Should return (very quickly) a nil-response
WHAT IF command: WEMPTY
Description: This web-service calls all functions and routines that all WHAT IF web-services have in common, but otherwise does nothing. So it is a good test to see if the web-services machine, and WHAT IF, are up and running
If any web-service fails then please try to run this TestEmpty web-service before mailing us. The correct response for this service is that it just gives you a TestEmptyResponse. If TestEmpty fails then most likely all services are down, or worse, the whole computer; and, most likely, we are already working at a solution. If this TestEmpty service fails, please try again the next (European) morning and only mail us if it still is down by that time.
If this TestEmpty service happily returns an empty response, while some other service fails, then please mail Gert Vriend (vriend@cmbi.umcn.nl) the name of the failing service, the corresponding WHAT IF command, and the PDB file that failed. (Preferably the 4-letter PDB identifier, but if the file is not in the PDB, mail the whole PDB file as an attachement.
As this is the first service, which means that this documentation is on top of the help page, the general info for all services will be placed here...
The documentation of each web-service contains a line like:
WHAT IF command: WSVXXX.
The funny six-character word WSVXXX (which is different for each service) is the command in WHAT IF that actually runs the WHAT IF options. So, using this word, you can find the corresponding documentation in the WHAT IF writeup.
WHAT IF license holders who want to have an in-house set up for WHAT IF based web-services can contact us and obtain all required material in an easier format than just downloading the scripts etc., that this documantation points at.
Please read the disclaimer, formal legal notice and informal legal notice that are applicable to the combined WHAT IF environment (except these explicit web-services!) and the results WHAT IF produced and produces, and that altogether are refered to as "material".
Web-service categories:
The following references are related to one or more of the web-services
Uploading / using PDB files
WHAT IF command: na
Description: To use WHAT-IF functions on your own PDB files, you have to upload them first. The result of this function is an ID that you can use in further calls to wiwsd services.
Downloading PDB files
WHAT IF command: na
Description: You can use this function to download PDB files. If you use the regular four letter code, you can retrieve standard PDB files, if you use the ID as returned by UploadPDB you can download a previously uploaded PDB file.
Surface accessibility dots for graphics
WHAT IF command: WSVDOT
Description: Calculates the positions of dots that are homogeneously distributed over the surface of the molecule (waters are not incorporated in the calculation).
Output is an array of structures that contain arrays filled with dots. A dot consist of three coordinates (x,y,z) and a number from 0-360 indicating the HUE value of the colour of the dot. Colours are on the Hue-wheel:
0 = Blue
60 = Purple
120 = Red
150 = Orange
180 = Yellow
240 = Green
300 = Light Green
360 = Blue (is zero again)
Surface accessibility
WHAT IF command: WSVACC
Description: Returns for each atom in the input file its solvent accessibility in Ångström2. Waters are neglected by this service.
This service returns the "accessible surface". The AtomAccessibilityMolecular service, that runs the WHAT IF option WSVACM, will calculate the "accessible molecular surface".
Accessibile molecular service
WHAT IF command: WSVACM
Description: Returns for each atom in the input file its accessibile molecular surface in Ångström2. Waters are neglected by this service.
This service returns the "accessible molecular surface". The AtomAccessibilityMolecular service, that runs the WHAT IF option WSVACC, will calculate the "accessible surface".
The computation method is described in:
Surface accessibility Plus extra output
WHAT IF command: WSVACP
Description: Returns for each atom in the input file its solvent accessibility in Ångström2. Waters are neglected by this service. A boolean is added to each atom indicating whether this atom is considered 'correct' by WHAT IF or not. Occupancy=0.0 is the most common reason for this boolean flag being returned as false.
This service returns the "accessible surface". The AtomAccessibilityMolecularPlus service, that runs the WHAT IF option WSVAMP, will calculate the "accessible molecular surface".
Accessibile molecular service
WHAT IF command: WSVAMP
Description: Returns for each atom in the input file its accessibile molecular surface in Ångström2. Waters are neglected by this service. A boolean is added to each atom indicating whether this atom is considered 'correct' by WHAT IF or not. Occupancy=0.0 is the most common reason for this boolean flag being returned as false.
