RE: RE: RE: Segmentation Fault during modelling with modeller6v
Subject: RE: RE: RE: Segmentation Fault during modelling with modeller6v
From: "Bozidar" <>
Date: Wed, 24 Apr 2002 04:47:56 -0400
Cc: <>, "'Andrej Sali'" <>
The problem with that one .ali file is the nature of the loops you
select/create. You have to really scrutinize that alignment, making sure
that one-residue gap insertion there is what really makes that alignment
better then some other possible arrangement.
As for the random seed: I don't think it makes any difference. Andrej
might be able to add something about this?
Sent: Wednesday, April 24, 2002 3:56 AM
Subject: re: RE: RE: Segmentation Fault during modelling with modeller6v
i started the job with SET GAP_EXTENSION = 0 0 yesterday with both
and one of the jobs has crashed againat the 100th model as well, the
is still running 450+models. The top and pir filesof the job that
I will start 10 jobs with each generating 125 models. To see if in every
the 100th model crashes. As soon as i have results I let you know. One
question about the seed, is it wise to take this randomly between -50000
-2 like -44656, -35435, -9835, - 15684, -378 ... or is it oke to take
order like -32768, - 16384, - 8192, -4096, -2048...
Thanks in advance
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On Tue Apr 23 18:03:13 2002, "Bozidar" <>
>These are the observations I got so far:
>1. Your OK job is OK with me also. It's still running (200+ models).
>2. Your crash job crashed at me as well at 99th model. What happened is
>that energy of the 100th model (which never got written out) went
>through the roof (NaN) and the system never recovered from it.
>The workaround is as follows: you can run this job in parallel. Instead
>of generating 1000 models in one run, you can start maybe 5 jobs that
>will generate 200 models each. All you need to do it to give a random
>seed number in the top files (between -50000 to -2) to each of them:
>SET RAND_SEED = -xvz
>Why this particular alignment crashes and not the other one is hard to
>say. As I mentioned in my earlier email, you are selecting 50% of your
>protein as loop region. Given the close similarity between two
>alignments, it might be that 5 vs. 4 loops results in formation of bad
>structure at some point (knots maybe), that simply collapses the
>Al least what we know is that MODELLER reports no errors and that it
>runs fine. I think that you have very specific case here, which will
>require careful modeling on your part, making sure you control each
>step of the way.
>Still, please let me know how happens with SET GAP_EXTENSION = 0 0
>Sent: Monday, April 22, 2002 3:52 AM
>Subject: re: RE: Segmentation Fault during modelling with modeller6v1
>Sorry for the delay. I send you the requested files. (ed)
>When running this top pir and pdb file the job crashes (crash.zip).
>When using another pir same top and pdb file everything goes
>oke(oke.zip). The log file a
>is included as zip file AVR4.zip in crash.zip. If there is anything
>want to know just ask.
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>- On Thu Apr 18 19:06:31 2002, "Bozidar Jerkovic"
>>1. Please send me complete set of input files plus log files and I'll
>>run it on 6v2 (not public yet) to see if it happens there.
>>2. Yes we went through this, as well. Prosa is not sensitive assessing
>>loops. Please read the comment on the use of statistical profile for
>>assessing loops, in Andras Fiser's Prot Sci 2000 loop modeling paper.
>>People should use modeller scores to rank them.
>>Sent: Tuesday, April 16, 2002 8:00 AM
>>Subject: Segmentation Fault during modelling with modeller6v1
>>I have been using modeller for 2 years now . I'm using modeller since
>>version 4. Recently I ran into a few problems maybe you can point me
>>1.) When running modeller 6V1 on a pentium III redhat 7.2 with all
>>recommended patches applied. The following problem occurred. After I
>>started a job doing loop modelling i generated 1000 models and every
>>thing went fine.
>>I changed the alignment a bit and try to run for an other 1000 models
>>crashes after 198 models. So i decided to run on a other machine,
>>one 1.7 Ghz Dual Xeon, same problem. What can be the source of the
>>The job crashes with segmentation fault error.
>>2.) I assessed the 1000 generated models with ProsaII to find the 20
>>best models. I also used the value from the objective function from
>>rank them. When doing this it was easy to see if there is any
>>between the rankings and guess what, there is none actual it seems
>>there an explanation for this and which one is right or did i do
>>wrong ? This surprised me since Andrej uses the ProsaII score in many
>>articles as an objective criterion for the quality of the models and
>>would expect the objective function of Modeller to be related in
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