Hi,

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?

Thanks, Bozidar

-----Original Message----- From: Kees-Jan.Francoijs@P450.BC.WAU.NL [mailto:Kees-Jan.Francoijs@P450.BC.WAU.NL] Sent: Wednesday, April 24, 2002 3:56 AM To: bozidar@salilab.org Subject: re: RE: RE: Segmentation Fault during modelling with modeller6v

Hi,

i started the job with SET GAP_EXTENSION = 0 0 yesterday with both alignments and one of the jobs has crashed againat the 100th model as well, the other job is still running 450+models. The top and pir filesof the job that crashed are attached.

I will start 10 jobs with each generating 125 models. To see if in every run 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 and -2 like -44656, -35435, -9835, - 15684, -378 ... or is it oke to take in order like -32768, - 16384, - 8192, -4096, -2048...

Thanks in advance

Kees-Jan Francoijs

- - - - - - - - - - - - - - Original Message - - - - - - - - - - - - - - On Tue Apr 23 18:03:13 2002, "Bozidar" bozidar@salilab.org wrote: > >Hi, > >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: 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 >- - - - - - - - - - - - - - Original Message - - - - - - - - - - - - - >- 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 >> >> > >- - - - - - - - - - - - End of Original Message - - - - - - - - - - - - > > >

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