Hi Maddy, Welcome to the relax mailing lists. This bug has been encountered before and was submitted as a bug report (https://gna.org/bugs/?14885) by Tiago Pais (tpais att itqb dott unl dott pt). I have fixed this bug but not released a new relax version yet with this fix. However you can download the new version of the script from http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/mf_multimodel.py?rev=10090&view=log (this is in comment #2 of the bug report). If you are new to this, then I would recommend using the 'full_analysis.py' script. This implements all of the new ideas and improvements in my 2 papers:
d'Auvergne, E. J. and Gooley, P. R. (2008). Optimisation of NMR dynamic models I. Minimisation algorithms and their performance within the model-free and Brownian rotational diffusion spaces. J. Biomol. NMR, 40(2), 107-119. (http://dx.doi.org/10.1007/s10858-007-9214-2) d'Auvergne, E. J. and Gooley, P. R. (2008). Optimisation of NMR dynamic models II. A new methodology for the dual optimisation of the model-free parameters and the Brownian rotational diffusion tensor. J. Biomol. NMR, 40(2), 121-133. (http://dx.doi.org/10.1007/s10858-007-9213-3) (actually it implements everything from my papers listed at http://www.nmr-relax.com/refs.html). Note the 'mf_multimodel.py' script only optimises the model-free models. It does not perform a full model-free analysis. For this you need multiple iterations (6 to 15 times) of model-free optimisation, model-free model elimination, model-free model selection, and then diffusion tensor optimisation. The 'full_analysis.py' script does all of this automatically for you. For this, multiple field strength data is a necessity, but that is what the biggest names in dynamics have been saying for years - single field strength data does not make the cut anymore. I hope this helps. Regards, Edward On 5 February 2010 17:44, M Strickland <[email protected]> wrote: > >> Dear mailing list, >> >> I am a new user of Relax and new to the field of dynamics as well. At the >> moment I am trying to run the multimodel.py script myself, but am having >> trouble getting relax to caluculate the m6 model. It will calculate the >> m0 to m5 models, but then an error message comes up for model 6. >> >> relax> pipe.create(pipe_name='m6', pipe_type='mf') >> >> relax> sequence.read(file='sequence.out', dir=None, mol_name_col=None, >> res_num_col=0, res_name_col=1, spin_num_col=None, spin_name_col=2, >> sep=None) >> Opening the file 'sequence.out' for reading. >> Mol_name Res_num Res_name Spin_num Spin_name >> None 1510 Ser None N >> None 1511 Asn None N >> None 1512 Glu None N >> None 1513 His None N >> None 1514 Asp None N >> None 1515 Asp None N >> None 1516 Cys None N >> None 1517 Gln None N >> None 1518 Val None N >> None 1519 Thr None N >> None 1520 Asn None N >> None 1521 Pro None N >> None 1522 Ser None N >> None 1523 Thr None N >> None 1524 Gly None N >> None 1525 His None N >> None 1526 Leu None N >> None 1527 Phe None N >> None 1528 Asp None N >> None 1529 Leu None N >> None 1530 Ser None N >> None 1531 Ser None N >> None 1532 Leu None N >> None 1533 Ser None N >> None 1534 Gly None N >> None 1535 Arg None N >> None 1536 Ala None N >> None 1537 Gly None N >> None 1538 Phe None N >> None 1539 Thr None N >> None 1540 Ala None N >> None 1541 Ala None N >> None 1542 Tyr None N >> None 1543 Ser None N >> None 1544 Glu None N >> None 1545 Lys None N >> None 1546 Gly None N >> None 1547 Leu None N >> None 1548 Val None N >> None 1549 Tyr None N >> None 1550 Met None N >> None 1551 Ser None N >> None 1552 Ile None N >> None 1553 Cys None N >> None 1554 Gly None N >> None 1555 Glu None N >> None 1556 Asn None N >> None 1557 Glu None N >> None 1558 Asn None N >> None 1559 Cys None N >> None 1560 Pro None N >> None 1561 Pro None N >> None 1562 Gly None N >> None 1563 Val None N >> None 1564 Gly None N >> None 1565 Ala None N >> None 1566 Cys None N >> None 1567 Phe None N >> None 1568 Gly None N >> None 1569 Gln None N >> None 1570 Thr None N >> None 1571 Arg None N >> None 1572 Ile None N >> None 1573 Ser None N >> None 1574 Val None N >> None 1575 Gly None N >> None 1576 Lys None N >> None 1577 Ala None N >> None 1578 Asn None N >> None 1579 Lys None N >> None 1580 Arg None N >> None 1581 Leu None N >> None 1582 Arg None N >> None 1583 Tyr None N >> None 1584 Val None N >> None 