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<head>
<title>
REP, REPLACE
</title>
</head>
<h1 align=center>
REP, REPLACE
</h1>
<hr size="3">
<font color=#880000>
<b>
NAME
<br>
</b>
</font>
REP, REPLACE - replace selected residues
<br><br>
<font color=#880000>
<b>
SYNOPSIS
<br>
</b>
</font>
REP
<br>
REPLACE
<br><br>
<font color=#880000>
<b>
DESCRIPTION
<br>
</b>
</font>
Replace the selected residues, using the sequence from the main sequence
buffer. At present (version 1.6), garlic is capable to replace protein
residues only. Do not use this command to replace nucleic bases or hetero
residues. After the replacement, the structure will need some refinement.
<br><br>
A residue is treated as selected if the first atom which belongs to this
residue is selected. For proteins, this is typically N (nitrogen).
<br><br>
The main sequence buffer has to be initialized before issuing the command
REPLACE. The number of residues in the main sequence buffer should be
equal to the number of selected residues.
<br><br>
<font color=#880000>
<b>
SINGLE RESIDUE REPLACEMENT
<br>
</b>
</font>
To replace a single residue, use the following commands:
<br>
select residue_sequence_number
<br>
sequence = new_residue_name
<br>
replace
<br><br>
Example:
<br>
sel 29
<br>
seq = ser
<br>
rep
<br><br>
<font color=#880000>
<b>
REPLACING THE ENTIRE SEQUENCE
<br>
</b>
</font>
The command REPLACE may be used to prepare the model of some protein using
the experimentally solved structure of the related protein. To replace the
entire protein sequence follow these general instructions:
<br>
(1) Prepare the file with the sequence of the unsolved protein
(use FASTA format).
<br>
(2) Find the related, experimentally solved protein structure.
<br>
(3) Fix insertions and deletions in the sequence of the unsolved protein.
<br>
(4) Start garlic and load the known structure.
<br>
(5) Exclude hetero residues from selection (first SEL HET, than SEL COM).
<br>
(6) If there is more than one chain restrict selection (RES chain_id/*/*/*).
<br>
(7) Load the new sequence (use the command SEQ LOAD).
<br>
(8) Replace the old sequence.
<br><br>
Don't forget that the number of selected residues should match the number
of residues in the sequence of the unsolved protein.
<br><br>
<font color=#880000>
<b>
TEMPLATE RESIDUES
<br>
</b>
</font>
The selected residues will be replaced with the residues from the template
file. Default template file contains 20 standard residues. This file should
be named residues.pdb and stored to at least one of the following
directories (listed in the search order):
<br>
(1) The current working directory.
<br>
(2) $HOME (user's home directory).
<br>
(3) $HOME/garlic (garlic subdirectory of the user's home directory).
<br>
(4) /usr/share/garlic (location for the system-wide file).
<br>
(5) /usr/local/lib/garlic (alternative location for the system-wide file).
<br>
(6) /usr/lib/garlic (another alternative location for the system-wide file).
<br><br>
If you want to add some extra residues (like modified amino-acids) to the
template file, make your own copy of the file residues.pdb and keep it either
in $HOME/garlic subdirectory or in your favorite working directory. It is
very easy to add residues to the template file: just copy and paste the
chosen exotic residue from the PDB file where you have it to the end of
garlic template file. Be sure to include hydrogen atoms! There is one more
thing: be sure that your residue does not have the same residue serial number
as the preceding residue. You don't have to worry about the position and
the orientation of your residue.
<br><br>
If you don't have the file residues.pdb,
<a href="residues.html">
click here
</a>
for html version. It is very easy to convert this version to the plain PDB,
just save it as the plain text.
<br><br>
<font color=#880000>
<b>
NOTES
<br>
</b>
</font>
(1) The command REPLACE resets the editing mode to default (no editing).
<br><br>
<font color=#880000>
<b>
RELATED COMMANDS
<br>
</b>
</font>
Use the command SELECT to define the residues which should be replaced and
SEQUENCE to define the residues which will be used as replacement.
BONDS REFRESH may be used to fix bad bonds, which may sometimes be generated
after executing the command REPLACE.
<br><br>
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