WHAT IF needs coordinates. Without coordinates the program is still a nice
database handler, and it can tell you what time it is, but without good
coordinates there is not much need for using WHAT IF.
WHAT IF can read and write PDB-files (Brookhaven protein data bank
format) and GROMOS files and it can read DIANA files. More formats will
be added upon request.
The central data structure in WHAT IF is the so-called 'soup'. The
soup is an assembly of water with
all molecules in it. WHAT IF knows six kinds of molecules:
1) protein;
2) drugs (or co-factors or ligands);
3) DNA/RNA;
4) single atomic molecules;
5) (groups of) water molecules.
6) drugs with an entry in the topology file
Because WHAT IF can only work with a finite number of molecules at one
time, water molecules are
taken together as one molecule, consisting of all the water molecules that
came from one source (eg. one input file, or one water position prediction).
The soup thanks it name to the fact that it consists of molecules
floating around in water. (However, there do not necessarily have to be water
molecules present).
The menu that is activated with the SOUP command allows you to manipulate
the soup. The WATER menu performs the addition or deletion of water in case
you want to add or delete them one by one rather than whole
groups of water at a time. Special operations on water
molecules (like automatic addition or deletion) are also performed from
the WATER menu (see chapter WATER).
Rather often this writeup refers to residues as input to an option.
In most cases however,
the input can also be drugs, etc. In such cases there does not always exist
clear documentation about what is allowed as input to the option.
You can use as rule of thumb
that if it is chemically sensible, WHAT IF will allow for it. In any
case, just try it. WHAT IF will not crash in case you try something that
is plain stupid or simply not (yet) not allowed.
Unfortunately the entire 'Who is who' in biomolecular computing,
crystallography, NMR or biophysics has once written the one and only universal
standard for protein coordinates. We therefore need an almost infinite number
of options to read or write coordinate files. Most of these option
have to do with interfacing to specific programs. These options are
described in the chapters that deal with these interfaces.
The command GETMOL is the general way of getting coordinates from a PDB
file into memory.
(With GETGRO you can read GROMOS formatted coordinate files).
GETMOL is a command from the general menu, which means that you can execute
it from every menu. You will be prompted for the name of the PDB file
and thereafter the symmetry matrices, and ALL coordinates are
read from this file and ADDED to the soup. If you want to start with an
empty soup, you should first execute the INISOU command from the soup
menu.
There are many ways to write coordinates to a file. Many options do so
automatically (eg. SHOHST, SPLINE, etc.). The generic command
however is MAKMOL in the SOUP menu. This command writes a PDB file.
Most coordinate related options are present in the soup menu. The commands
GETGRO and GETMOL can be executed from ALL menus.
Whenever WHAT IF adds coordinates to the soup these coordinates need a set
name. This set name is very handy if you want to remember which molecule in
the soup came from which input file. If you are prompted for the set name
and just hit return, the set name will be made identical to the file name.
The command GETMOL will cause WHAT IF to prompt you for a PDB file. It will
then read all coordinates from this file, and add them to the soup.
If the file is not found in your local directory,
but it exists in the central PDB directory on your machine,
you will be asked if you want to use this PDB file instead. Make your local
WHAT IF manager aware of the the notes
on the configuration files if WHAT IF can not find the standard PDB directory.
(The standard PDB directory must be put in the CCONFI.FIG file).
If the file is also not there, WHAT IF will try to get it from my machine,
swift.embl-heidelberg.de.
If you are working at a company, and you are not allowed to use the internet for
such frivolous things as downloading PDB files, you should delete the
script 'getpdbfile' from the dbdata directory.
The command GETGRO will cause WHAT IF to prompt you for a formatted
GROMOS coordinate file. It will
then read all coordinates from this file, and add them to the soup.
The command GETDSP will cause WHAT IF to prompt you for a
DSSP file. It will
then read all C-alpha coordinates from this file, and add them to
the soup. See the chapter on DSSP for details.