This service returns the "accessible molecular surface". The AtomAccessibilityMolecular service, that runs the WHAT IF option WSVACP, will calculate the "accessible surface".
Residue accessibility (BB,SCH,TOT + resOK flag)
WHAT IF command: WSVAM2
Description: Returns for each residue the backbone solvent accessibility, sidechain solvent accessibility, total solvent accessibility (sum of other two), plus a flag that is T or F. T when all atoms in this residue are OK, F when one or more are not OK.
This service returns the "accessible molecular surface". The ResidueAccessibilitySolvent service, that runs the WHAT IF option WSVAR2, will do the same but with "accessible surface"
Entity accessibility (+ resOK flag)
WHAT IF command: TSVAM2
Description: Returns for each entity the backbone, side chain, and totalsolvent accessibility, plus a flag that is T or F. T when all atoms in this entity are OK, F when one or more are not OK.
For sugars and ligands the backbone is not defined, so their backbone accessibility is zero, and the side chain and total accessibility are the same.
This service returns the "accessible molecular surface". The TotAccessibilitySolvent service, that runs the WHAT IF option TSVAR2, will do the same but with "accessible surface".
The accessible surface is always larger than the accessible molecular surface.
Residue accessibility (BB,SCH,TOT + resOK flag
WHAT IF command: WSVAR2
Description: Returns for each residue the backbone molecular accessible surface, sidechain molecular accessible surface, total molecular accessible surface (sum of other two), plus a flag that is T or F. T when all atoms in this residue are OK, F when one or more are not OK.
This service returns the "accessible surface". The ResidueAccessibilitySolvent service, that runs the WHAT IF option WSVAM2, will do the same but with "accessible molecular surface"
Entity accessibility (+ resOK flag)
WHAT IF command: TSVAR2
Description: Returns for each entity the backbone, side chain, and totalmolecular accessibility, plus a flag that is T or F. T when all atoms in this entity are OK, F when one or more are not OK.
For sugars and ligands the backbone is not defined, so their backbone accessibility is zero, and the side chain and total accessibility are the same.
This service returns the "molecular surface". The TotAccessibilitySolvent service, that runs the WHAT IF option TSVAM2, will do the same but with "solvent accessible surface"
Residue accessibility plus residue vacuum accessibility.
WHAT IF command: WSVAR3
Description: Returns for each residue the accessible surface, and the vacuum accessible surface. The latter is defined as the accessibility of the residue when taken out of the protein together with the the backbone atoms of any residue it is covalently bound to.
This service returns the "accessible surface". The ResidueAccessibilityVacuumMolecular service, that runs the WHAT IF option WSVAM3, will do the same but with "accessible molecular surface".
The accessible surface is always larger than the accessible molecular surface.
Molecular accessible surface plus its vacuum value per persidue.
WHAT IF command: WSVAM3
Description: Returns for each residue the molecular surface, and the vacuum molecular surface. The latter is defined as the molecular surface of the residue when taken out of the protein together with the the backbone atoms of any residue it is covalently bound to.
This service returns the "molecular surface". The ResidueAccessibilityVacuum service, that runs the WHAT IF option WSVAR3, will do the same but with "accessible surface"
Backbone torsion angles (φ,ψ,ω)
WHAT IF command: WSVCHB
Description: Returns for each residue all its backbone torsion angles: φ, ψ, ω (in degrees).
φ, ψ and ω are returned as 999 if they don't exist (like φ that doesn't exist in an N-terminal residue....
Torsion angles (φ,ψ,ω,χ1-5)
WHAT IF command: WSVCHI
Description: Returns for each residue all its torsion angles: φ, ψ, ω, χ1-χ4 (in degrees).
φ, ψ, and ω are returned as 999.9 if they don't exist. χ-angles are listed only if they exist and are returned as 999.9 when they are not meaningful (i.e. when one of the atoms defining defining that χ-angle is missing from the PDB file or has all coordinates zero.
Cysteine (bridge) torsion angles
WHAT IF command: WSVCYT
Description: Returns for each cysteine (bridge) all its torsion angles (in degrees).
