This menu is called PIRPSQ in honor of one of the few institutions that
still makes their programs available for a minimal (or zero) fee. Part
of their products is re-distributed with permission with WHAT IF.
PIR and PSQ are trademarks I think. See the acknowledgements at the end
of this writeup.
WHAT IF is not a dedicate sequence manipulation package. If your main interest
is sequence work, I strongly recommend that you look into GCG. However, a
limited set of sequence alignment and sequence analysis options is
available in WHAT IF.
The PIRPSQ menu in WHAT IF only accepts sequences in PIR format. If you do not
know which
format that is, you can use the SOUPIR option to create a sequence file
as an example.
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* *
* This menu is about to become obsolete. Most of its *
* functions are performed by the WALIGN menu already. *
* *
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The command GETPIR will cause WHAT IF to prompt you for the name of a PIR
format sequence file. If the file is acceptable to WHAT IF, it will read
this sequence.
The command DIRPIR will cause WHAT IF to show you the number,
the length, and the name of
all presently active PIR sequence files. The numbers are needed to tell
WHAT IF which sequences you want to use. So if WHAT IF asks you for example
something like "Give the first sequence" you should give a number, and not
the name of the sequence.
The command SHOPIR will cause WHAT IF to prompt you for the number of a
sequence file. It will then type this file at the terminal. If the DOLOG option
is used, the file will be written in the log-file too. If you do not know
the number of the pir file you want to see, you can use the DIRPIR command.
The command DELPIR will cause WHAT IF to prompt you for the number of a
sequence. It will then remove this sequence from WHAT IF's memory. Remember
that the actual sequence file will not be deleted from disk, so you can
always get this sequence back in memory with the GETPIR command.
The command INIPIR will cause WHAT IF to initialize all sequence
file related parameters. The files on disk will not be removed.
The command SAVPIR causes WHAT IF to prompt you for a file name. It will
then write all pir menu related parameters, variables and file names in
this file. You can then later get back to the present situation with the
RESPIR command.
The command RESPIR will cause WHAT IF to prompt you for the name of a file
that was written with the SAVPIR (see above) command. It will then
initialize all present pir related parameters, and restore them from this file.
The command BLDPIR will cause WHAT IF to prompt you for a pir file for which
there are coordinates in the soup. You will also be prompted for the
corresponding range in the soup. Then you will be prompted for another,
aligned, pir file. WHAT IF will then automatically build the unknown
structure using the homology with the known structure. You are asked if you want
quick (and dirty) modeling, or that you want to use the better, but
much slower method. It is suggested that you first try to use the quick and dirty
method, and inspect the modelling result to see if the alignment needs
repair. Thereafter you just do everything again with the slow but better
method. This can take
a lot of CPU time (up to 3 hours for a big protein)!!
Be aware that WHAT IF exactly does what you ask it to do. If your alignment
is flunky, then the model building will be flunky!