Hi all,
A few basic questions related to a simple R1 (or R2 or NOE) analysis in relax:
1) Default lists created by Sparky look like this:
Assignment w1 w2 Data Height
R1N-H 126.139 8.573 108076
Q4N-H 118.070 8.861 50515
F5N-H 119.682 7.577 111977
T6N-H 113.163 8.827 95306
R7N-H 120.731 8.903 108430
A8N-H 126.058 10.299 92981
Q9N-H 118.747 8.300 127858
W10N-H 122.375 9.005 102254
F11N-H 121.361 8.698 114173
A12N-H 122.049 8.175 59426
I13N-H 118.046 7.753 129168
Q14N-H 111.972 7.184 73155
H15N-H 106.081 7.773 119082
I16N-H 122.326 8.294 156604
S17N-H 120.624 7.734 133194
L18N-H 128.309 8.660 163834
N19N-H 115.816 8.450 241597
According to the relax manual, we need to convert lists to the following format:
Assignment w1 w2 Data Height
ARG1N-HN 126.139 8.573 108076
GLN4N-HN 118.07 8.861 50515
PHE5N-HN 119.682 7.577 111977
THR6N-HN 113.163 8.827 95306
ARG7N-HN 120.731 8.903 108430
ALA8N-HN 126.058 10.299 92981
GLN9N-HN 118.747 8.3 127858
TRP10N-HN 122.375 9.005 102254
PHE11N-HN 121.361 8.698 114173
ALA12N-HN 122.049 8.175 59426
ILE13N-HN 118.046 7.753 129168
GLN14N-HN 111.972 7.184 73155
HIS15N-HN 106.081 7.773 119082
ILE16N-HN 122.326 8.294 156604
SER17N-HN 120.624 7.734 133194
LEU18N-HN 128.309 8.66 163834
ASN19N-HN 115.816 8.45 241597
First, do we need to add any unused/unassigned residues like this or is this
irrelevant:
PRO2N-HN None None None
PRO3N-HN None None None
?
2) Does anyone have a script to automatically convert Sparky lists to the right
format for relax? This is a tedious process to run manually.
3) After modifying the sample script to run a simple R1 analysis with our own
modified Sparky lists and PDB, the 'python relax_fit.py' command yielded the
following error:
File "relax_fit.py", line 26, in <module>
pipe.create('rx', 'relax_fit')
NameError: name 'pipe' is not defined
Any idea what's going on? Are we using the command correctly?
Thanks,
Nick Doucet
--
Nicolas Doucet
Assistant Professor
INRS - Institut Armand-Frappier
University of Quebec
Institut Pasteur International Network
531 Boulevard des Prairies
Laval (Quebec) H7V 1B7 CANADA
Phone: (450) 687-5010 #4212
Fax: (450) 686-5501
Email: [email protected]
Web: http://www.profs.inrs.ca/ndoucet/
--
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