1 3
<br>
group save united.pdb
</td>
<td align="left">
Group structures 1 and 3 and store as a single structure
<br>
consisting of two chains to the output file united.pdb .
</td>
<tr>
<td align="left">
gro 2 5
<br>
gro ssc xyz.pdb
</td>
<td align="left">
Group structures 2 and 5 and store as a single chain
<br>
to the output file called xyz.pdb .
</td>
</table>
<br>
<font color=#880000>
<b>
RELATED COMMANDS
<br>
</b>
</font>
CATCH is used to catch only one structure. The command CATCH breaks the group
formed by the command GROUP.
<br><br>
<hr size="3">
</html>
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