Pyadmin: 7 revisions

2014-03-28T01:42:58Z

7 revisions

Dalyte: Authors corrected.

2012-02-13T22:17:21Z

Authors corrected.

Tlinnet: /* Example 1 */

2012-01-15T15:01:54Z

Example 1

Tlinnet at 23:21, 13 January 2012

2012-01-13T23:21:24Z

Tlinnet: moved SelectPISAContacts to Ccp4 pisa: small letters

2011-12-14T16:55:13Z

moved SelectPISAContacts to Ccp4 pisa: small letters

Tlinnet at 16:53, 14 December 2011

2011-12-14T16:53:12Z

Show changes

Dalyte: Minor edit

2011-06-27T21:17:14Z

Minor edit

Dalyte: added new script to parse PISA output

2011-06-19T20:45:06Z

added new script to parse PISA output

New page

== 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 ==
<source lang="python">
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')
</source>

== Code repository ==

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

[[Category:Script_Library]] [[Category:ThirdParty Scripts]] [[Category:Structural Biology Scripts]]

@@ Line 2: / Line 2: @@
 |type      = script
 |filename  = ccp4_pisa.py
-|author    = [[User:Dalyte|Gerhard]]
+|author    = [[User:Dalyte|Gerhard Reitmayr and Dalia Daujotyte]]
 |license   = GPL
 }}

← Older revision		Revision as of 15:01, 15 January 2012
Line 29:		Line 29:


−	[[Category:Script_Library]] [[Category:ThirdParty Scripts]] [[Category:Structural Biology Scripts]]	+	[[Category:Script_Library]]
		+	[[Category:ThirdParty Scripts]]
		+	[[Category:Structural Biology Scripts]]
		+	[[Category:Pymol-script-repo]]

@@ Line 2: / Line 2: @@
 |type      = script
 |filename  = ccp4_pisa.py
-|author    = [[Users:Dalyte|Gerhard]]
+|author    = [[User:Dalyte|Gerhard]]
 |license   = GPL
 }}

← Older revision	Revision as of 01:42, 28 March 2014
(No difference)

← Older revision	Revision as of 16:55, 14 December 2011
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@@ Line 142: / Line 142: @@
 except:
      # for debugging
-     parsePISAContacts('../pisa/interfaces_2uz4.pisa')
+     parsePISAContacts('../pisa/interfaces_2c7r.pisa')
 </source>

Ccp4 pisa - Revision history