These are the torsion angles over the following five bonds, respectively: Cαi - Cβi; Cβi - Sγi; Sγi - Sγj; Sγj - Cβj; Cβj - Cαj.
Lists cysteine bridges
WHAT IF command: WSVCYS
Description: Show Cysteine bridges.
Lists cysteine bridges
WHAT IF command: WSVCNP
Description: Show Cysteine bridges, but skip those that are between Pisa generated copies.
This option was needed for one particular HOPE application...
Lists free cysteines
WHAT IF command: WSVCYS
Description: Show Cysteine bridges.
A cysteine is called free when it neither is involved in a cysteine bridge, nor functions as a ligand to a metal
Lists cysteines bound to metal
WHAT IF command: WSVCYM
Description: Show cysteines that are bound to a metal.
Metals are either included when they are covalently bound to a cysteine (as can sometimes be observed for Pb, for example), or when the cysteine S-gamma is a ligand of the metal. The output consists of a row of cysteine-metal pairs.
Lists interatomic bumps
WHAT IF command: WSVBMP
Description: Show Interatomic bumps The output are those pairs of atoms considered a bump, and their degree of interpenetration. A bump is listed if the Van der Waals' radii of two atoms interpenetrate more than 0.25 Ångström.
Side chain - side chain contacts
WHAT IF command: WSLCON
Description: For each amino acid its atomic contacts are counted with everything but water. All distances are scored using a way too simple force-field.
Two atoms are in contact when there is less than 0.5 Ångström between their Van der Waals surfaces.
These contact scores are added up for all side chain atoms, and returned to the caller as a single value that relates (poorly) to the effects if the side chain studied is mutated.
Side chain - side chain contacts
WHAT IF command: WSLCNR
Description: For each amino acid its atomic contacts are counted with everything but water. All distances are scored using a way too simple force-field.
Two atoms are in contact when there is less than 1.5 Ångström between their Van der Waals surfaces.
These contact scores are added up for all side chain atoms, and returned to the caller as a single value that relates (poorly) to the effects if the side chain studied is mutated.
Side chain - side chain contacts
WHAT IF command: WSLCN2
Description: For each amino acid its side chain contacts (excluding Cβ) are counted with everything but water. All distances are scored using a way too simple force-field.
Two atoms are in contact when there is less than 0.5 Ångström between their Van der Waals surfaces.
These contact scores are added up for all side chain atoms, and returned to the caller as a single value that relates (poorly) to the effects if the side chain studied is mutated.
Side chain - side chain contacts
WHAT IF command: WSLCN3
Description: For each amino acid its side chain contacts (excluding Cβ) are counted with everything but water. All distances are scored using a way too simple force-field.
Two atoms are in contact when there is less than 1.5 Ångström between their Van der Waals surfaces.
These contact scores are added up for all side chain atoms, and returned to the caller as a single value that relates (poorly) to the effects if the side chain studied is mutated.
Side chain integrated multimer contacts
WHAT IF command: WSVANP
Description: For each amino acid in the input file the contacts with other protein chains in the multimer are counted. This is a simple count, and has no linear relation to any form of contact energy
Side chain integrated nucleic contacts
WHAT IF command: WSVHDC
Description: For each amino acid in the input file the contacts with nucleic acids are counted. This is a simple count, and has no linear relation to any form of contact energy
Lists interactions with nucleic acids
WHAT IF command: WSVANU
Description: Show protein - nucleic acid interactions
The output are those pairs of atoms of which one is protein and the other nucleic acid, that have less than 1.0 Ångström between their Van der Waals' surfaces.
Side chain integrated ion-contact energie
WHAT IF command: WSVHIC
Description: For each amino acid in the input file the ion contacts are counted. Depending on the distance they get a score ranging from 1.0 for close contacts to 0.25 for weak contacts. These contact scores are added up for all ions for all side chain atoms, and returned to the caller as a single value that relates (poorly) to the energetic contribution of this particular contact to the total folding energy.
Side chain integrated ion-contact energie
WHAT IF command: WSLHIC
Description: For each amino acid in the input file the ion contacts are counted. Depending on the distance they get a score ranging from 1.0 for close contacts to 0.25 for weak contacts. These contact scores are added up for all ions for all side chain atoms, and returned to the caller as a single value that relates (poorly) to the energetic contribution of this particular contact to the total folding energy.
