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PdbStat Manual on-line

ist of available commands:

click on any of them to get some description along with examples of use.

  Commands/Keywords currently recognized by PDBSTAT

  The commands/keywords currently recognized by PDBSTAT are given below. 
  Type "help " for more information on each PDBSTAT function.

align	analyze	bye \| quit	class	clear	close
chain	check	chiral	delete	debug	dump
dist \| noe	energy	expand	evaluate	find	fit
fix	get	help	history	hydrogen	hyper
kabsch	ident	info	intialize	log \| change	load \| read
missing	order	rama	relax	reset	restore
rotate	save	see\|show\|list	set	rmsd	to
trans	version	what	write

  Other kind/commands/keywords of help
   codes(amino codes) 	 amino(amino geometry)

Useful taks:

performed with PdbStat, commands and output.

align

it will try to align two structures using Smith-Waterman algorithm with BLOSUM62 back

analyze

Once a set of coordinates and restraints have been read this command will analyze the set of constraints giving several statistics. back

bye | quit

to abandon the program

class

Classify models based on energy. If one has loaded a set of models that have somehow stored energy for each one this command will classify them based on that value back

clear

Clear the screen by simply adding 60 blank lines. back

close

Search for close contacts in the molecule. The program asks interactively for the structure # you want and for the cutoff to consider a 'close contact'. Then it displays on the screen some of the calculations being done with some of the contacts and finally tells the user that the whole list is written to a file usually named 'name_of_your_file_Close_contacts' where name_of_your_file is the name of the file where the structure/s is/are. back

chain

Change the 'Chain Id' in a structure or family. If you read a file with a family of structures you can change the 'Chain Identification' in the PDB format for the letter you want (or number or ...). It is useful in some applications. back

check | chiral

Check 'chirality' in the molecule. This option has evolved a lot and now it checks a lot of things in the molecule like chirality (backbone and side chain), bad omegas, Ramachandran (trying to detect bad Ramachandran angles ...) The check is too strict in the sense that for Ramachandran for example it points as _BAD_ all residues that lie in 4th quadrant. No check for glycine is done, all residues are treated the same. back

delete

Delete a model or a range of models

 
   Syntax:  del[ete] {}
            del[ete] bad { rama | energy

   Deletes a model from the list stored in memory. The command takes one or two 
   numbers.  In the first case the model # is deleted and then the whole list is 
   re-numbered. In the second the program deletes from number 'first' to number
   'second' and then re-numbers. If you give no number the program asks for one 
   (or a range)

   Example:    del 1       ->   Deletes model 1
               del 1 5     ->   Deletes from 1 to 5 (1,2,3,4 and 5)

   In 1998 was been extended a little. Now the user can delete models based in 
   RMSD, ENERGY and values or Ramachandran or Chirality.

   Examples:  del bad rama   -> Deletes models with bad Ramach. values
              del bad energy -> Deletes models with E > cutoff
              del bad rmsd   -> Deletes models with Rmsd > cutoff

   Please note that the user should set the cutoff value for RMSD or ENERGY, 
   for that please see  set  command.

back

debug

Choose debug level to debug code

   Syntax:  deb[ug] {}

   Sets the value of DEBUG, the debug level. The level of debug is controlled by 
   the variable DEBUG. Any value greater than 0 means some printing. Values greater 
   than 5 can give LOTS of printing with some options, so be careful as the print 
   out can get huge. At starting time DEBUG has a value of 0, i.e.  no debug.

back

evaluate

Evaluate different measurements in a model

 
   Syntax:  eva[luate] { options } 
 
   Used to evaluate distances, angles or dihedrals in a molecule. Also it can give 
   the user information about a residue evaluating distances, angles and dihedrals 
   for that residue. A list of available evaluation is given below. 
   Type "help evaluate " for more information 
 
   Options:
          distances      angle     dihedral    residue     OMEGA	PHI  PSI
          ramachandran   gyration  dar

back

expand

Iterative expansion of FindCore core.

 Syntax:  expa [ core | daop ]  [ log | norm ] [ domain id ]

The most common use will be: expa -bb core. It takes all defaults for the expansion of the core. back

find

FindCore algorithm.

 
  Syntax:  find [ -bb | -heavy | -all | -noe ... ]
 
  FindCore - the 'FindCore' algorithm of Snyder and Montelione 
                  (PROTEINS, 59:673-686, June 2005)
  
  Output - superimpositions (one file, named _1.pdb, for each domain) of 
  the ensemble each with (scaled) 'Order Parameters' in the B-factor field of the 
  first model as well as a file, named _b.pdb with coordinate uncertainties 
  in the B-factor field and additionally statistics describing ensemble written to the 
  standard output
  