The command MAKMOL is the only correct way to write PDB files. You will be
prompted for a template coordinate file. The header of this template
file will be copied to the output PDB-file. Thereafter you will be prompted
for the name of the PDB-file to be created. Last you will be prompted for
the residue ranges.
The command MAKMLR does the same as MAKMOL, but additionally
prompts you for a ROW number. Only atoms that are tagged (set to TRUE)
in that ROW will be written to the output PDB file.
The command SAVSOU will cause WHAT IF to prompt you for a save-file number.
If will then create a file (numbered as requested) and puts all presently
available data in the soup (molecules, residues, atoms, secondary
structure, accessibilities, etc.) in this file. You can later use RESSOU
to restore the soup from this file.
If you have previously saved the soup in a save-file with the SAVSOU command,
you can use the RESSOU command to restore the soup from that save-file. Be
aware that RESSOU will first destroy ALL data presently in the soup.
The command SAVSTA will cause WHAT IF to prompt you for a save-file number.
If will then create a file (numbered as requested) and puts all presently
available data in the soup (molecules, residues, atoms, secondary
structure, accessibilities, etc.) in this file. So far all is similar
as for SAVSOU, but SAVSTA additionally tries to save the interactive
status (scale, translation, view etc., MOL-items, labels, objects on/off etc.).
You can later use RESSTA to restore the status from this file.
If you have previously saved the status in a save-file with the SAVSTA command,
you can use the RESSTA command to restore the status from that save-file. Be
aware that RESSTA will first destroy ALL data presently in the soup.
To make WHAT IF understand protons, copy the file TOPOLOGY.H from the
dbdata area in the WHAT IF account to your local area, and call it
TOPOLOGY.FIL.
See the command ADDHYD in the REFINE menu for `dreaming-up` proton
coordinates.
The command SOUP brings you in the menu from which you can manipulate the
soup. At present soup consists of water with molecules in it. These molecules
can be protein, DNA/RNA, single atomic ligands such as ions, or drug.
Everything not recognized
by WHAT IF will be called drug. So, co-factors like FAD, or complex solvent
molecules like MPD will be called drugs. Ions like Cu2+ Ca2+ etc. will be
called non-water solvent molecules or single atomic entities.
The commands in the soup menu can be logically grouped as follows:
1) look at the soup;
2) cut or paste proteins;
3) delete or insert molecules or residues;
4) save or restore amino acids;
5) cys-cys bridge related options.
6) other options.
In the SOUP menu you will find the command MORE. This command can be used to
increase the number of options in the SOUP menu. Normally only the most used
commands in this menu are visible, but MORE will also make the less frequently
used options visible in the menu. LESS deactivates the options that you activated
with MORE.
The command SHOSOU will cause WHAT IF to show you the contents of the soup. The
number of molecules will be shown, as well as their names. The molecules will
be divided in the following classes: -1 = undefined; 0 = indicative of a
program bug; 1 = protein; 2 = drug; 3 = DNA/RNA; 4 = solvent, non-water;
5 = water.
The ranges of residues spanned by molecules and the total content per molecule
class are also shown.
A typical results from the SHOSOU command looks like:
Contents of the SOUP: *1
Protein .................... : 2 *2
Drug, ligand or co-factor .. : 1
DNA or RNA ................. : 0
Single atom entity ......... : 7
(Groups of) water .......... : 1
Drug with known topology ... : 0
Molecule Range Type Set name *3
1 1 ( 1) 316 ( 316)E Protein tnl *4
2 317 ( 322) 318 ( 323)D Protein tnl *4
3 319 ( O2 ) 319 ( O2 )E K O2 <- tnl *5
4 320 ( 317) 320 ( 317) CA tnl *6
5 321 ( 318) 321 ( 318) CA tnl
6 322 ( 319) 322 ( 319) CA tnl
7 323 ( 320) 323 ( 320) CA tnl
8 324 ( 321) 324 ( 321) ZN tnl
9 325 ( 324) 325 ( 324) DMS tnl *7
10 326 ( O2 ) 326 ( O2 )D L O2 <- tnl *8
11 327 ( HOH ) 327 ( HOH ) water ( 157) tnl *9
1) This is the header of the SHOSOU output
2) First the contents of the soup is counted
3) This is the header of the real thing of the SHOSOU command.
