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 system.
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
Happy modeling, 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: firstname.lastname@example.org 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 else you want to know just ask.
Kees-Jan Francoijs - - - - - - - - - - - - - - Original Message - - - - - - - - - - - - - - On Thu Apr 18 19:06:31 2002, "Bozidar Jerkovic" email@example.com 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: firstname.lastname@example.org >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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