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
<[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>
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