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/