Author: bugman
Date: Tue Sep 25 18:46:03 2012
New Revision: 17567
URL: http://svn.gna.org/viewcvs/relax?rev=17567&view=rev
Log:
Fix for bug #20197 (https://gna.org/bugs/?20197) - the PyMOL and Molmol macro
failure.
The macro creation now only operates on spins called 'N' and assumes these
are the backbone
nitrogens. The sidechain tryptophan indole NH data will need to be detected
and added later.
Modified:
trunk/specific_fns/model_free/macro_base.py
Modified: trunk/specific_fns/model_free/macro_base.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_fns/model_free/macro_base.py?rev=17567&r1=17566&r2=17567&view=diff
==============================================================================
--- trunk/specific_fns/model_free/macro_base.py (original)
+++ trunk/specific_fns/model_free/macro_base.py Tue Sep 25 18:46:03 2012
@@ -73,27 +73,6 @@
@type spin_id: str
"""
- # Test the validity of the data (only a single spin per residue).
- #################################################################
-
- # Init some variables.
- prev_res_num = None
- num = 0
-
- # Loop over the spins.
- for spin, mol_name, res_num, res_name in spin_loop(spin_id,
full_info=True):
- # No relaxation data, so skip.
- if not hasattr(spin, 'ri_data'):
- continue
-
- # More than one spin.
- if prev_res_num == res_num:
- raise RelaxError("Only a single spin per residue is allowed
for the classic macro style.")
-
- # Update the previous residue number.
- prev_res_num = res_num
-
-
# Generate the macro header.
############################
@@ -114,8 +93,9 @@
if not hasattr(spin, 's2') or spin.s2 == None:
continue
- # S2 width and colour.
- self.classic_order_param(res_num, spin.s2, colour_start,
colour_end, colour_list)
+ # S2 width and colour for the backbone NH.
+ if spin.name == 'N':
+ self.classic_order_param(res_num, spin.s2, colour_start,
colour_end, colour_list)
# S2f.
@@ -128,13 +108,15 @@
if not spin.select:
continue
- # Colour residues which don't have an S2f value white.
- if not hasattr(spin, 's2f') or spin.s2f == None:
- self.classic_colour(res_num=res_num, width=0.3,
rgb_array=[1, 1, 1])
-
- # S2f width and colour.
- else:
- self.classic_order_param(res_num, spin.s2f,
colour_start, colour_end, colour_list)
+ # The backbone NH.
+ if spin.name == 'N':
+ # Colour residues which don't have an S2f value white.
+ if not hasattr(spin, 's2f') or spin.s2f == None:
+ self.classic_colour(res_num=res_num, width=0.3,
rgb_array=[1, 1, 1])
+
+ # S2f width and colour.
+ else:
+ self.classic_order_param(res_num, spin.s2f,
colour_start, colour_end, colour_list)
# S2s.
@@ -147,13 +129,15 @@
if not spin.select:
continue
- # Colour residues which don't have an S2s value white.
- if not hasattr(spin, 's2s') or spin.s2s == None:
- self.classic_colour(res_num=res_num, width=0.3,
rgb_array=[1, 1, 1])
-
- # S2s width and colour.
- else:
- self.classic_order_param(res_num, spin.s2s,
colour_start, colour_end, colour_list)
+ # The backbone NH.
+ if spin.name == 'N':
+ # Colour residues which don't have an S2s value white.
+ if not hasattr(spin, 's2s') or spin.s2s == None:
+ self.classic_colour(res_num=res_num, width=0.3,
rgb_array=[1, 1, 1])
+
+ # S2s width and colour.
+ else:
+ self.classic_order_param(res_num, spin.s2s,
colour_start, colour_end, colour_list)
# Amplitude of fast motions.
@@ -172,25 +156,27 @@
else:
model = spin.model
- # S2f width and colour (for models m5 to m8).
- if hasattr(spin, 's2f') and spin.s2f != None:
- self.classic_order_param(res_num, spin.s2f,
colour_start, colour_end, colour_list)
-
- # S2 width and colour (for models m1 and m3).
