Seb, I've come up with a simple fix for this bug. The files attached to the bug report were perfect for debugging this! Thank you so much! Normally it would have taken me hours to find the problem, instead because of these files it took less than 5 min!!! However before I make a new relax release, would you be able to check that the bug has been fixed in you full data set? It seems resolved in the data files attached to the report, but I just want to be completely sure.
Cheers, Edward On Fri, Apr 11, 2008 at 7:39 PM, Sébastien Morin <[EMAIL PROTECTED]> wrote: > > URL: > <http://gna.org/bugs/?11476> > > Summary: Model "m0" instances break the minimise() function > Project: relax > Submitted by: semor > Submitted on: Friday 04/11/2008 at 13:39 > Category: relax's source code > Severity: 6 - Security > Priority: 9 - Immediate > Status: None > Privacy: Public > Assigned to: None > Originator Name: > Originator Email: > Open/Closed: Open > Discussion Lock: Any > Release: Repository: 1.2 line > Operating System: GNU/Linux > > _______________________________________________________ > > Details: > > Hi, > > This bug was found as a result of digging into bug 11454 (Constraint > incorrectly supplied when using the "full_analysis.py" script) > > I had a look at some "final" run with 500 simulations and found out > something. > > The simulations are affected by a break of the minimise() function when > encountering model "m0" for a given residue... > > See, for example, errors for S2 for residues before residue 218 (for which > "m0" was chosen) and after this residue. Before the residue, errors in S2 are > fine, but after they are excessively small... > > ============================== > ... > 216 val 1 error N m7 ... 0.031361478644779991 > 217 thr 1 error N m7 ... 0.038211292618960502 > 218 gly 1 error N m0 ... None > 219 asn 1 error N m1 ... 1.112698441354078e-15 > 220 leu 1 error N m3 ... 3.2268254799268261e-15 > ... > ============================== > > If we have a look at some simulations, for example simulations 1, 2 and 3 : > > ============================== > ... > 216 val 0 sim_1 N m7 ... 0.78494175630280139 > 217 thr 0 sim_1 N m7 ... 0.82059932724210649 > 218 gly 0 sim_1 N m0 ... None > 219 asn 0 sim_1 N m1 ... 0.9225077650606851 > 220 leu 0 sim_1 N m3 ... 0.84861925081698242 > ... > 216 val 1 sim_2 N m7 ... 0.81063701088779105 > 217 thr 1 sim_2 N m7 ... 0.8206973815627201 > 218 gly 1 sim_2 N m0 ... None > 219 asn 1 sim_2 N m1 ... 0.9225077650606851 > 220 leu 1 sim_2 N m3 ... 0.84861925081698242 > ... > 216 val 1 sim_3 N m7 ... 0.83600457272281326 > 217 thr 1 sim_3 N m7 ... 0.81752904637249857 > 218 gly 1 sim_3 N m0 ... None > 219 asn 1 sim_3 N m1 ... 0.9225077650606851 > 220 leu 1 sim_3 N m3 ... 0.84861925081698242 > ... > ============================== > > we see that simulated values vary for residues before 218 (with model "m0"), > but never vary (obviously are not simulated) for residues following this > first instance of model "m0" in the sequence. > > In the log file, the error is seen as "The constraints have been incorrectly > supplied." as in bug 11454. > > Joined is a simple reproduction kit for the bug. This includes a short > script, a "ellipsoid.bz2" file to initiate the simulations, a small pdb file > and several results files (log, saved state, results). > > This bug is a really serious one. > > > > > _______________________________________________________ > > File Attachments: > > > ------------------------------------------------------- > Date: Friday 04/11/2008 at 13:39 Name: ellipsoid.bz2 Size: 2kB By: semor > > <http://gna.org/bugs/download.php?file_id=4179> > ------------------------------------------------------- > Date: Friday 04/11/2008 at 13:39 Name: log__final.bz2 Size: 2kB By: semor > > <http://gna.org/bugs/download.php?file_id=4180> > ------------------------------------------------------- > Date: Friday 04/11/2008 at 13:39 Name: full_analysis.py Size: 2kB By: > semor > > <http://gna.org/bugs/download.php?file_id=4181> > ------------------------------------------------------- > Date: Friday 04/11/2008 at 13:39 Name: results.bz2 Size: 53kB By: semor > > <http://gna.org/bugs/download.php?file_id=4182> > > _______________________________________________________ > > Reply to this item at: > > <http://gna.org/bugs/?11476> > > _______________________________________________ > Message sent via/by Gna! > http://gna.org/ > > > _______________________________________________ > relax (http://nmr-relax.com) > > This is the relax-devel 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-devel > _______________________________________________ relax (http://nmr-relax.com) This is the relax-devel 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-devel