The set name (that is the name the user gave to the ensemble of molecules
added to the soup with one single GETMOL or GETGRO, etc., command.
4) Molecule one is a protein with chain identifier E. This protein has 316
amino acids. The second protein is a two residue peptide with chain identifier D.
5) The third molecule is the C-terminal oxygen of chain E. It is attached
to a Lysine (that is indicated by the character K) and the arrow indicates
that it is bound to something.
6) Molecules 5 till 8 are single atomic entities (together with the two
C-terminal oxygens they form the seven single atomic entities mentioned
in the top half of the output.
7) DMS probably stands for DMSO, and is a drug, ligand or co-factor. For
WHAT IF drug, ligand, and co-factor are all the same thing.
8) This is the C-terminal oxygen of the second molecule. You can see that
because the O2 indicates that it is a C-terminal oxygen. The D indicates that
it is part of the D chain and the arrow indicates that it is bound to
something. The L indicates that it is bound to a Leucine.
9) This is a group of 157 water molecules.
The general command LISTR causes WHAT IF to show you the entire amino
acid sequence. Depending on
the parameters (see the chapter on parameters) you get the sequence in one-
or three- letter code, optionally the amino acid frequency distribution and
the amino acid neighbor matrix are shown for proteins.
(See the chapter on parameter
setting for that, the default is showing only the sequence).
A typical LISTR output looks like:
Molecule number 1
1- 10 ILE THR GLY THR SER THR VAL GLY VAL GLY
11- 20 ARG GLY VAL LEU GLY ASP GLN LYS ASN ILE
........
311- 316 ASP ALA VAL GLY VAL LYS
Molecule number 2
317- 318 VAL LYS
Molecule number 3
........
Molecule number 10
Molecule number 11
Only for molecules that consist of residues (i.e. protein and nucleic acids)
will the sequence be listed. Only the presence of all other molecules is
indicated by simply counting them.
The general command LISTRR will, when given,
prompt you for a residue range, and show for that range the internal
residue number, the residue type, and the original name/number as read from
the Brookhaven file.
LISTRR output typically looks like:
Res. # : 1 ILE ( 3 ) E Set-name : tnl
Res. # : 2 THR ( 4 ) E Set-name : tnl
Res. # : 3 GLY ( 5 ) E Set-name : tnl
Res. # : 4 THR ( 6 ) E S Set-name : tnl
Res. # : 5 SER ( 7 ) E S Set-name : tnl
Res. # : 6 THR ( 8 ) E S Set-name : tnl
........
*1 *2 *3 *4 *5 *6
1) The sequential residue number (WHAT IF's residue number)
2) The residue type
3) The PDB file residue number. This sequence starts with residue 3, indicating
that the first two residues are invisible in the density map.
4) The chain identifier (in this case E)
5) The secondary structure
6) The set name
The general command LISTA can be used to look at atoms, grouped per
residue. WHAT IF
will prompt you for a residue range, and will then show for every requested
residue both the amino acid information like name, type, etc. and the atomic
information like coordinates, B-factor, Van der Waals radius, color (if
already set), charges (if already calculated) etc. This option also works
on drugs, water, etc.
Remember that you can use control/O (character O) to skip output to the
terminal in case you accidentally asked for too much output.