- elif model == 'm1' or model == 'm3':
- self.classic_order_param(res_num, spin.s2, colour_start,
colour_end, colour_list)
-
- # S2 width and colour (for models m2 and m4 when te <= 200
ps).
- elif (model == 'm2' or model == 'm4') and spin.te <= 200e-12:
- self.classic_order_param(res_num, spin.s2, colour_start,
colour_end, colour_list)
-
- # White bonds (for models m2 and m4 when te > 200 ps).
- elif (model == 'm2' or model == 'm4') and spin.te > 200e-12:
- self.classic_colour(res_num=res_num, width=0.3,
rgb_array=[1, 1, 1])
-
- # Catch errors.
- else:
- raise RelaxFault
+ # The backbone NH.
+ if spin.name == 'N':
+ # S2f width and colour (for models m5 to m8).
+ if hasattr(spin, 's2f') and spin.s2f != None:
+ self.classic_order_param(res_num, spin.s2f,
colour_start, colour_end, colour_list)
+
+ # S2 width and colour (for models m1 and m3).
+ elif model == 'm1' or model == 'm3':
+ self.classic_order_param(res_num, spin.s2,
colour_start, colour_end, colour_list)
+
+ # S2 width and colour (for models m2 and m4 when te <=
200 ps).
+ elif (model == 'm2' or model == 'm4') and spin.te <=
200e-12:
+ self.classic_order_param(res_num, spin.s2,
colour_start, colour_end, colour_list)
+
+ # White bonds (for models m2 and m4 when te > 200 ps).
+ elif (model == 'm2' or model == 'm4') and spin.te >
200e-12:
+ self.classic_colour(res_num=res_num, width=0.3,
rgb_array=[1, 1, 1])
+
+ # Catch errors.
+ else:
+ raise RelaxFault
# Amplitude of slow motions.
@@ -209,17 +195,19 @@
else:
model = spin.model
- # S2 width and colour (for models m5 to m8).
- if hasattr(spin, 'ts') and spin.ts != None:
- self.classic_order_param(res_num, spin.s2, colour_start,
colour_end, colour_list)
-
- # S2 width and colour (for models m2 and m4 when te > 200
ps).
- elif (model == 'm2' or model == 'm4') and spin.te > 200 *
1e-12:
- self.classic_order_param(res_num, spin.s2, colour_start,
colour_end, colour_list)
-
- # White bonds for fast motions.
- else:
- self.classic_colour(res_num=res_num, width=0.3,
rgb_array=[1, 1, 1])
+ # The backbone NH.
+ if spin.name == 'N':
+ # S2 width and colour (for models m5 to m8).
+ if hasattr(spin, 'ts') and spin.ts != None:
+ self.classic_order_param(res_num, spin.s2,
colour_start, colour_end, colour_list)
+
+ # S2 width and colour (for models m2 and m4 when te >
200 ps).
+ elif (model == 'm2' or model == 'm4') and spin.te > 200
* 1e-12:
+ self.classic_order_param(res_num, spin.s2,
colour_start, colour_end, colour_list)
+
+ # White bonds for fast motions.
+ else:
+ self.classic_colour(res_num=res_num, width=0.3,
rgb_array=[1, 1, 1])
# te.
#####
@@ -235,8 +223,9 @@
if not hasattr(spin, 'te') or spin.te == None:
continue
- # te width and colour.
- self.classic_correlation_time(res_num, spin.te,
colour_start, colour_end, colour_list)
+ # te width and colour (backbone NH).
+ if spin.name == 'N':
+ self.classic_correlation_time(res_num, spin.te,
colour_start, colour_end, colour_list)
# tf.
@@ -253,8 +242,9 @@
if not hasattr(spin, 'tf') or spin.tf == None:
continue
- # tf width and colour.
- self.classic_correlation_time(res_num, spin.tf,
colour_start, colour_end, colour_list)
+ # tf width and colour (backbone NH).
+ if spin.name == 'N':
+ self.classic_correlation_time(res_num, spin.tf,
colour_start, colour_end, colour_list)
# ts.
@@ -277,8 +267,9 @@
if colour_end == None:
colour_end = 'black'
- # ts width and colour.
- self.classic_correlation_time(res_num, spin.ts / 10.0,
colour_start, colour_end, colour_list)
+ # ts width and colour (backbone NH).