The contacted metal ions are listed too.
Side chain integrated ion-contact energie
WHAT IF command: WSVHIN
Description: For each amino acid in the input file the ion contacts are counted. Depending on the distance they get a score ranging from 1.0 for close contacts to 0.25 for weak contacts. These contact scores are added up for all ions for all side chain atoms, and returned to the caller as a single value that relates (poorly) to the energetic contribution of this particular contact to the total folding energy.
Side chain integrated ion-contact energie
WHAT IF command: WSLHIN
Description: For each amino acid in the input file the ion contacts are counted. Depending on the distance they get a score ranging from 1.0 for close contacts to 0.25 for weak contacts. These contact scores are added up for all ions for all side chain atoms, and returned to the caller as a single value that relates (poorly) to the energetic contribution of this particular contact to the total folding energy.
The contacted metal ions are listed too.
Lists interactions with drug-like ligands
WHAT IF command: WSVLC2
Description: Show drug-like ligand interactions
The output are those pairs of atoms of which one is a drug like ligand and the other macromolecule, that have less than 1.0 Ångström between their Van der Waals' surfaces.
Compared to the ShowLigandContacts (WSVLIC) service, this one essentially skips contacts with ions.
Lists interactions with drug-like ligands
WHAT IF command: WSVLC3
Description: Show drug-like ligand interactions
The output lists all residues that have a contact with (at least one) a drug-like ligand, and the shortest atom-to-atom amino acid - ligand contact distance, and all ligands this amino acid makes a contact with. A residue and a ligand are called in contact if they share a pair of atoms that have less than 1.0 Ångström between their Van der Waals' surfaces.
Compared to the ShowLigandContacts (WSVLIC) service, this one essentially skips contacts with ions, sugars, crystallisation additives, and other small things.
Lists interactions with ligands
WHAT IF command: WSVLIC
Description: Show ligand interactions
The output are those pairs of atoms of which one is ligand and the other macromolecule, that have less than 1.0 Ångström between their Van der Waals' surfaces.
This service considers drugs, metabolites, lipids, co-factors, and ions all as ligands. ATP, ADP, NADPH, etc are considered as ligands unless they have the same name as nucleotides.
Side chain salt bridge counter
WHAT IF command: WSVHSB
Description: For each amino acid in the input file its side chain salt bridges are counted, valued, and added up. The total quasi salt bridge energy is returned to the caller as a single value that probably relates poorly to the energetic contribution of this particular salt bridge to the total folding energy.
So, a salt bridge between the N-terminus and a Glu side chain is counted for the Glu, but not for the N-terminal residue, because we only check side chain salt bridges.
Two residues are said to have a saltbridge if a negative atom in the one residue is within 8.0 Ånström of a positive atom in the other residue.
Side chain salt bridge counter
WHAT IF command: WSLHSB
Description: For each amino acid in the input file its side chain salt bridges are counted, valued, and added up. The total quasi salt bridge energy is returned to the caller as a single value that probably relates poorly to the energetic contribution of this particular salt bridge to the total folding energy.
So, a salt bridge between the N-terminus and a Glu side chain is counted for the Glu, but not for the C-terminal residue, because we only check side chain salt bridges.
All saltbridge partners are listed too.
Two residues are said to have a saltbridge if a negative atom in the one residue is within 8.0 Ånström of a positive atom in the other residue.
Lists potential hydrogenbonds
WHAT IF command: WSVHB-
Description: Lists potential hydrogenbonds between amino acids and anything but water. See ShowHydrogenBonds if you want to include hydrogenbonds with water too.
The hydrogen bonding network is not optimised, and Asn, Gln, and His flips are not worked out prior to analyzing the hydrogen bonds.
Output is a list of records, each record consisting of: The atoms making the hydrogenbond
Four hydrogenbond geometric parameters:
1) Donor Acceptor distance
2) Proton Acceptor distance
3) The deviation from 180 degrees over the acceptor
4) The deviation from 180 degrees over the proton
In case of bi-directional hydrogen bonds, both are listed, one-after-the-other
Side chain integrated H-bond energie
WHAT IF command: WSVHBF
Description: For each amino acid in the input file the H-bond enthalpy is calculated for each side chain atom. All these enthalpies are added up and the total enthalpy is returned.
