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nmr_cnstr.py
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nmr_cnstr.py
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'''
See more here: http://www.pymolwiki.org/index.php/nmr_cnstr
##############################################################################################################
# Pymol Script: For visualizing the NMR constrains (DYANA & CNS format), on top of the calculated structure. #
# Author: Evangelos Papadopoulos. #
# previous affiliation: Dept. of Biochemistry and Biophysics, #
# Arrhenius Laboratories, #
# Stockholm University #
# SE-106 91 Stockholm, Sweden #
# email:evangelos.papadopoulos@gmail.com #
# 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 #
# #
##############################################################################################################
'''
from __future__ import print_function
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 += 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 += 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)