+ if spin.name == 'N':
+ self.classic_correlation_time(res_num, spin.ts / 10.0,
colour_start, colour_end, colour_list)
# Timescale of fast motions.
@@ -297,18 +288,20 @@
else:
model = spin.model
- # tf width and colour (for models m5 to m8).
- if hasattr(spin, 'tf') and spin.tf != None:
- self.classic_correlation_time(res_num, spin.tf,
colour_start, colour_end, colour_list)
-
- # te width and colour (for models m2 and m4 when te <= 200
ps).
- elif (model == 'm2' or model == 'm4') and spin.te <= 200e-12:
- self.classic_correlation_time(res_num, spin.te,
colour_start, colour_end, colour_list)
-
- # All other residues are assumed to have a fast correlation
time of zero (statistically zero, not real zero!).
- # Colour these bonds white.
- else:
- self.classic_colour(res_num=res_num, width=0.3,
rgb_array=[1, 1, 1])
+ # The backbone NH.
+ if spin.name == 'N':
+ # tf width and colour (for models m5 to m8).
+ if hasattr(spin, 'tf') and spin.tf != None:
+ self.classic_correlation_time(res_num, spin.tf,
colour_start, colour_end, colour_list)
+
+ # te width and colour (for models m2 and m4 when te <=
200 ps).
+ elif (model == 'm2' or model == 'm4') and spin.te <=
200e-12:
+ self.classic_correlation_time(res_num, spin.te,
colour_start, colour_end, colour_list)
+
+ # All other residues are assumed to have a fast
correlation time of zero (statistically zero, not real zero!).
+ # Colour these bonds white.
+ else:
+ self.classic_colour(res_num=res_num, width=0.3,
rgb_array=[1, 1, 1])
# Timescale of slow motions.
@@ -333,17 +326,19 @@
if colour_end == None:
colour_end = 'black'
- # ts width and colour (for models m5 to m8).
- if hasattr(spin, 'ts') and spin.ts != None:
- self.classic_correlation_time(res_num, spin.ts / 10.0,
colour_start, colour_end, colour_list)
-
- # te width and colour (for models m2 and m4 when te > 200
ps).
- elif (model == 'm2' or model == 'm4') and spin.te > 200e-12:
- self.classic_correlation_time(res_num, spin.te / 10.0,
colour_start, colour_end, colour_list)
-
- # White bonds for the rest.
- else:
- self.classic_colour(res_num=res_num, width=0.3,
rgb_array=[1, 1, 1])
+ # The backbone NH.
+ if spin.name == 'N':
+ # ts width and colour (for models m5 to m8).
+ if hasattr(spin, 'ts') and spin.ts != None:
+ self.classic_correlation_time(res_num, spin.ts /
10.0, colour_start, colour_end, colour_list)
+
+ # te width and colour (for models m2 and m4 when te >
200 ps).
+ elif (model == 'm2' or model == 'm4') and spin.te >
200e-12:
+ self.classic_correlation_time(res_num, spin.te /
10.0, colour_start, colour_end, colour_list)
+
+ # White bonds for the rest.
+ else:
+ self.classic_colour(res_num=res_num, width=0.3,
rgb_array=[1, 1, 1])
# Rex.
@@ -356,13 +351,15 @@
if not spin.select:
continue
- # Residues which chemical exchange.
- if hasattr(spin, 'rex') and spin.rex != None:
- self.classic_rex(res_num, spin.rex, colour_start,
colour_end, colour_list)
-
- # White bonds for the rest.
- else:
- self.classic_colour(res_num=res_num, width=0.3,
rgb_array=[1, 1, 1])
+ # The backbone NH.
+ if spin.name == 'N':
+ # Residues which chemical exchange.
+ if hasattr(spin, 'rex') and spin.rex != None:
+ self.classic_rex(res_num, spin.rex, colour_start,
colour_end, colour_list)
+
+ # White bonds for the rest.
+ else:
+ self.classic_colour(res_num=res_num, width=0.3,
rgb_array=[1, 1, 1])
# Unknown data type.
r17567 - /trunk/specific_fns/model_free/macro_base.py