Ccp4 pisa

Overview

The script selects atoms from the list of the contacts found by PISA. First, we run PISA on our pdb file to find the interfaces. Then by using the selectPISAContacts script in PyMOL we separately select atoms for all interface types and individual interfaces. This generates many selections, two for each interface, allowing quick manipulation of (sometimes) extensive lists in PISA log file.

Usage

selectPISAContacts( pisafile )

Examples

The script parses the XML output files from the PISA service or command line tool. A short description of how to download the XML output files is available here http://www.ebi.ac.uk/msd-srv/prot_int/pi_download.html.

(For example, the following URL downloads the interfaces in 2c7r.pdb http://www.ebi.ac.uk/pdbe/pisa/cgi-bin/interfaces.pisa?2c7r)

Make sure you've run the selectPISAContacts script first.

fetch 2c7r
selectPISAContacts interfaces_2c7r.pisa

The Code

from xml.etree import ElementTree

def parseElement( element ):
    """ creates a dict for the sub elements of the element"""
    result = { }
    for l in range(len(element)):
        if element[l].text != None:
            result[element[l].tag.strip()] = element[l].text.strip()
    return result;

def parseBond( elementDir ):
    """ puts bond information into tuples"""
    return ((elementDir['chain-1'], elementDir['seqnum-1'], elementDir['atname-1']), (elementDir['chain-2'], elementDir['seqnum-2'], elementDir['atname-2']))

def parseInterface( interface, bondname ):
    """ parses a single interface into the interface id, the two chain names connected 
        and two lists of atoms for each chain"""
    bonds = interface.findall(bondname)
    id = interface.find('id').text.strip()
    if len(bonds) == 0:
        return None
    left = []
    right = []
    for b in bonds:
        l, r = parseBond(parseElement(b))
        left.append(l)
        right.append(r)
    left_chain = left[0][0]
    right_chain = right[0][0]
    if left_chain > right_chain:
        return id, (right_chain, left_chain), right, left
    return id, (left_chain, right_chain), left, right

def createSelectionList( atomlist ):
    """creates a PYMOL selection string for a list of atoms"""
    atomnames = [chain+'/'+res+'/'+atom for chain, res, atom in atomlist]
    return " or ".join(atomnames)

def createInterfaceSelection( interface, prefix ):
    """creates two selections for an interfaces"""
    id, e, l, r = interface
    leftname = prefix+'_' + str(id) + '_' + e[0] + e[1]
    rightname = prefix+'_' + str(id) + '_' + e[1] + e[0]
    if e[0] == e[1]:
        leftname = leftname + '1'
        rightname = rightname + '2'
    leftlist = createSelectionList(l)
    rightlist = createSelectionList(r)
    try:
        cmd.select(leftname, leftlist)
        cmd.select(rightname, rightlist)
    except:
        print leftname, '\t', leftlist
        print rightname, '\t', rightlist
    return leftname, rightname

def parsePISAContacts( filename ):
    """ parse a PISA contact file and create atoms selections for all interfaces
        
        For each interface, two selections are created containing the atoms of 
        the interface on each chain. The selection names follow the convention 
        bondtype_#Id_Chain1Chain2. If Chain1 equals Chain2 then the two selections are 
        numbered. 
        
        bondtype corresponds to h-bonds, salt-bridges, ss-bonds and cov-bonds and
        are marked with the prefixes hb, sb, ss and cov.
        
        For example, all h-bonds in interface 3 between chain A and D create the selections
        hb_3_AD and hb_3_DA.
        
        Salt-bridges in interface 4 between chain A and a symmetry copy of A creates the selections
        sb_4_AA1 and sb_4_AA2.
    
    PARAMS
        filename 
            filename of the PISA contacts file
    
    RETURNS
        a set of selections in PYMOL. 

    REPOSITORY
        https://github.com/GerhardR/pymol-scripts

    AUTHOR
        Gerhard Reitmayr and Dalia Daujotyte, 2011.
    """
    
    bond_types = [
        ('h-bonds', 'h-bonds/bond', 'hb'),
        ('salt-bridges', 'salt-bridges/bond', 'sb'),
        ('ss-bonds', 'ss-bonds/bond', 'ss'),
        ('cov-bonds', 'cov-bonds/bond', 'cv')
    ]
    
    tree = ElementTree.parse(open(filename))
    interfaces = tree.findall('//interface')
    
    result = []
    for name, path, prefix in bond_types:
        allcontacts = [edge for edge in [parseInterface(i, path) for i in interfaces] if edge != None]
        
        allselections = []
        for c in allcontacts:
            allselections.extend( createInterfaceSelection(c, prefix) )
        
        result.append(len(allselections)/2)
        if len(allselections) > 0:
            try:
                cmd.select(name, " or ".join(allselections))
            except:
                print name, '\t', " or ".join(allselections)
    
    print 'selectPISAContacts found interfaces with', 
    for number, type in zip(result, bond_types):
        print number, type[0], ",",

try:
    cmd.extend("selectPISAContacts", parsePISAContacts)
except:
    # for debugging
    parsePISAContacts('../pisa/interfaces_2uz4.pisa')

Code repository

The latest version of this script and related scripts is available at https://github.com/GerhardR/pymol-scripts.