Residues that have no hydrogen bonding side chain atoms get the value 0.0. The hydrogenbonding network is optimized (see references) before the hydrogenbonds are analysed. Surface located water molecules are deleted before the network optimisation to make this a CPU-technically doable web service. Contact us if you need this facility with water molecules included, perhaps we can work something out.
Side chain integrated H-bond energie, surface waters excluded
WHAT IF command: WSVHBN
Description: For each amino acid in the input file the H-bond enthalpy is calculated for each side chain atom. All these enthalpies are added up and the total enthalpy is returned.
Residues that have no hydrogen-bonding side chain atoms get the value 0.0. The hydrogenbonding network is optimized (see references) before the hydrogenbonds are analysed. All water molecules are deleted before the network optimisation to make this a CPU-technically doable web service. Contact us if you need this facility with water molecules included, perhaps we can work something out.
Lists salt bridges
WHAT IF command: WSVSBR
Description: Show saltbridges
The output are those pairs of atoms considered a salt-bridge, and their inter-atomic distance. Histidines are not included in this calculation.
Lists salt bridges
WHAT IF command: WSVSB2
Description: Show saltbridges
The output are those pairs of atoms considered a salt-bridge, and their inter-atomic distance. All histidines are considered positively charged in this calculation.
Lists potential hydrogenbonds
WHAT IF command: WSVHBO
Description: Lists potential hydrogenbonds between amino acids and anything.
The hydrogen bonding network is not optimised, and Asn, Gln, and His flips are not worked out prior to analyzing the hydrogen bonds.
Output is a list of records, each record consisting of: The atoms making the hydrogenbond
Four hydrogenbond geometric parameters:
1) Donor Acceptor distance
2) Proton Acceptor distance
3) The deviation from 180 degrees over the acceptor
4) The deviation from 180 degrees over the proton
In case of bi-directional hydrogen bonds, both are listed one-after-the-other
Packing quality (old style)
WHAT IF command: WSVQUA
Description: Returns for each residue is packing normality. The normal score for proteins solved correctly at high resolution is about -0.4. A score of -5.0 or lower indicates a (very) poorly packed residue. If low scores are seen more than a few times, or a series of times in a row, one should start worrying about those residues.
This work is described in:
Quality control of protein models: Directional atomic contact analysis.
G. Vriend, C. Sander. J.Appl.Cryst. (1993) 26, 47-60.
Packing quality for whole entry(old style)
WHAT IF command: WSVQUM
Description: Returns packing normality for whole entry. The normal score for proteins solved correctly at high resolution is about -0.4. A score of -3.0 or lower indicates a (very) poorly packed molecule.
This work is described in:
Quality control of protein models: Directional atomic contact analysis.
G. Vriend, C. Sander. J.Appl.Cryst. (1993) 26, 47-60.
Inside - outside distribution normality
WHAT IF command: WSVINO
Description: Returns an inside - outside normality score that is callibrated against PDB files ofwater-soluble molecules. One score is returned for each molecule > 50 amino acids andone score for the whole file. Per molecule(s) scored the first residue, the last residue, and a score are lsited
Improper dihedral value score
WHAT IF command: WSVCHN
Description: Returns for each residue the sum of all improper dihedral Z-scores observable in that residue. One thus expects larger residues to generally score higher than small residues.
Improper dihedral value score
WHAT IF command: WSVCHX
Description: Returns for each residue the maximum of all its improper dihedral Z-scores.
Returns per amino acid a series of values.
WHAT IF command: WSVBFA
Description: Returns per amino acid (in this order) the values :
Average B-factor of all atoms;
B-factor of the alpha carbon;
Average B-factor of four backbone atoms;
Average B-factor of the side chain atoms;
Average B-factor of the outer (maximally 4) side chain atoms;
Please be aware that for glycine the Calpha is used as side chain, for alanine the Cbeta is its whole side chain; and for many (small) amino acid types will the latter two values be identical.
