Re: [bug #11476] Model "m0" instances break the minimise() functionRe: [bug #11476] Model "m0" instances break the minimise() function|
Hi Ed, Cool ! This is really an elegant bug fix ! I tried it on my small dataset (the one in the bug report) and it worked fine as for you. I also tried it on a bigger dataset for the final run and it was also fine : simulations are made for every residues before or after encountering model "m0" and errors for residues following the one with model "m0" are now much more realistic... I'll try to be aware of any bug this change could have introduced, but as of now, it seems FINE. Thanks for solving this bug so quickly !!!!! Cheers, ! Séb :) Edward d'Auvergne wrote: 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 <NO-REPLY.INVALID-ADDRESS@xxxxxxx> 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 relax-devel@xxxxxxx 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 |