PdbStat

Introduction

The PdbStat program, written and actively developed by our colleague Roberto Tejero (Universita de Valencia), is routinely used in the Montelione lab for the analysis, conversion, and manipulation of coordinate and constraint files for protein structure determination. The program is also an integral component of the Protein Structure Validation Software package [1] used across the NESG consortium.

The current version of the software is PdbStat 5.1 (July, 2008). There is no separate publication for PdbStat; we cite this program using Bhattacharya et al, 2007 [1]. Also, there is no official manual for the program. Below are a number of basic stand-alone PdbStat commands and common uses. Going forward, we can continue to add to this document as more applications are developed.

Anyone interested in obtaining the latest version of PdbStat can contact Roberto at: roberto.tejero@uv.es

Commands and Applications

Starting the program

    pdbstat

Menu of Commands

menu gives a list of commands and keywords recognized by PdbStat (also get this using the command: help command)

Here are the recognized PdbStat commands for version 5.1:

PdbStat> menu

Commands/Keywords currently recognized by PDBSTAT

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

   align     analyze     author      bye         class
   clear     close       chain       check       chiral
   delete    debug       dump        energy      evaluate 
   find      fit         fix         get         help
   history   hydrogen    hyper       kabsch      ident/chain
   info      initialize  log/change  load        menu
   missing   order       phi         quit        rama
   read      relax       reset       restore     rotate
   save      see         set         show        rmsd
   to        trans       version     what        write

  homology commands: 
   get      change       homology    homa

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

Help documents for specific commands

Each command has a short help document describing its usage and options.
Syntax:
help {topic} {subtopic}

Example: PdbStat> help read

Read Syntax: rea[d] {<arg1>} {<arg2>} {<arg3>}

        arg1 can be:  coo[rdinates] or con[straints] or seq[uence]
        arg2 can be:  pdb or con[gen] or cha[rmm] or dis[man]
        arg3 can be:  the name of the file.

        Examples:   read coord pdb filename.pdb
                    read seq filename
                    read cons congen filename
                    read cons diana filename

Read coordinates/constraints/sequence in specified format from file. This 
command is able to open the file read it locating the number of structures 
stored and then read them.

The user needs to type only <read> then a interactive cycle with questions
begins. The program offers the different formats available, so after read
is typed the program offers <coords/cons/seq> and then after that the
program offers the different formats <pdb,disman,....> 

Preparation of final CNS coordinates for PDB deposition

Before we deposit our final coordinates we would like to order our models in order of lowest conformation energy. Also, we want to perform backbone superposition of the coordinates using ordered [S(phi) + S(psi) > 1.8] residues only. Finally, we want to rotate the ensemble to a desired orientation, which will be the orientation that appears when a user downloads our coordinates from the Protein Data Bank (www.rcsb.org). The final coordinates are saved in the original (CNS) format and IUPAC format for RPF analysis [2].

To prepare the final coordinates file for PDB deposition use the following protocol:

PdbStat:

  rea coo pdb [filename]	             #read file with concatenated CNS pdb files
  all					     #select all the models
  class				             #classify the models by energy
  order 0.9			             #determine ordered residues; phi/psi cut-off 0.9
  rmsd best backbone	        	     #backbone rmsd
  [return]			             #creates an rmsd output file
  write coo pdb [overlayed file]	     #write overlayed coordinates 

Next, open the overlayed coordinates in Molmol and get the desired rotation. Use writetransform command to write the rotation matrix to a file.
Back in PdbStat:

  rea coo pdb [overlayed.pdb]                #read the overlayed coordinates  (all models)
  rotate file [filename]		      #apply rotation matrix
  write coo pdb [final.pdb]		      #write new coordinates
  to iupac				      #converts atom nomenclature to IUPAC
  write coo pdb [final_iupac.pdb]             #write IUPAC coordinates for RPF analysis 

Selecting specific models / residues / atoms.

A powerful option in PdbStat is the ability to select specific residues and/or atoms for further analysis. This is extremely useful for superposition and RMSD evaluation of selected residues/atoms.
Syntax and Examples:

#syntax
    sel[ect]  {model(s)}    {residue(s)}   {atom(s)}                
#select backbone atoms of residues 5-25,30-50 in models 1,3-5,7-10
    sele  1,3-5,7-10  5-25,30-50  backbone           
#select N,C,CA,O atoms of residues 5-50 in all models 
    sele  *  5-50  n,c,ca,o                                  
#combine selection with superposition  
    sele  *  5-50,60-85  *
    rmsd sele backbone

Conversion of coordinate and constraint formats

In the course of a structure refinement we regularly have to convert between different coordinate and constraint formats for different structure programs (i.e., CYANA, XPLOR/CNS, ECEPP). We routinely use PdbStat for this.
Examples:

# converting CYANA to XPLOR/CNS coordinates:
   rea coor pdb [CYANA.pdb]             #read CYANA models (all)
   to xplor                             #converts to xplor; fixes stereospecfic labels 
   write                                #answer questions
        > WRITER: Output file name ?:_  4cns.pdb
        > WRITER: Coords, constraints, aco or sequence file? :_  coor
        > WRITER: ... backbone, heavy, full set? (back/heavy/all/select): all
        > WRITER: What model ?_ : all
        > WRITER:  --  All models to be written 
        > COORD_writer: Format  (pdb/congen/RasMol) ? : pdb   
# converting CYANA to XPLOR/CNS distance constraints:
    rea coor pdb [CYANA.pdb]            #read CYANA models; you have to read in a pdb or sequence file before the constraints
    rea cons cyana [CYANA.upl]          #read CYANA upls file
    write                               #write to CNS format; add 10% to upper bound; make lower bound van der Waals (1.8 A)
        > WRITER: Output file name ?:_  4cns_noe.tbl 
        > WRITER: Coords, constraints, aco or sequence file? :_  cons
        > WRITER_constr: Output format 
               [congen|discover|ecepp|disman|dyana|cyana|diana|xplor|cns]? : cns
        > XPLOR_writer: percentage range for upper bound (upp+range)?: 10
        > XPLOR_writer: range for lower bound (low-range)?: vdw
        > XPLOR_writer: ... writing ... wait 
# converting CYANA to XPLOR/CNS dihedral constraints:
     rea aco cyana [CYANA.aco]
     write
         > WRITER: Output file name ?:_  4cns_dihe.tbl
         > WRITER: Coords, constraints, aco or sequence file? :_  aco              
         > WRITER_constr: Output format (congen | discover | impact | disman | diana | xplor | cns)? : cns