Typically LISTA output looks per residue like:
Residue: 37 ASP ( 37 ) E (Prp= 0.00)
Atom X Y Z Acc B WT VdW Colr AtOK Val
N 18.2 59.6 -5.1 0.0 16.7 1.0 1.7 340 + 0.00
CA 17.0 58.8 -5.2 1.7 16.0 1.0 1.8 240 + 0.00
C 16.9 57.7 -4.1 1.6 23.4 1.0 1.8 240 + 0.00
O 16.1 56.9 -4.2 2.7 19.6 1.0 1.4 120 + 0.00
CB 16.8 58.2 -6.6 3.5 16.8 1.0 1.8 240 + 0.00
CG 16.6 59.3 -7.6 4.0 43.8 1.0 1.8 240 + 0.00
OD1 16.0 60.4 -7.1 7.6 41.3 1.0 1.4 120 + 0.00
OD2 17.0 59.2 -8.7 6.0 42.4 1.0 1.4 120 + 0.00
*1 *2 *2 *2 *3 *4 *5 *6 *7 *8 *9
The first line gives about the same information as the LISTAA output
for one residue. Prp is the residue property value. Several options
calculate one value for each residue. Often the result is than stored
in this so-called residue property value.
The second line is just a header. Between these first two lines more
information can be given in case this residue is member of a family,
or in case WHAT IF has corrected or mutated this residue.
1) the atom names
2) the coordinates in Angstroms
3) The accessible molecular surface area (only zeros indicates buried
or not calculated yet)
4) The crystallographic B-factor. >60 means this atom is for sure not here....
5) Weight. This is almost always 1.0. If 0.0 the coordinates were modeled.
If between 0.0 and 1.0, alternative conformations have been observed.
6) The Van der Waals radius for this atom. (See the SETVDW menu).
7) The colur for this atom. (See the colour menu).
8) Is-atom-OK flag. Atoms that are wrong according to WHAT IF get a
minus in this column.
9) The atomic value. Several options calculate values for each atom. Often
the result is than stored in this so-called atomic value.
The general command LISTAA functions similar to LISTA, the difference
being that LISTA
prompts you for one range of residues, waters, drugs, etc. LISTAA will prompt
you for multiple ranges (as usual, give 0 (zero) after providing all
ranges of interest). Per residue the output is the same as for LISTA.
Sometimes one wants to find the location of a sequence pattern, e.g.
Arg-Gly-Asp in a very big structure. The general command SHOPAT
can aid with
this. SHOPAT prompts you for three residue types (you can give
multiple types at each position). For every occurence of the pattern
the first position will be listed.
The sidechains of all observed patterns will be displayed.
You always have to give pattersn of length 3. If you want patterns of length
2, use ALL as residue type at position 3 in the pattern. In this case
however, an accidental occurence of your dipeptide pattern at the
C-terminus will remain undetected.
WHAT IF decides whether two residues are covalently bound by looking at the
distance between the alpha carbon coordinates. Sometimes it makes multiple
molecules out of one protein when you don't want that. The cut and paste
commands are available to overrule WHAT IF's ideas about this. Also it
is nice to fool WHAT IF sometimes by telling that all proteins are one big
molecule shortly before you run an option that can only work on one
molecule at a time.
The command PASTE will cause WHAT IF to prompt you for the C-terminal
residue of a molecule. It will then paste this residue and the N-terminal
residue of the next molecule in the soup, thereby making one molecule out
of the two. If you try to paste at a position where you previously placed a
cut-mark (see CUT), first this cut-mark will be removed and thereafter
a PASTE flag will be placed. If due to your pasting a C-terminal oxygen
would be left in the middle of a molecule, you will be asked if you
want to delete this extra oxygen.
The command PASTAL will cause WHAT IF to execute the PASTE command (see above)
automatically for all residues in the soup. PASTAL will first execute the
INIPAS command (see below), so all previously set cut-flags and paste-flags
are removed first. Thereafter all proteins will be pasted and all nucleic
acids will be pasted. Proteins will not be pasted to nucleic acids. If due
to your pasting one or more C-terminal oxygens
would be left in the middle of a molecule, you will be asked if you
want to delete these extra oxygens. Two
molecules that are in the soup separated from each other by a third one can
never become one molecule, no matter how close they are in space, or how
often you try to PASTE them.