Only atoms are used that seem intact. If no intact atoms are found for any of the categoriesthe value of 99.99 will be returned.
Backbone angle N-Calpha-C (angle over the C-alpha)
WHAT IF command: WSVTAU
Description: For each canonical amino acid in the input file the backbone angle tau is listed.
Symmetry contact counter
WHAT IF command: WSVSMC
Description: Returns for each residue the number of symmetry contacts made by that whole residue.
Two atoms (of which one in `another` asymmetric unit) are called in contact if the distance between their Van der Waals' surfaces is less than 0.25 Ångström.
Symmetry contact counter
WHAT IF command: TSVSMC
Description: Returns for each thing the number of symmetry contacts made by that whole thing. A thing can be amino acid, nucleic acid, water, sugar, liagnd, ion, drug, etc.
Two atoms (of which one in `another` asymmetric unit) are called in contact if the distance between their Van der Waals' surfaces is less than 0.25 Ångström.
Symmetry contact counter
WHAT IF command: WSVSMS
Description: Returns for each amino acid the number of symmetry contacts made by it's side chain. For glycine the Calpha is considered its side chain.
Two atoms (of which one in `another` asymmetric unit) are called in contact if the distance between their Van der Waals' surfaces is less than 0.25 Ångström.
Contacts with symmetry related water molecules are not taken into account.
List bumps of mutant protein
WHAT IF command: WSVMBA
Description: Returns for each residue in the mutated protein the integrated bump value after optimally executing the mutatation. Two atoms (of which one in `another` asymmetric unit) are called bumping if their Van der Waals' surfaces penetrate more than than 0.5 Ångström.
This Web service accepts as input information about a mutation described by a residue number as integer, i.e. the number associated to this residue in the PDB file, and the new residue type as a string. Residue types can be given in 1-letter code (ACDEFGHIKLMNPQRSTVWY) or in 3-letter code (Ala, Cys, Asp, etc). Residue types are not case sensitive.The bump calculation is preceded by the execution of the requested mutation.
Sequence profile
WHAT IF command: WSVPRF
Description: Warning. This service only returns results for PDB files known by HSSP, and those are the protein-containing subset of what the wwPDB distributes.
This option reads the Profile from HSSP files, and returns thoseprofile values. It also returns a thing called reliability. This is simply the number of sequences aligned at this position divided by the total number of sequences in the HSSP alignment.
Sequence variability
WHAT IF command: WSVVAR
Description: Warning. This service only returns results for PDB files known by HSSP, and those are the protein-containing subset of what the wwPDB distributes.
This option reads the VAR column from HSSP files, and returns thosevalues.
Lists likely rotamers
WHAT IF command: WSVROT
Description: Show Rotamer likelyhoods for all 20 amino acid types at each position in the protein. Output is a list of records, each record consisting of:
Lists accessibilities and symmetry contact details
WHAT IF command: WSVJOP
Description: Show accessibilities and symmetry contact details, decomposed in classes. Output is a list of records, each record consisting of:
Proline mutation value
WHAT IF command: WSVPRO
Description: This service determines for each position the molecule that is further than two positions away from a terminus a score that relates to the chance that a proline, when introduced at this position, would increase the stability of the whole protein.
This option runs over all amino acids in the whole PDB file. If your PDB files holds too many amino acids (too many is somewhere between 500 and 1000) this option will time out and you should use ProlineMutationValueRange several times instead.
Residue happiness value
WHAT IF command: WSVHAP
Description: This service determines for each position the molecule that is further than two positions away from a terminus a score that relates to the chance that a mutation at this position is could increase the stability of the whole protein.
This option can time out when run over more than 500 amino acids. In those cases you should use this option several times instead giving the full range at once.
Proline mutation value
WHAT IF command: WSVPRR
Description: This service determines for each position the given range (that is further than two positions away from any terminus) a score that relates to the chance that a proline, when introduced at this position, would increase the stability of the whole protein.
WHAT IF's interpretation of PDB sequence
WHAT IF command: WSVSEQ
Description: The sequence in a PDB file is not uniquely defined. This server returns what WHAT IF thinks is the sequence in the PDB file you uploaded.