1585 Asp None N >> None 1586 Gln None N >> None 1587 Val None N >> None 1588 Leu None N >> None 1589 Gln None N >> None 1590 Leu None N >> None 1591 Val None N >> None 1592 Tyr None N >> None 1593 Lys None N >> None 1594 Asp None N >> None 1595 Gly None N >> None 1596 Ser None N >> None 1597 Pro None N >> None 1598 Cys None N >> None 1599 Pro None N >> None 1600 Ser None N >> None 1601 Lys None N >> None 1602 Ser None N >> None 1603 Gly None N >> None 1604 Leu None N >> None 1605 Ser None N >> None 1606 Tyr None N >> None 1607 Lys None N >> None 1608 Ser None N >> None 1609 Val None N >> None 1610 Ile None N >> None 1611 Ser None N >> None 1612 Phe None N >> None 1613 Val None N >> None 1614 Cys None N >> None 1615 Arg None N >> None 1616 Pro None N >> None 1617 Glu None N >> None 1618 Ala None N >> None 1619 Gly None N >> None 1620 Pro None N >> None 1621 Thr None N >> None 1622 Asn None N >> None 1623 Arg None N >> None 1624 Pro None N >> None 1625 Met None N >> None 1626 Leu None N >> None 1627 Ile None N >> None 1628 Ser None N >> None 1629 Leu None N >> None 1630 Asp None N >> None 1631 Lys None N >> None 1632 Gln None N >> None 1633 Thr None N >> None 1634 Cys None N >> None 1635 Thr None N >> None 1636 Leu None N >> None 1637 Phe None N >> None 1638 Phe None N >> None 1639 Ser None N >> None 1640 Trp None N >> None 1641 His None N >> None 1642 Thr None N >> None 1643 Pro None N >> None 1644 Leu None N >> None 1645 Ala None N >> None 1646 Cys None N >> None 1647 Glu None N >> None 1648 Gln None N >> None 1649 Ala None N >> None 1650 Thr None N >> None 1651 Lys None N >> None 1652 Glu None N >> None 1653 His None N >> >> relax> structure.read_pdb(file='structure.pdb', dir=None, read_mol=None, >> set_mol_name=None, read_model=None, set_model_num=None, parser='internal') >> >> Internal relax PDB parser. >> Opening the file 'structure.pdb' for reading. >> Adding molecule 'structure_mol1' to model None (from the original molecule >> number 1 of model None) >> >> relax> relax_data.read(ri_label='R1', frq_label='600', frq=600000000.0, >> file='R1.out', dir=None, mol_name_col=None, res_num_col=0, res_name_col=1, >> spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None) >> Opening the file 'R1.out' for reading. >> >> relax> relax_data.read(ri_label='R2', frq_label='600', frq=600000000.0, >> file='R2.out', dir=None, mol_name_col=None, res_num_col=0, res_name_col=1, >> spin_num_col=None, spin_name_col=None, data_col=2, error_col=3, sep=None) >> Opening the file 'R2.out' for reading. >> >> relax> relax_data.read(ri_label='NOE', frq_label='600', frq=600000000.0, >> file='NOE.out', dir=None, mol_name_col=None, res_num_col=0, >> res_name_col=1, spin_num_col=None, spin_name_col=None, data_col=2, >> error_col=3, sep=None) >> Opening the file 'NOE.out' for reading. >> >> relax> diffusion_tensor.init(params=1e-08, time_scale=1.0, d_scale=1.0, >> angle_units='deg', param_types=0, spheroid_type=None, fixed=True) >> >> relax> value.set(val=1.0200000000000001e-10, param='bond_length', >> spin_id=None) >> >> relax> value.set(val=-0.00017199999999999998, param='csa', spin_id=None) >> >> relax> value.set(val='15N', param='heteronucleus', spin_id=None) >> >> relax> value.set(val='1H', param='proton', spin_id=None) >> >> relax> model_free.select_model(model='m6', spin_id=None) >> >> relax> grid_search(lower=None, upper=None, inc=11, constraints=True, >> verbosity=1) >> RelaxError: All parameters are fixed. >> >> >> ------------------------------------------------------------------------------------------------------------------------------------------- >> >> Any ideas? Should I be setting the spin id? I don't understand why model >> 6 is the problem in particular. >> >> I'd be very grateful if you could help me out - I feel a bit overwhelmed! >> >> Maddy Strickland >> >> (University of Bristol, 2nd year PhD) >> >> > > > > > -- > > > > _______________________________________________ > relax (http://nmr-relax.com) > > This is the relax-users mailing list > [email protected] > > To unsubscribe from this list, get a password > reminder, or change your subscription options, > visit the list information page at > https://mail.gna.org/listinfo/relax-users > _______________________________________________ relax (http://nmr-relax.com) This is the relax-users mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-users