The command CUT will cause WHAT IF to prompt you for a residue number. It
will then act like a protease at the C-terminal side of this residue. Thus
if this was not the C-terminal residue of a molecule, the molecule you are
cutting will change into two molecules. If you try to cut at a position
where you previously placed a paste-mark first this paste-mark
will be removed and thereafter a cut mark will be placed. If due to your
cutting a C-terminal oxygen
would be needed in the middle of a molecule, you will be asked if you
want to add this extra oxygen.
The command INIPAS will cause WHAT IF to remove all manually set cut and
paste flags. It will thereafter re-determine what it thinks are independent
molecules and what not. Hereby it uses solely distance criteria. Also two
molecules that are in the soup separated from each other by a third one can
never become one molecule, no matter how close they are in space.
The command SHOPAS can be used to list all presently set cut and paste flags.
If you want to try mutations (see mutating residues) you often might want to
go back to the original situation later. You can of course every time write
in between PDB-files, but there is also the possibility to save and later
restore residues. This is a much faster procedure, and it costs less disk space.
The command SAVAA will cause WHAT IF to prompt you for the number of a residue.
It will then write the residue in a file. You can later restore this residue
with the RESAA command. You can in principle abuse the combination of
this option and the RESAA option wildly....
The command RESAA will cause WHAT IF to prompt you for the number of a residue.
You will also be prompted for the type of residue you want to insert. This must
be the type that was used during the SAVAA operation.
It will then add this residue from its file
into the soup immediately after a residue for which you will be prompted.
If you want to
replace the residue in the soup with the restored residue, you should
delete that residue in the soup, and insert the saved residue after the residue
N-terminal of the one you are replacing. You can either first
restore the previously
saved residue after residue N in the soup, and then delete residue N, or
first delete residue N, and then insert after N-1.
The real WHAT IF hackers can abuse the SAVAA and RESAA options to do rather
complicated modifications of molecules.....
There are many ways to correct, delete, insert, or mutate
amino acids, from many menus
throughout WHAT IF. Direct correction, deletion and insertion
operations can only be performed from the soup menu.
WARNING: many parameters are no longer correct after changes have
been made in the
soup. These parameters involve ROWS, H-BONDS, DGLOOP, accessibilities,
groups, SALT BRIDGES, or more general, all information that depends on
(pointers to) amino acids.
This commands removes all molecules from the soup. Other parameters like
groups, matrices, maps, etc. will remain untouched. The INISOU command
is irreversible!
This command causes WHAT IF to prompt you for the number of the
molecule to be deleted. If you give molecule 0 nothing
will be deleted.
This command causes WHAT IF to perform the SHOSOU command first, and then prompt
you for the numbers of the molecules to be deleted. You can give
multiple ranges of molecules. End the list of molecule ranges with a zero.
If you enter only molecule 0 nothing will be deleted.
The command DELETE will cause WHAT IF to prompt you for a residue number.
That residue will than be deleted from the soup, without any structural
corrections in the environment.
The command CORAA will cause WHAT IF to prompt you for a residue range. All
atoms in this range that are missing will be created by WHAT IF, provided that
at least the backbone N, C-alpha and C are present. You will be asked by
WHAT IF if you also want to correct bad inter atomic distances. If you answer with
YES, WHAT IF will move atoms around till the bad inter atomic distances are
better. However, this option will also displace some atoms that are actually
placed correctly, and that might not be desired.
Don't worry about all
kinds of error messages. These are caused by errors which when elsewhere
in WHAT IF occurring, are fatal, but here don't matter too much.
Be aware that this option only accepts amino acids.
The command CORALL will cause WHAT IF to execute the CORAA option without asking
for the range, because it assumes that all amino acids in the soup should
be corrected (at least those that are wrong). All
atoms in this range that are missing will be created by WHAT IF, provided that
at least the backbone N, C-alpha and C are present. You will be asked by
WHAT IF if you also want to correct bad inter atomic distances. If you answer with
YES, WHAT IF will move atoms around till the bad inter atomic distances are
better. However, this option will also displace some atoms that are actually
placed correctly, and that might not be desired.
