Nmr cnstr

This script will display the NMR constrains used for a structure calculation atop a structure. Usage: Save this as "NMRcnstr.py" load your protein in PyMOL, and run the script. type upl('fname') or cns('fname') where fname is the filename with the NMR constrains you want to display. It is still a very preliminary version.

##############################################################################################################
# Pymol Script: For visualizing the NMR constrains (DYANA & CNS format), on top of the calculated structure. #
#               Author: Evangelos Papadopoulos.                                                              #
#  current affiliation: Dept. of Biochemistry and Biophysics,                                                #
#                       Arrhenius Laboratories,                                                              #
#                       Stockholm University                                                                 #
#                       SE-106 91 Stockholm, Sweden                                                          #
#                email:evangelos@dbb.su.se   tel: +468164580                                                 #
#                NOTES: This is a preliminary version.   
#
#     '''Reference:''' please if you find this script usefull add the following reference:
#     NMR Solution Structure of the Peptide Fragment 1-30, Derived from Unprocessed Mouse Doppel  
#     Protein, in DHPC Micelles. Biochemistry. 2006 Jan 10;45(1):159-166. PMID: 16388591
#      
##############################################################################################################



def upl(fname):

	f=open(fname,'r')
	i=1
	upl=f.readline()
#
	while upl<>'':
	
		print upl,i
		cns=string.split(upl)
		cmd.dist('upl'+str(i),'i. '+cns[0]+' & n. '+cns[2],'i. '+cns[3]+' & n. '+cns[5])
		upl=f.readline()
		i=i+1
#
	f.close()
	cmd.hide('labels')
	cmd.set ('dash_gap', 0.05)
	cmd.do ("orient")
	cmd.set ('movie_delay', 1500)

def cns(fname):

	f=open(fname,'r')
	i=1
	upl=f.readline()
	print upl,i
	while upl<>'':
		if upl=='\n': 
			upl=f.readline()
			continue
		cns=string.split(upl)
		print cns,i
		if cns[0]=='assign' : 
			print 'CNS'
			if cns[5]=='HB*': print 'CNS***'
			cmd.dist('upl'+str(i),'i. '+cns[2]+' & n. '+cns[5],'i. '+cns[7]+' & n. '+cns[10])
		i=i+1
		upl=f.readline()
		print '*'+upl+'*',i
	
	f.close()
	cmd.set ('dash_gap', 0.05)
	cmd.hide('labels')
	cmd.do ("orient")
	cmd.set ('movie_delay', 1500)