If you are interested in SELECTing residues before executing an option, look
at the command CHOOSE.
If your only interest is searching in the structure database, you dont need
WHAT IF. The program SRS (URL=http://www.embl-heidelberg.de/srs/srsc) uses
the same PDBFINDER as WHAT IF. SRS searches faster and more flexible than WHAT IF.
However, if you want to select files as a pre-filter for the WHAT IF relational
structure-sequence database SCAN3D, you should use this SELECT menu.
The selection is made in a relational way. This means that one can say things
like: "I want to use all proteases with resolution better than 2.5 Angstrom,
and R-factor less than 20.0", or things like that.
This relationallity is just like in the SEARCH menu, and in the SCAN3D menu
obtained by creating arrays of logicals or pointers. In the SELECT menu these
arrays are called columns. The above mentioned selection could be made in
five steps:
Step 1) Use the SELTXT command to select all proteases. Make this column 1.
Step 2) Use the SELNMB command to select proteins solved with a resolution
better than 2.5 Angstrom. Make this column 2.
Step 3) Use the SELNMB command to select all proteins for which the R-factor
from the crystallographic refinement is better than 20.0. Make this column 3.
Step 4) Use the command SELAND to do a logical AND on the columns 1 and 2.
Make this column 4.
Step 5) Do another AND on the columns 3 and 4 to get the final answer. Make
this column 5.
After that you can use several commands to look at the results. E.g. SELSHO
or SELHIT. You can
use the SELUSE command to make the result permanent, i.e. force SCAN3D to only
look in those proteins that are tagged true in a certain column in
the SELECT MENU.
The data used by WHAT IF in the SELECT menu is all stored in the file
PDBFIND.TXT. You find this file in the dbdata directory.
We update this file continuously, so a real entry is likely to
contain more information than the example listed below.
A typical entry in this
file roughly looks like:
ID : 1CRN
Header : PLANT SEED PROTEIN
Date : 1981-04-30
Compound : Crambin
Source : Abyssinian Cabbage (Crambe Abyssinica) Seed
Author : W.A.Hendrickson
Author : M.M.Teeter
Exp-Method : X
Resolution : 1.50
R-Factor : 0.11
HSSP-N-Align : 8
T-Frac-Helix : 0.48
T-Frac-Beta : 0.09
T-Nres-Prot : 46
Chain : _
Sec-Struc : 46
Helix : 22
i,i+3 : 3
Beta : 4
Anti-Hb : 4
Amino-Acids : 46
CYSS : 6
Sequence : TTCCPSIVARSNFNVCRLPGTPEAICATYTGCIIIPGATCPGDYAN
But dont count on this too much because more fields will be added in the future.
Examples of planned extensions are: Quality of the entry; Symmetry information
(SCALE and CRYST info, but corrected); pointers to other databases, etc.
Several options exist to search in the database. You can search for numerical
values, texts strings, sequence patterns, etc.
Many entries in PDBFIND.TXT hold numerical information (R-factor, Resolution,
Number of amino acids, etc.). The SELNMB command will allow you to
select the keyword of a numerical value, and a range for this value. All
entries that have the requested value in the requested range will be set
to true in the corresponding column. You will be prompted for the column
number and the column name.
The commands SELAND and SELOR can be used to combine selected columns. Other
combination possibilities can be added on request.
Many entries in PDBFIND.TXT hold textual information (Authors, Experimental
method, coumpound, source, het atom groups). The SELTXT command will allow you
to select the keyword of a text value, and a range for this value. All
entries that have the requested text as a subtext in the line that
starts with the requested keyword will be set
to true in the corresponding column. You will be prompted for the column
number and the column name.
The commands SELAND and SELOR can be used to combine selected columns. Other
combination possibilities can be added on request.
The command SELAND will cause WHAT IF to prompt you for two input columns and
one output column (which may be the same as one of the input columns). It
will then do a logical AND on the two input columns, and store the result in
the output column.
The command SELOR will cause WHAT IF to prompt you for two input columns and
one output column (which may be the same as one of the input columns). It
will then do a logical OR on the two input columns, and store the result in
the output column.
The command SELINV will cause WHAT IF to prompt you for one input and one output
column. The output column may be the same as the input column. It will then
copy the input column to the output column, and toggle all TRUEs to
FALSEs and vice versa in this output column.
The command SELSHO will cause WHAT IF to show you the number of hits in every
created column. It will also show for each column how it was created.
The command SELHIT will cause WHAT IF to prompt you for a column number. It
will then show part of the information from the entries in PDBFIND.TXT that
have a TRUE in the given column. See also SELLST for a similar option
that gives less output.
The command SELLST will cause WHAT IF to prompt you for a column number. It
will then show a small part of the information from the entries in PDBFIND.TXT
that have a TRUE in the given column. See also SELHIT for a similar option
that gives more output.
Several other commands exist:
The command SELINI will cause WHAT IF to initialize all parameters and
variables that are related to the SELECT menu operations. This initialization
is irreversible.
The command SELUSE will cause WHAT IF to prompt you for a column.
It will mark all entries in the SCAN3D database active that are true in this
column. That means that future searches with SCAN3D will no longer look
in the whole database, but in the subset of the SCAN3D database that was
selected with thgis option. Use column 0 (zero) if you want to (re-)activate
all SCAN3D entries (so, issue the SELUSE 0 command).