Don't worry about all
kinds of error messages. These are caused by errors which when elsewhere
in WHAT IF occurring, are fatal, but here don't matter too much.
Be aware that this option only works on amino acids.
The command CNTBAD will cause WHAT IF to look at all residues in
the soup. It will count all residues that it thinks are perfect, and all
that it thinks are bad. It will list all bad residues.
WHAT IF normally determines which cysteines are bridged by simple distance
criteria. Every pair of cysteine S-gammas closer than 2.5 Angstrom trigger
a cys-cys bridge.
There are a few commands to manipulate this.
The command SHOCYS will cause WHAT IF to list all cysteine bridges presently
known to it. This includes the self determined ones, and the user set
cysteine bridges.
Typically SHOCYS output looks like:
The following Cys-Cys bridges are found:
4 CYS ( 4) - 32 CYS ( 32) *1
16 CYS ( 16) - 26 CYS ( 26)
3 CYS ( 3) - *2
The total number of cysteines is: 5
1) Cys 4 is bridged with Cys 32 (and 16 with 26).
2) Cys 3 is unpaired
The command SETCYS will cause WHAT IF to prompt you for the first and for the
second cysteine in a cys-cys bridge. This can of course only be done if there
are at least two unpaired cysteines available.
The command INICYS will cause WHAT IF to remove all flags for manually set
cys-cys bridges, and set all cys-cys bridges according to distance criteria
again.
The following commands are also available from the soup menu:
At present WHAT IF treats C-terminal oxygens still as single atomic individual
molecules. This will be changed in version 6.0. However, till that time, you can
use the ADDOXT command to add C-terminal oxygens where needed. This is for
example needed after you remove one or more residues, and create new
C-termini.
The command GETDBF can be used to get a protein from WHAT IF's relational
structure database in the soup. The command GETDBF will cause WHAT IF to
prompt you for the number of a database file. You can use the INDEX command
in the SCAN3D menu to see which proteins all are available.
You will be asked if you want to initialize the soup first. If you answer
with YES, the command INISOU (see above) will automatically be executed first.
If you answer with NO, the requested protein will be added to the soup.
The command MAKDNA will cause WHAT IF to display a mini menu that allows
you to create a DNA molecule. Further information will be provided as soon
as this option is bug free. Till that time, use MAKDNA with great care.
The command NEWUNQ will cause WHAT IF to renumber the unique identifiers
(=PDB identifiers) for the residues in your soup. They will be numbered
1, 2, 3, ... etc. You can use RENUMB if you want alternative numbering
schemes.
The command SETCHA will cause WHAT IF to prompt you for a range(s) of residues
and for a (new) chain identifier. A chain identifier must be a single character.
It will give all selected residues the chosen chain identifier.
The use of this option is a requirement if you want to generate a PDB file
that should later be manipualted with the RasMol program.
Be aware that this option can get you in deep trouble....
If you give the first half of a chain a different chain identifier from the second
half, you actually converted that one chain into two chains. Every character
is allowed as chain identifier. WHAT IF has no problems with that, but the
official PDB nomenclature only allows for capital A-Z, and several other
programs might count on you using only those chain identifiers.
If you give two disconnected chains the same chain identifier than a few WHAT IF
options might start giving funny results, and other programs will become
unpredictable.
In summary, this is an option that requires some thinking....
The command SOUCOP will cause WHAT IF to prompt you for a range of residues.
It will then make an exact copy of this range after the last protein in the
soup.
This is a nice option for rearranging your soup without the usual edit
procedures. It is also a useful option for loop transplants.
Not all commands are immediately active in the SOUP menu. By typing
MORE, more commands will be activated. (Use LESS to deactivate the
extra commands again).