  Usage:    findcore < options >        Options:  {-all | -heavy | -noe | -bb} 
            
      -all                   use all atoms in calculations
      -heavy                 use only heavy atoms
      -noe                   use only H atoms
      -bb                    use only N,CA,C' backbone (default is -bb)
      -p prior               alt. prior to use for Bayesian correction in domain
                             detection method (default is 0.33)
      -e critical_precision  value of 'epsilon' measure of precision below which 
                             to use alternative prior (default is 0.37)
      -rmsdToModel N         calculate RMSD to the N'th model rather than to a 
                             mean model 
      -biasOfModel N         calculate RMSD between model N and average of other 
                             models rather than RMSD to mean
      -X2ForModel N          calculate X2 statistic describing distance of model 
                             N from spread of other models.  This procedure does 
                             a jackknife calculation to evaluate significance of 
                             X2 statistic and writes the superimposition for each 
                             calculation in the jackknife also in this method, the 
                             file named _b.pdb contains scaled p-values 
                             for local X2 statistics in the B-factor field.
                             The actual p-values are reported in a file called 
                             .local_pValues
  Note - the -rmsdToModel, -biasOfModel and -X2ForModel change the default superimposition
         behavior of this and are mutually exclusive of each other: please use zero or one
         of these options, not more than one

  Theory
  FindCore uses a completely different method for determining well-defined residues.  
  It does not use DAOP at all and only uses the inter-atom distance variance matrix 
  (IVM).  An element (i,j) in this matrix is defined as the variance in the distance 
  between atoms i and j across the ensemble. For each atom i, corresponding to a row 
  in the IVM matrix, and a value of variance, e2, an order parameter Te(i) is defined 
  as the number of elements in row smaller that e2.  The critical value of the parameter 
  e2 should minimise the kurtosis of the set {Te(i)}.  The set of order parameters at 
  the critical value of e2 is then split into non-overlaping subsets such that intrasubset 
  variances are minimized. The optimal susbsets thus define the well-defined (high values 
  of order parameters) and the ill-defined (low values of the order parameters).  The 
  well-defined atoms are then analysed using Ward’s clustering algorithm and separated 
  into individual domains if needed.  The cutoff for clustering is provided by the 
  Chauvenet criterion.

back

fit

Fit to a model specified by user

 
  Syntax:	 fit [model number] [sele|back|heavy ..]  

  Fits sets of coordinates (selected, backbone, heavy..) defined at command 
  line to those of a specified model. If model is not specified, model 1 is 
  taken a the one to fit coordinates to.  At the same time gives the RMSD 
  coord for the fitting.

  Args can be none (--model 1 is taken as the one to fit--) or a model number 
  and any of selected, backbone, heavy.

   back

missing

Try to find missing atoms in model/s

 
  Syntax:  mis[ssing] [model number | all | *]

  Searches models for missing atoms. Currently PDBSTAT has a Library of atom 
  names (GenCons.Lib) which stores all atoms names in different conventions: 
  DISMAN, DIANA, X-PLOR, CONGEN, PDB. This options checks if the atom names 
  in file are in the Library and also checks if the atoms in Library are in the 
  file or some of the names are missing. (It takes into account the protonation 
  state of residues and if residue is first or last where H atoms and OXT can 
  be missing).

  The args can be model number or 'all' or '*' if the user likes to look for 
  missing atoms in *ALL* the models stored in memory.

back

noe

Commands related to NOEs (or distance restraints)

 
  Syntax:  noe | cons  < matrix | analysis | clean | to >
           noe delete < intra | seq | medium | long | ambi | side | back >

  Command used to operate in several ways over the set of distance restraints 
  (or NOEs) stored in memory.  It can take several args

    matrix   -- produces a distance matrix
    analysis -- performs some statistical analysis on the restraints 
    clean    -- cleans the set marking meaningles or duplicated restraints
    to       -- transforms the atom naming convention in the distance
                to several formats: 
                PDB        follow PDB rules
                IUPAC      IUPAC rules for atom naming
                XPLOR      XPLOR rule
                CONGEN     
                DYANA
                DIANA
                CYANA

back

set

Sets different things in the program, like atom properties, rmsd cutoff, ...

  Syntax: set [ prop | rmsd | ener | cutupl | cutaco ]

  Examples:  set rmsd  1.50
             set ener -98.0
             set prop 
      	      set cutupl 1.0     -- or  set cut_upl
      set cutaco 10.0    -- or  set cut_aco 

  This command is used to set different things in the program. The most 
  interesting ones from user point of view should be rmsd and/or energy 
  as these set the RMSD cutoff value to consider an rmsd good or bad. 
  The same comment applies for energy cutoff. If these values are set we 
  can delete for example ALL models with bad values, i.e. the following 
  sequence of commands: 
      > order 0.85 
      > rmsd best 
      > set rmsd 1.5 
      > del bad rmsd

  The example above deletes all models with rmsd values greater than 1.5

  'set prop' is used to set atom properties in the model. Usually this is 
             done at read time.

  'set thres 1.0' is used to define the threshold for printing residual 
                  distance violations

back

version

Prints version and some dimensions of the program running

 
  Syntax:  ver[sion]
           dim[ensions]
 
  Mainly it gives you some info about current dimensions for your 
  executable. You can get something looking like this:

  > MAIN: ===========> CURRENT SETS <==============
  > MAIN: -- Version Version 2.0  -   Oct, 1994 --
  > MAIN: -----------------------------------------
  > MAIN:                                      
  > MAIN:   Max. Number of models   :      61
  > MAIN:   Max. number of residues :     100
  > MAIN:   Max. number of atoms    :    1600
  > MAIN:   Max. Number of noes     :    3200
  > MAIN:   Max. Number of JCOUP    :     200
  > MAIN:                                      
  > MAIN: =========================================

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