Constraint Violations

One can analyze constraint violations using PdbStat. It is best to convert the coordinates and constraints to IUPAC format; this is the approach used internally within PSVS.
Commands:

   rea coo pdb [filename]
   to iupac                            #convert coordinates to IUPAC format
   rea cons [format] [filename]        #read distance constraints; specify format
   noe to iupac                        #convert distance constraints to IUPAC
   rea aco [format] [filename]         #read dihedral constraints; specify format
   set cutu 0.2                        #set cut-off for distance violations to 0.2 A
   see viol noe [sum/ave/center]       #see noe violations using sum/average/center averaging
   see cutaco 1                        #set cut-off for dihedral violations to 1 deg.
   see viol aco                        #see dihedral violations above threshold 

Sorting of Distance Constraints

There are a number of options in PdbStat for sorting or culling distance constraints.

   cons clean                    #keep conformationally-restricting constraints; also removes duplicates
   noe analysis                  #NOE statistics (as in PSVS)
   noe delete intra              #delete all intra NOE constraints
   noe keep long                 #keep only long range (||i-j|| >/= 5) NOE constraints
   noe keep ilv                  #keep NOE constraints consistent with ILV labeling 

Commands for Obtaining Various Metrics

The “eval”, “show”, and “see” commands allow one to evaluate several types of metrics in a structure or ensemble.

   eval [procheck/rama]                #get Procheck/Ramachandran statistics for model(s)
   eval dist * 68 sg 119 nd1           #get 68-SG to 119-ND1 distance across all models
   eval [phi || psi || omega] 1        #get phi/psi/omega torsion angles in model 1
   see lib [residue]                   #see library definitions for residue type
   select 1 119 *                      #use select and see in tandem
   see coo                             #coordinates for residue 119 in model 1 

Other Functions

   # renumbering / resetting residue numbering
     reset * 10                          #sets first residue in file to 10
     reset *                             #resets coordinates to original
   # ordering ensemble using FindCore algorithm [3]:
     find [ -bb || -heavy || -all || -noe ]
   # contact map generation based on coordinates or constraints
      contact
        > DRAW_cntct: from coordinates or constraints (coor/cons) ?:_ coor
        > MAIN_cntct: What model do you want (1-20) or average ?_ :ave
        > do_average_coords(): Making average for backbone atoms 
        > do_average_coords(): Calculating center of masses 
        > do_average_coords(): Calling optimal rotation for backbone 
        > do_average_coords(): Calc. average coordinates backbone 
        > MAIN_cntct: distance cutoff ?:_   4.5
        > MAIN_cntct: atom type (hydr, heavy, all) ?:_  hydr                   #writes a postscript file 

Updates

Version 5.4

Several new functions have been added to PdbStat and a new version of the program (PdbStat 5.4) was released in April 2011.  Below is a summary of new functions added to the program.

1.  Reading and analyzing residual dipolar couplings.

Example:

# reading two rdc files in cyana format (i.e., after a CYANA 3.0 structure calculation with RDCs):

   rea rdc cyana [file1.rdc]            #read CYANA rdc file #1
   rea rdc cyana [file2.rdc]            #read CYANA rdc file #2
   set nmedia 2                         #set the number of media to 2         
   eval dar                             #get Da and R for each media   
   #now write the rdc constraints out in CNS format   
   write dar 1   
   write dar 2   
   write rdc cns [filename_rdc1.tbl] 1
   write rdc cns [filename_rdc2.tbl] 2

2.  Reading and converting hydrogen bond constraints.

Example:

# reading hydrogen bond constraints in CYANA format and converting to CNS:

   rea coo pdb final.pdb                  #read CYANA pdb file
   rea upl cyana hbonds.upl               #read CYANA hbonds upl file
   rea lol cyana hbonds.lol               #read CYANA hbonds lol file         
   write cons cns [filename_hbond.tbl]    #write hbond constraints in CNS format

3.  Reading and converting metal ion constraints.

Example:

# reading metal ion constraints in CYANA format and converting to CNS:

   rea coo pdb final.pdb                  #read CYANA pdb file
   rea upl cyana metal.upl                #read CYANA metal ion upl file
   rea lol cyana metal.lol                #read CYANA metal ion lol         
   write cons cns [filename_metal.tbl]    #write metal ion constraints in CNS format

References

1. Bhattacharya, A., Tejero, R., and Montelione, G. T. (2007) Evaluating protein structures determined by structural genomics consortia. Proteins 66, 778-795.
2. Huang, Y. J., Powers, R., and Montelione, G.T. (2005) Protein NMR Recall, Precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics. J. Am. Chem. Soc. 127, 1665-1674.
3. Snyder, D. A. and Montelione, G. T. (2005) Clustering algorithms for identifying core atom sets and for assessing the precision of protein structure ensembles. Proteins 59, 673-686.