Names of HET groups found in PDB header
WHAT IF command: WSVHET
Description: The PDB has, for obscure reasons, decided to have atoms and hetatoms. Ligands, lipids, and ions tend to become hetatoms, and so do sometimes also groups that are attached to amino acids.
The PDB tries to give every molecule that consists of hetatoms a unique three letter code and a unique name, but dont rely on this...
This web-service returns for each molecule that consists of hetatoms its unique three three letter code and its unique name. If a common name is given (a HETSYM name in PDB terms), this common name is returned rather than the formal name
Reduced DSSP output
WHAT IF command: WSVHST
Description: Returns for each residue the DSSP determined secondary structure in three-state (HSC).
Reduced DSSP output plus phi-psi interpretation
WHAT IF command: WSVHSL
Description: Returns for each residue the DSSP determined secondary structure in three-state (HSC). It than determines (coarsly) what the secondary structure roughly is according to the local phi-psi angles and adds a character (UHST). U for unknown or none of the others; H for helix; S for strand; T for the left handed helix area where phi and psi both are positive (or psi perhaps a bit negative but not much).
Use residue in database or not
WHAT IF command: WSVUDB
Description: Returns for each residue a value that tells you whether you can use this residue in database applications or that you better do not use it. The values are up to 1.0. 1.0 means that this is a perfect residue to use in training sets, in statistics, in databases, etcetera.
Each residue starts with 1.0 points. After that points are subtracted:
-0.75 Bad Cα
-0.50 Bad other backbone atom
-0.60 Bad Cβ (not for Gly)
-0.40 One or more other bad side chain atoms
-0.35 N- or C-terminal residue (or next to invisible residue)
-0.25 Next to residue from previous line
-0.40 For non-canonical residue
-0.40 For Gly or Pro
-0.10 Next to one of previous two lines
-0.15 Cα has high B-factor
-0.10 Other backbone atoms has high B-factor
-0.08 Cβ has high B-factor
A B-factor is called high if it is either >60.0, or > 2.5 times the average B-factor of all Cαs in the whole file.
Use file in database or not
WHAT IF command: WSVUFI
Description: Returns for each PDB file a series of values that tell you whether you can use this file in database applications or that you better do not use it.
You get up to 25 values returned to you. If any value is worse than I think is perhaps somewhat acceptable, then the rest of the values ;will not be calculated. You will have to determine yourself whether you use this file or not
-1 No protein found
Number of NMR MODELs found
Resolution found in X-ray file; should fall in [0.1;2.5]
Number of residues (amino acids, nucleotides, sugares) must be 5000 or less
Number of amino acids must be 25 or more
Number of waters (must be less than 25% of all atoms in PDB file)
Number of atoms in ligands, drugs, lipid, etc (must be less than 15% of all atoms in PDB file)
Percentage residues with one or more bad/missing atoms (cutoff 25%)
Percentage bad/missing backbone atoms (cutoff 10%)
Ramachandran Z-score (cutoff -5.0)
Chi-1 / Chi-2 normality score (cutoff -5.0)
RMS-Z score on bonds (cutoff <0.25,1.50>)
RMS-Z score on angles (cutoff <0.25,1.50>)
Bumps score (no cutoff set (yet))
Old-style packing quality
Inside-Outside distribution score (above cutoff of 1.16 is wrong or membrane protein)
.......
25) +1 means fine, use this molecule; -1 means better dont use this molecule
Debug cq test service that returns the coordinates in PDB format.
WHAT IF command: WSVECH
Description: This service returns the PDB file that you upload in PDB format. Most HEADERcards are skipped, so are ANISOU cards, and a few more administrative things.
Moves waters to symmetry related position closest to solute.
WHAT IF command: WSVMWA
Description: For a crystallographer, a position in the "next cell" is just as good as a position in the cell where all the protein etcetera sits. For the users of a structure this can at times be inconvenient.
This web-service returns water atoms that have been moved to a position closer to the solute. These atoms are returned in a file in PDB format. The atom numbers, B-factor, etc., are the same as the atom numbers, B-factors, etc., from which they were generated.
Moves waters to symmetry related position closest to solute.
WHAT IF command: WSVMWX
Description: For a crystallographer, a position in the "next cell" is just as good as a position in the cell where all the protein etcetera sits. For the users of a structure this can at times be inconvenient.
