If you are supposed to enter a residue number or a residue range, you can respond in several ways. The first possibility is to just type the residue number(s) which WHAT IF has assigned to your residue(s) (or drugs, or waters). These are just sequential numbers, starting with 1 for the first residue encountered, etc. Use the List a file server in the Administration server class to see how WHAT IF assigned the numbers to your PDB entry.
Whenever you are prompted for a residue or residue range without any specification of the residue type, you can also enter drugs, ions or water groups. The few times that that is not considered valid input, WHAT IF will tell you what it thinks about the input.
W A R N I N G. Be aware that most servers will prompt you for only one residue and not for a residue range.
If your input file used a different scheme for the numbering of residues you can give those number(s) by typing O (the character O, not the digit zero) followed by the original residue number(s) (Which, in contrast to the strict PDB rules, do not need to be numerical, WHAT IF will also accept names like 17A etc.). Use O as the first character of the line, and not for every residue. This holds for all options throughout WHAT IF. The original names are always listed by WHAT IF in brackets.
Input by picking an atom is not possible when using the servers, but
for the interactive version of WHAT IF the help looks like:
If you give just only P, you will be asked to pick the residue(s) in the
graphics window. In this case you can pick any atom in the residue(s)
you want. I suggest you test if certain options function as expected with P
input the day before you have to give the big demonstration to the director
general of your company...
If you want to input all residues (protein, sugar and DNA/RNA) as a range, you can just type ALL.
If you want to input all amino acids, DNA/RNA, sugars, co-factors, and water in one shot, you can type TOT.
In case you want to enter one entire molecule you can give M followed by the molecule number (as assigned to the molecule by WHAT IF). Of course, when asked for a molecule you can type just the molecule number, although giving an M in front of the molecule number will not hurt the WHAT IF performance.
In case you have multiple copies of one molecule (for example before and after a Molecular Dynamics run) you can type U followed by first the molecule number and then the two original residue names. U3 17A 123 will use the residues 17A till 123 (according to the original, PDB given numbering scheme) from the third molecule in the soup.
In case you have multiple copies of one molecule (for example before and after a molecular dynamics run) you can type S followed by first the molecule number and then the two sequential residue names. S3 18 24 will use the 18-th till 24-th residue from the third molecule.
Input of families is not possible when using the servers, but
for the interactive version of WHAT IF the help looks like:
A family is defined as a group of one or more amino acids consecutively
located in the sequence. Families are not something very intelligent
or so, it is just a way of giving names to
stretches of amino acids. One can for example give all major secondary structure
elements their own name. Families can be used at several occasions as input for options.
It is for example possible to give families a color, or delete all
residues from a family.
Commands that are related to usage of families are easily recognized because
they have the three letter combination FAM in their name. The CLUFAM option
brings you in the menu that deals with families and clusters.
Whenever you are prompted for one or more ranges you can also enter a family name.
Input of clusters is not possible when using the servers, but
for the interactive version of WHAT IF the help looks like:
A cluster is a group of residues that does not need to sit next to each
other in the sequence. In a way clusters are sets of families.
Commands that are related to usage of clusters are easily recognized because
they have the three letter combination CLU in their name. The CLUFAM option
brings you in the menu that deals with families and clusters.
Whenever you are prompted for multiple ranges you can also enter a cluster name.
When you are prompted for a range of residues you can also type PROT,
WATER, DRUG or NUC. This will add the protein, water, ligands or nucleic
acids, respectively, to the list of selected residues. -PROT,
-WATER, -DRUG and -NUC will remove protein, water, ligands or nucleic
acids, respectively, from the list of selected residues.
So, the command LISTAA TOT -PROT -WATER will list all nucleic acids
and co-factors in the soup.
If you are prompted for a (range) of residue(s) you can give LAST if you want to address the last residue (amino acid, nucleic acid or sugar) in the soup. If you want to address the last entity (and this can also be water group, C-terminal oxygen, N-terminal protons, ligand, etc.) you can enter END (actually END-OF-SOUP, but just END is enough).
The table below lists all possible inputs when you are prompted for residue ranges (X and Y are residue numbers in the WHAT IF soup; P and Q are PDB residue identifiers, * means any number):
P Ask the user to pick residues in the graphics window PL Take the residue that was last picked X Y Simple residue range OP Q PDB identifiers M* Whole molecule * S* X Y The X-th till Y-th residue in molecule * U* P Q The residues P till Q in molecule * ALL All residues (amino acids, nucleic acids and sugars) TOT The whole soup LAST The last residue (amino acid, nucleic acid or sugar) END (actual END-OF-SOUP) the last thing in the soup PROT All amino acids NUC All nucleic acids SUG All sugars WATER All water groups DRUG All drugs, ligands, ions ION All single atomic molecules (not C-terminal oxygens) OXT All C-terminal oxygens HELIX All helical residues (in proteins) STRAND All residues in strands 4BUNDL All residues in 4-helix bundles BURIED All buried residues (default cutoff < 2 A surface area) ACCESS All accessible residues (default cutoff < 2 A surface area) CLUNAM All residues in cluster are selected by giving cluster name FAMNAM All residues in family are selected by giving family name
The input listed below will remove things from the list of selected residues etc. Nothing goes wrong if you try to remove a residue that was not selected yet.
-PROT All proteins -WATER All water -DRUG All drugs, ligand, ions -NUC All nucleic acids -SUG All sugars -ALL All residues -HELIX All helical residues -STRAND All strand residues -ION All ions -OXT All C-terminal oxygens