R1, R2 and/or NOE Analysis with RelaxR1, R2 and/or NOE Analysis with Relax| 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: nicolas.doucet@xxxxxxxxxxx -- |