RE: RE: Segmentation Fault during modelling with modeller6v1 - modeller_usage

22 Apr 2002


      Hi,
I am running your examples. It will be 4 days before I can generate 1000
loops. In the mean time please not that you are selecting 2 residues on
each side of every loop:
SET GAP_EXTENSION = 2 2
That, along with the loop resides, selects almost 50% of your protein:
SEGMENT  RESNUM   AA ---  RESNUM   AA    LEN
      1   11 :  CYS  ---   26 :  ASP      16
      2   43 :  PRO  ---   47 :  VAL       5
      3   50 :  ALA  ---   58 :  PRO       9
      4   63 :  TRP  ---   68 :  GLY       6
which is computationaly rather extensive calculation (given the ab
inition nature of loop modeling).
After consulting the loop expert Andras Fiser, he suggested that you
change your selection to zero residues:
SET GAP_EXTENSION = 0 0
More later...
Thanks,
Bozidar
-----Original Message-----
From: Kees-Jan.Francoijs@P450.BC.WAU.NL
[mailto:Kees-Jan.Francoijs@P450.BC.WAU.NL] 
Sent: Monday, April 22, 2002 3:52 AM
To: bozidar@oboe.rockefeller.edu
Subject: re: RE: Segmentation Fault during modelling with modeller6v1
Hi,
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
else you 
want to know just ask.
with regards
Kees-Jan Francoijs
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On Thu Apr 18 19:06:31 2002, "Bozidar Jerkovic"
bozidar@oboe.rockefeller.edu wrote:
>
>Hi,
>
>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.
>
>Thanks,
>Bozidar
>
>
>-----Original Message-----
>From: Kees-Jan.Francoijs@P450.BC.WAU.NL 
>[mailto:Kees-Jan.Francoijs@P450.BC.WAU.NL]
>Sent: Tuesday, April 16, 2002 8:00 AM
>To: bozidar@oboe.rockefeller.edu
>Subject: Segmentation Fault during modelling with modeller6v1
>
>
>Hi Bozidar,
>
>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 in
>the right
>direction.
>
>Two Questions:
>
>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
>the job 
>crashes after 198 models. So i decided to run on a other machine,
>different 
>one 1.7 Ghz Dual Xeon,  same problem. What can be the source of the
>problem. 
>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 
>modeller to
>rank them. When doing this it was easy to see if there is any
>correlation 
>between the rankings and guess what,  there is none actual it seems
>random. Is 
>there an explanation for this and which one is right or did i do
>something 
>wrong ? This surprised me since Andrej uses the ProsaII score in many
of
>his 
>articles as an objective criterion for the quality of the models and
one
>would expect the objective function of Modeller to be related in
>quality.
>
>
>with regards
>
>C.J.J Francoijs
>
>
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