This web-service returns water atoms that have been moved to a position closer to the solute. These atoms are returned in a file in PDB format. The atom numbers, B-factor, etc., are the same as the atom numbers, B-factors, etc., from which they were generated.
Lists residues in almost PDBXML format.
WHAT IF command: WSVLAT
Description: Lists residues in a format the PDB should actually have chosen.
The output uses the PDBXML nomenclature but a smarter schema so that it fits better in the Edam ontology.
Not all information is returned to the user. In case of alternate atoms, the one most likely to be there most of the time will be returned. Anisotropic B-factor information also is not passed on from the input PDB file to this XML output.
Makes a series of corrections, mainly in amino acids.
WHAT IF command: WSVCOA
Description: Before returning the coordinates in XML format, WHAT IF applies a series of small `corrections`:
Adds polar hydrogens to the macromolecules.
WHAT IF command: WSVCO2
Description: The hydrogenbond optimisation routines are used to calculate optimal positions for polar protons. This module does not take symmetry into account and doubles waters that sit between symmetry related positions.
Adds polar hydrogens to the macromolecules.
WHAT IF command: WSVCO3
Description: The hydrogenbond optimisation routines are used to calculate optimal positions for polar protons. This module takes symmetry into account. Therefore there is no need to double the watermolecules that sit at symmetry-positions and thus actually contactthe solute at multiple positions.
Produces a shell of symmetry contacting residues.
WHAT IF command: WSVSS1
Description:
Produces a shell of symmetry contacting residues.
WHAT IF command: WSVSS1
Description: All residues that can be generated from the assymmetric unit by applying the space group symmetry matrices and whole cell translations and that make a contact with any residue in the asymmetric unit are calculated and returned to the caller.
Two residues are said to have a contact if any of their atoms make a contact. Two atoms are said to make a contact if the shortest distance between their Van der Waals radii is less than the cutoff.
For this server the cutoff is 2.5 Ånström.
Produces a shell of symmetry contacting residues.
WHAT IF command: WSVSS1
Description: All residues that can be generated from the assymmetric unit by applying the space group symmetry matrices and whole cell translations and that make a contact with any residue in the asymmetric unit are calculated and returned to the caller.
Two residues are said to have a contact if any of their atoms make a contact. Two atoms are said to make a contact if the shortest distance between their Van der Waals radii is less than the cutoff.
For this server the cutoff is 5.0 Ånström.
Produces a shell of symmetry contacting residues.
WHAT IF command: WSVSST
Description: All residues that can be generated from the assymmetric unit by applying the space group symmetry matrices and whole cell translations and that make a contact with any residue in the asymmetric unit are calculated and returned to the caller.
Two residues are said to have a contact if any of their atoms make a contact. Two atoms are said to make a contact if the shortest distance between their Van der Waals radii is less than the cutoff.
For this server the cutoff is 10.0 Ånström.
Phi, psi, as reals and grid-indices, and the cleaned secondary structure
WHAT IF command: WSVWTH
Description: Only Wouter can use this thing... Per residue you receive the original DSSP determination (where loop and turn both are C) and a character that indicates why (if) these two are different:
- : Unaltered
1 : Terminus
2 : Short strand
3 : Irregular helix
4 : N not H-bonded (-pro)
5 : O not H-bonded
6 : First or last Helical turn
7 : Total helix shorter than 10
Gives the old and the cleaned secondary structure
WHAT IF command: WSVWH2
Description: Only Wouter should use this thing...
Side chain integrated multimer contacts
WHAT IF command: WSVANP
Description: For each amino acid in the input file the contacts with other protein chains in the multimer are counted. This is a simple count, and has no linear relation to any form of contact energy
Proline mutation value
WHAT IF command: WSVPRO
Description: This service determines for each position the molecule that is further than two positions away from a terminus a score that relates to the chance that a proline, when introduced at this position, would increase the stability of the whole protein.
This option runs over all amino acids in the whole PDB file. If your PDB files holds too many amino acids (too many is somewhere between 500 and 1000) this option will time out and you should use ProlineMutationValueRange several times instead.