The following options are so-called hidden options:
The command DVADOM will force WHAT IF to overrule its internal
determination of which atoms are bad, and treat them all
as OK. You can see if atoms are bad when you type LISTA. The
AT OK column has + for good atoms and - for bad atoms.
One of the most common errors in the residue nomenclature in PDB-like files
is the addition of a fourth character to it (e.g. HISA, ASPH). The GETUS3
command can be used
to overcome this problem.
The command GETUS3 will cause WHAT IF to prompt you for a PDB file. It will
then read all coordinates from this file, and add them to the soup.
The fourth character of the residue name will be skipped upon reading.
If WHAT IF gets confused it sometimes starts spitting incomprehesible
messages at you such as "Soup out of sync". These messages are mainly meant
for us, but that does
not help you much, because your session is about to crash. The best thing to do
in such cases is to run the STATUS command. That produces a lot of
seemingly useless output, but it might rescue your session. After STATUS,
try to use MAKMOL to save your soup, kill WHAT IF, and start again.
This is mainly a debug routine. The very experienced user might read the
comments in the routine MOL010 to see what kind of pointers are all listed.
The command CLNSOU removes all drugs, co-factors, water, ions, etc. from the
soup. Also, in case proteins and/or DNA/RNA overlap severely in space, the
molecule with the highest number in the soup gets deleted. This is a rather
harsh and irreversible option. Use SAVSOU before you use this option?
Sometimes DNA molecules are present in the PDB file in the wrong order (i.e.
the last residue is given first). In these cases INVERT can be used to
invert the order of the bases in the molecule. WHAT IF is not very
clever when dealing with DNA (mainly because I never work with DNA), so
if WHAT IF gets confused about DNA molecules, try this option.
Alternatively, use the FIXDNA option.
By the way, you can also use this option (without any guarantees) on
stretches of protein....
The command MERGED allows you to merge multiple drugs into one single
drug molecule. This is a handy option if you run out of possible molecules
in the soup because of billions of single ions or something similar.
If you want to delete a base pair from the soup, that might be rather
cumbersome work because you have to do a lot of residue number calculations.
With the DELDNA option you can delete an entire base pair by proving the
residue number of just one of the bases.
This option will look at the basepair hydrogen bonding for DNA/RNA
and list which bases are paired. Typically HBODNA output looks like:
47 DADE ( 1 ) - 54 DTHY ( 96 )
48 DTHY ( 2 ) - 53 DADE ( 95 )
49 DCYT ( 3 ) - 52 DGUA ( 94 )
50 DGUA ( 4 ) - 51 DCYT ( 93 )
Which indicates that 47 DADE is paired with 54 DTHY, etc.
The option SHEARD will ask you for a molecule and a range on the DNA
Your molecule will be moved one basepair along the DNA. If there are
no large curvature differences, all contacts between the DNA backbone
and the molecule you are moving should be similar before and after the
move. This option has no incorporated intelligence for base
specific interactions. So it is possible that this option leads
to chemically nonsensical situations....
Often you see all kinds of junk bound to your beautiful protein,
e.g. a C-terminal oxygen, a phosphate group, a heam group, etc.
If you want to get rid of this binding, use NOBOTO.
Be aware that this situation is short-lived. WHAT IF very rapidly
re-builds all information about what is bound to what. Normally
NOBOTO is cancelled after the next option. Sometimes already
during the next option. So in practice, this might be a rather useles
option.
Sometimes DNA molecules are present in the PDB file with the wrong residues
(i.e. the O3* sits at the wrong base). In these cases FIXDNA can be used to
correct the positions of O3* atoms in the molecule. WHAT IF is not very
clever when dealing with DNA (mainly because I never work with DNA), so
if WHAT IF gets confused about DNA molecules, try this option.
Alternatively, use the INVERT option.
The command SHOTOP will cause WHAT IF to show you most information that it
obtained from the last topology file that was read in. This is normally
the topology file that get read automatically upon starting WHAT IF.
This option does not work properly yet.
The option PASRNG will prompt you for a range and execute the PASTE
option on this whole range.